docs_docsify/reference.md
## Agepyramid
### Description
Age Pyramid
### Usage
agepyramid(data, age, gender, female)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>age</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>gender</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>female</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$pyramidTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
Tables can be converted to data frames with `asDF` or `as.data.frame`.
For example:
`results$pyramidTable$asDF`
`as.data.frame(results$pyramidTable)`
---
## AgepyramidClass
### Description
Age Pyramid
Age Pyramid
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::agepyramidBase` ->
`agepyramidClass`
### Methods
#### Public methods
- [`agepyramidClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="agepyramidBase"
data-id="initialize"></span>
[`ClinicoPath::agepyramidBase$initialize()`](../../ClinicoPath/html/agepyramidBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
agepyramidClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Agreement
### Description
Function for Interrater Reliability.
### Usage
agreement(data, vars, sft = FALSE, wght = "unweighted", exct = FALSE)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>vars</code></td>
<td><p>A string naming the variable from <code>data</code> that contains the diagnosis given by the observer, variable can be categorical, ordinal or numeric.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>sft</code></td>
<td><p>Boolean selection whether to show frequency table. Default is 'false'.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>wght</code></td>
<td><p>A list for the argument weight (wght), for weighted kappa analysis. Default is 'unweighted'. 'squared' or 'equal' should be selected only with ordinal variables. The function gives error if the variable type is not ordinal.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>exct</code></td>
<td><p>Boolean selection whether to use exact kappa. Effects only more than 3 observers.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$irrtable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
Tables can be converted to data frames with `asDF` or `as.data.frame`.
For example:
`results$irrtable$asDF`
`as.data.frame(results$irrtable)`
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## AgreementClass
### Description
Interrater Reliability Analysis
Interrater Reliability Analysis
### Value
Table
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::agreementBase` -> `agreementClass`
### Methods
#### Public methods
- [`agreementClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="agreementBase"
data-id="initialize"></span>
[`ClinicoPath::agreementBase$initialize()`](../../ClinicoPath/html/agreementBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
agreementClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Alluvial
### Description
Alluvial Diagrams
### Usage
alluvial(
data,
vars,
condensationvar,
excl = TRUE,
marg = FALSE,
fill = "first_variable",
bin = "default",
orient = "vert",
usetitle = FALSE,
mytitle = "Alluvial Plot"
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>vars</code></td>
<td><p>a string naming the variables from <code>data</code> that contains the values used for the Alluvial Diagram.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>condensationvar</code></td>
<td><p>The primary variable to be used for condensation.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>marg</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>fill</code></td>
<td><p>A list for the argument fill for selecting the variable to be represented by color. Default is 'first_variable'.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>bin</code></td>
<td><p>labels for the bins from low to high</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>orient</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>usetitle</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>mytitle</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
---
## AlluvialClass
### Description
Alluvial Plot
Alluvial Plot
### Value
Alluvial Plot
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::alluvialBase` -> `alluvialClass`
### Methods
#### Public methods
- [`alluvialClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="alluvialBase"
data-id="initialize"></span>
[`ClinicoPath::alluvialBase$initialize()`](../../ClinicoPath/html/alluvialBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
alluvialClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Benford
### Description
Benford Analysis
### Usage
benford(data, var)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>var</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$text2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
---
## Checkdata
### Description
Checking data
### Usage
checkdata(data, dep)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$missingvals</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$minvals</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$maxvals</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
Tables can be converted to data frames with `asDF` or `as.data.frame`.
For example:
`results$minvals$asDF`
`as.data.frame(results$minvals)`
---
## Chisq.multcomp
### Description
Title
### Usage
chisq.multcomp(x, p.method = "fdr")
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>x</code></td>
<td><p>vector</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>p.method</code></td>
<td><p>fdr</p></td>
</tr>
</tbody>
</table>
---
## CiSingle
### Description
Confidence interval for a mean
### Usage
ciSingle(data, deps, splitBy, ciWidth = 95)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>deps</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>splitBy</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>ciWidth</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$conflevel</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$citable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
Tables can be converted to data frames with `asDF` or `as.data.frame`.
For example:
`results$citable$asDF`
`as.data.frame(results$citable)`
---
## Classification
### Description
Decision tree
### Usage
classification(
data,
dep,
indep,
testSize = 0.33,
noOfFolds = 10,
testing,
reporting = list("classifMetrices"),
classifier,
minSplit = 20,
minBucket = 0,
complecity = 0.01,
maxCompete = 4,
maxSurrogate = 5,
unsurrogate = 2,
noCrossValidations = 10,
maxDepth = 30,
noOfTrees = 10,
maxDepthRandFor = 30,
sampleFraction = 1,
splitRule,
plotDecisionTree = FALSE,
predictedFreq = FALSE,
printRandForest = FALSE,
predictedFreqRF = FALSE
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>indep</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>testSize</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>noOfFolds</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>testing</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>reporting</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>classifier</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>minSplit</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>minBucket</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>complecity</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>maxCompete</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>maxSurrogate</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>unsurrogate</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>noCrossValidations</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>maxDepth</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>noOfTrees</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>maxDepthRandFor</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>sampleFraction</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>splitRule</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>plotDecisionTree</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>predictedFreq</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>printRandForest</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>predictedFreqRF</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$modelSettings</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$confusion$matrix</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$classificationMetrics$general</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$classificationMetrics$class</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$rocCurvePlot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$decisionTreeModel</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$predictedFreqPlot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$printRandForest$randomForestModel</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
---
## ClinicoPath-package
### Description
`ClinicoPath` ClinicoPath help researchers to generate natural language
summaries of their dataset, generate cross tables with statistical
tests, and survival analysis with survival tables, survival plots, and
natural language summaries.
For more documentation, see the
[Website](https://sbalci.github.io/ClinicoPathJamoviModule/).
### Details
`ClinicoPath`
### Author(s)
**Maintainer**: Serdar Balci <drserdarbalci@gmail.com>
([ORCID](https://orcid.org/0000-0002-7852-3851))
### See Also
Useful links:
- <https://www.serdarbalci.com/ClinicoPathJamoviModule>
- <https://github.com/sbalci/ClinicoPathJamoviModule/>
- <https://github.com/sbalci/ClinicoPathDescriptives/>
- <https://github.com/sbalci/jsurvival>
- <https://github.com/sbalci/meddecide>
- <https://github.com/sbalci/jjstatsplot>
- <https://sbalci.github.io/ClinicoPathJamoviModule/>
- Report bugs at
<https://github.com/sbalci/ClinicoPathJamoviModule/issues/>
---
## ComparingSurvival
### Description
Comparing Survival Outcomes
### Usage
comparingSurvival(
data,
times,
status,
groups,
ciyn = FALSE,
loglogyn = FALSE,
timeunits = "None"
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>times</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>status</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>groups</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>ciyn</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>loglogyn</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>timeunits</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$compsurvTable1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$compsurvTable2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$compsurvTable3</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
Tables can be converted to data frames with `asDF` or `as.data.frame`.
For example:
`results$compsurvTable1$asDF`
`as.data.frame(results$compsurvTable1)`
---
## Competingsurvival
### Description
Overall, Cause Specific, and Competing Survival.
### Usage
competingsurvival(
data,
explanatory,
overalltime,
outcome,
dod,
dooc,
awd,
awod,
analysistype = "overall"
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>explanatory</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>overalltime</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>outcome</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>dod</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dooc</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>awd</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>awod</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>analysistype</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## CompetingsurvivalClass
### Description
Competing Survival Analysis
Competing Survival Analysis
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::competingsurvivalBase` ->
`competingsurvivalClass`
### Methods
#### Public methods
- [`competingsurvivalClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath"
topic="competingsurvivalBase" data-id="initialize"></span>
[`ClinicoPath::competingsurvivalBase$initialize()`](../../ClinicoPath/html/competingsurvivalBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
competingsurvivalClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## ContTables
### Description
The X² test of association (not to be confused with the X² goodness of
fit) is used to test whether two categorical variables are independent
or associated. If the p-value is low, it suggests the variables are not
independent, and that there is a relationship between the two variables.
### Usage
contTables(
data,
rows,
cols,
counts = NULL,
layers = NULL,
chiSq = TRUE,
chiSqCorr = FALSE,
likeRat = FALSE,
fisher = FALSE,
contCoef = FALSE,
phiCra = FALSE,
logOdds = FALSE,
odds = FALSE,
relRisk = FALSE,
ci = TRUE,
ciWidth = 95,
gamma = FALSE,
taub = FALSE,
obs = TRUE,
exp = FALSE,
pcRow = FALSE,
pcCol = FALSE,
pcTot = FALSE,
formula
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>the data as a data frame</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>rows</code></td>
<td><p>the variable to use as the rows in the contingency table (not necessary when providing a formula, see the examples)</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>cols</code></td>
<td><p>the variable to use as the columns in the contingency table (not necessary when providing a formula, see the examples)</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>counts</code></td>
<td><p>the variable to use as the counts in the contingency table (not necessary when providing a formula, see the examples)</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>layers</code></td>
<td><p>the variables to use to split the contingency table (not necessary when providing a formula, see the examples)</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>chiSq</code></td>
<td><p><code>TRUE</code> (default) or <code>FALSE</code>, provide X²</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>chiSqCorr</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide X² with continuity correction</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>likeRat</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide the likelihood ratio</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>fisher</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide Fisher's exact test</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>contCoef</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide the contingency coefficient</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>phiCra</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide Phi and Cramer's V</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>logOdds</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide the log odds ratio (only available for 2x2 tables)</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>odds</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide the odds ratio (only available for 2x2 tables)</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>relRisk</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide the relative risk (only available for 2x2 tables)</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>ci</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide confidence intervals for the comparative measures</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>ciWidth</code></td>
<td><p>a number between 50 and 99.9 (default: 95), width of the confidence intervals to provide</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>gamma</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide gamma</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>taub</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide Kendall's tau-b</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>obs</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide the observed counts</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>exp</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide the expected counts</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>pcRow</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide row percentages</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>pcCol</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide column percentages</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>pcTot</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide total percentages</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>formula</code></td>
<td><p>(optional) the formula to use, see the examples</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$freqs</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table of proportions</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$chiSq</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table of X² test results</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$odds</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table of comparative measures</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$nom</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table of the 'nominal' test results</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$gamma</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table of the gamma test results</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$taub</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table of the Kendall's tau-b test results</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
Tables can be converted to data frames with `asDF` or `as.data.frame`.
For example:
`results$freqs$asDF`
`as.data.frame(results$freqs)`
### Examples
```r
## Not run:
# data('HairEyeColor')
# dat <- as.data.frame(HairEyeColor)
# contTables(formula = Freq ~ Hair:Eye, dat)
#
# CONTINGENCY TABLES
#
# Contingency Tables
# -----------------------------------------------------
#Hair BrownBlueHazelGreenTotal
# -----------------------------------------------------
#Black 68 20 155 108
#Brown 119 84 54 29 286
#Red 26 17 14 14 71
#Blond7 94 10 16 127
#Total 220 215 93 64 592
# -----------------------------------------------------
#
#
# X² Tests
# -------------------------------
# Valuedfp
# -------------------------------
#X² 138 9< .001
#N 592
# -------------------------------
#
# Alternatively, omit the left of the formula (`Freq`) if each row
# represents a single observation:
# contTables(formula = ~ Hair:Eye, dat)
## End(Not run)
```
---
## ContTablesPaired
### Description
McNemar test
### Usage
contTablesPaired(
data,
rows,
cols,
counts = NULL,
chiSq = TRUE,
chiSqCorr = FALSE,
exact = FALSE,
pcRow = FALSE,
pcCol = FALSE,
formula
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>the data as a data frame</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>rows</code></td>
<td><p>the variable to use as the rows in the contingency table (not necessary when providing a formula, see the examples)</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>cols</code></td>
<td><p>the variable to use as the columns in the contingency table (not necessary when providing a formula, see the examples)</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>counts</code></td>
<td><p>the variable to use as the counts in the contingency table (not necessary when providing a formula, see the examples)</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>chiSq</code></td>
<td><p><code>TRUE</code> (default) or <code>FALSE</code>, provide X²</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>chiSqCorr</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide X² with continuity correction</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>exact</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide an exact log odds ratio (requires exact2x2 to be installed)</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>pcRow</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide row percentages</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>pcCol</code></td>
<td><p><code>TRUE</code> or <code>FALSE</code> (default), provide column percentages</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>formula</code></td>
<td><p>(optional) the formula to use, see the examples</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$freqs</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a proportions table</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$test</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table of test results</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
Tables can be converted to data frames with `asDF` or `as.data.frame`.
For example:
`results$freqs$asDF`
`as.data.frame(results$freqs)`
### Examples
```r
dat <- data.frame(
`1st survey` = c('Approve', 'Approve', 'Disapprove', 'Disapprove'),
`2nd survey` = c('Approve', 'Disapprove', 'Approve', 'Disapprove'),
`Counts` = c(794, 150, 86, 570),
check.names=FALSE)
contTablesPaired(formula = Counts ~ `1st survey`:`2nd survey`, data = dat)
#
# PAIRED SAMPLES CONTINGENCY TABLES
#
# Contingency Tables
# ------------------------------------------------
#1st surveyApproveDisapproveTotal
# ------------------------------------------------
#Approve 794 150 944
#Disapprove 86 570 656
#Total 880 720 1600
# ------------------------------------------------
#
#
# McNemar Test
# -----------------------------------------------------
#Valuedfp
# -----------------------------------------------------
#X² 17.4 1< .001
#X² continuity correction 16.8 1< .001
# -----------------------------------------------------
#
# Alternatively, omit the left of the formula (`Counts`) from the
# formula if each row represents a single observation:
contTablesPaired(formula = ~ `1st survey`:`2nd survey`, data = dat)
```
---
## Correlation
### Description
Function for Correlation.
### Usage
correlation(data, vars)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>vars</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## CorrelationClass
### Description
Correlation Analysis
Correlation Analysis
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::correlationBase` ->
`correlationClass`
### Methods
#### Public methods
- [`correlationClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="correlationBase"
data-id="initialize"></span>
[`ClinicoPath::correlationBase$initialize()`](../../ClinicoPath/html/correlationBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
correlationClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Crosstable
### Description
Function for making Cross Tables.
### Usage
crosstable(
data,
vars,
group,
sty = "nejm",
excl = TRUE,
cont = "mean",
pcat = "chisq"
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>vars</code></td>
<td><p>variable in the rows</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>group</code></td>
<td><p>variable in the column</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>sty</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>cont</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>pcat</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$tablestyle1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$tablestyle2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$tablestyle3</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$tablestyle4</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## CrosstableClass
### Description
Cross Table
Cross Table
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::crosstableBase` ->
`crosstableClass`
### Methods
#### Public methods
- [`crosstableClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="crosstableBase"
data-id="initialize"></span>
[`ClinicoPath::crosstableBase$initialize()`](../../ClinicoPath/html/crosstableBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
crosstableClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Decision
### Description
Function for Medical Decision Analysis. Sensitivity, specificity,
positive predictive value, negative predictive value.
### Usage
decision(
data,
gold,
goldPositive,
newtest,
testPositive,
pp = FALSE,
pprob = 0.3,
od = FALSE,
fnote = FALSE,
ci = FALSE,
fagan = FALSE
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>gold</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>goldPositive</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>newtest</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>testPositive</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>pp</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>pprob</code></td>
<td><p>Prior probability (disease prevelance in the community). Requires a value between 0.001 and 0.999, default 0.300.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>od</code></td>
<td><p>Boolean selection whether to show frequency table. Default is 'false'.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>fnote</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>ci</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>fagan</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$text1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$cTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$nTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$ratioTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$epirTable_ratio</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$epirTable_number</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
Tables can be converted to data frames with `asDF` or `as.data.frame`.
For example:
`results$cTable$asDF`
`as.data.frame(results$cTable)`
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## Decision2
### Description
Function for Medical Decision Analysis. Sensitivity, specificity,
positive predictive value, negative predictive value.
### Usage
decision2(data, gold, goldPositive, newtest, testPositive)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>gold</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>goldPositive</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>newtest</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>testPositive</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$cTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
Tables can be converted to data frames with `asDF` or `as.data.frame`.
For example:
`results$cTable$asDF`
`as.data.frame(results$cTable)`
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## Decisioncalculator
### Description
Function for Medical Decision Calculator.
### Usage
decisioncalculator(
TP = 90,
TN = 80,
FP = 30,
FN = 20,
pp = FALSE,
pprob = 0.3,
fnote = FALSE,
ci = FALSE,
fagan = FALSE
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>TP</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>TN</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>FP</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>FN</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>pp</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>pprob</code></td>
<td><p>Prior probability (disease prevelance in the community). Requires a value between 0.001 and 0.999, default 0.300.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>fnote</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>ci</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>fagan</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$cTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$nTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$ratioTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$epirTable_ratio</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$epirTable_number</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
Tables can be converted to data frames with `asDF` or `as.data.frame`.
For example:
`results$cTable$asDF`
`as.data.frame(results$cTable)`
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## DecisioncalculatorClass
### Description
Decision Calculator
Decision Calculator
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::decisioncalculatorBase` ->
`decisioncalculatorClass`
### Methods
#### Public methods
- [`decisioncalculatorClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath"
topic="decisioncalculatorBase" data-id="initialize"></span>
[`ClinicoPath::decisioncalculatorBase$initialize()`](../../ClinicoPath/html/decisioncalculatorBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
decisioncalculatorClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## DecisionClass
### Description
Medical Decision Making
Medical Decision Making
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::decisionBase` -> `decisionClass`
### Methods
#### Public methods
- [`decisionClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="decisionBase"
data-id="initialize"></span>
[`ClinicoPath::decisionBase$initialize()`](../../ClinicoPath/html/decisionBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
decisionClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Dendogram
### Description
Dendogram
### Usage
dendogram(data, dep, group, alt = "notequal", varEq = TRUE)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>group</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>alt</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>varEq</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
---
## Gtsummary
### Description
Tables via gtsummary
### Usage
gtsummary(data, dep, group, alt = "notequal", varEq = TRUE)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>group</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>alt</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>varEq</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$gtsum1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
---
## GtsummaryClass
### Description
Tables via gtsummary
Tables via gtsummary
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::gtsummaryBase` -> `gtsummaryClass`
### Methods
#### Public methods
- [`gtsummaryClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="gtsummaryBase"
data-id="initialize"></span>
[`ClinicoPath::gtsummaryBase$initialize()`](../../ClinicoPath/html/gtsummaryBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
gtsummaryClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Histopathology
### Description
Fake histopathology research data.
Fake histopathology research data.
### Usage
data(histopathology)
data(histopathology)
### Format
A data frame
A data frame
---
## Icccoeff
### Description
Function for Interclass Correlation Coefficient Calculation.
### Usage
icccoeff(data, vars)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>vars</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## IcccoeffClass
### Description
Interclass Correlation Coefficient
Also see
<http://www.cookbook-r.com/Statistical_analysis/Inter-rater_reliability/#ordinal-data-weighted-kappa>
Interclass Correlation Coefficient
Also see
<http://www.cookbook-r.com/Statistical_analysis/Inter-rater_reliability/#ordinal-data-weighted-kappa>
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::icccoeffBase` -> `icccoeffClass`
### Methods
#### Public methods
- [`icccoeffClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="icccoeffBase"
data-id="initialize"></span>
[`ClinicoPath::icccoeffBase$initialize()`](../../ClinicoPath/html/icccoeffBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
icccoeffClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Jjbarstats
### Description
'Wrapper Function for ggstatsplot::ggbarstats and
ggstatsplot::grouped\_ggbarstats to generate Bar Charts.'
### Usage
jjbarstats(data, dep, group, grvar, excl = TRUE, originaltheme = FALSE)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>group</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>grvar</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>originaltheme</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## Jjbarstats2
### Description
'Wrapper Function for ggstatsplot::ggbarstats and
ggstatsplot::grouped\_ggbarstats to generate Bar Charts.'
### Usage
jjbarstats2(
data,
dep,
group,
grvar,
direction = "independent",
excl = TRUE,
originaltheme = FALSE
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>group</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>grvar</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>direction</code></td>
<td><p>select measurement type (repeated or independent)</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>originaltheme</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## Jjbarstats2Class
### Description
Bar Charts
Bar Charts
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::jjbarstats2Base` ->
`jjbarstats2Class`
### Methods
#### Public methods
- [`jjbarstats2Class$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="jjbarstats2Base"
data-id="initialize"></span>
[`ClinicoPath::jjbarstats2Base$initialize()`](../../ClinicoPath/html/jjbarstats2Base.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
jjbarstats2Class$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## JjbarstatsClass
### Description
Bar Charts
Bar Charts
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::jjbarstatsBase` ->
`jjbarstatsClass`
### Methods
#### Public methods
- [`jjbarstatsClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="jjbarstatsBase"
data-id="initialize"></span>
[`ClinicoPath::jjbarstatsBase$initialize()`](../../ClinicoPath/html/jjbarstatsBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
jjbarstatsClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Jjbetweenstats
### Description
Violin Plots to Compare Between Groups
### Usage
jjbetweenstats(
data,
dep,
group,
grvar = NULL,
excl = TRUE,
typestatistics = "parametric",
pairwisecomparisons = TRUE,
pairwisedisplay = "significant",
padjustmethod = "holm",
plottype = "boxviolin",
originaltheme = FALSE
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>group</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>grvar</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>typestatistics</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>pairwisecomparisons</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>pairwisedisplay</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>padjustmethod</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>plottype</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>originaltheme</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## JjbetweenstatsClass
### Description
Violin Plots to Compare Between Groups
Violin Plots to Compare Between Groups
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::jjbetweenstatsBase` ->
`jjbetweenstatsClass`
### Methods
#### Public methods
- [`jjbetweenstatsClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="jjbetweenstatsBase"
data-id="initialize"></span>
[`ClinicoPath::jjbetweenstatsBase$initialize()`](../../ClinicoPath/html/jjbetweenstatsBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
jjbetweenstatsClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Jjcorrmat
### Description
Correlation Matrix
### Usage
jjcorrmat(
data,
dep,
grvar,
excl = TRUE,
typestatistics = "parametric",
originaltheme = FALSE
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>grvar</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>typestatistics</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>originaltheme</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## JjcorrmatClass
### Description
Correlation Matrix
Correlation Matrix
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::jjcorrmatBase` -> `jjcorrmatClass`
### Methods
#### Public methods
- [`jjcorrmatClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="jjcorrmatBase"
data-id="initialize"></span>
[`ClinicoPath::jjcorrmatBase$initialize()`](../../ClinicoPath/html/jjcorrmatBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
jjcorrmatClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Jjdotplotstats
### Description
Dot Chart
### Usage
jjdotplotstats(
data,
dep,
group,
grvar,
excl = TRUE,
typestatistics = "parametric",
originaltheme = FALSE
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>group</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>grvar</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>typestatistics</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>originaltheme</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## JjdotplotstatsClass
### Description
Dot Chart
Dot Chart
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::jjdotplotstatsBase` ->
`jjdotplotstatsClass`
### Methods
#### Public methods
- [`jjdotplotstatsClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="jjdotplotstatsBase"
data-id="initialize"></span>
[`ClinicoPath::jjdotplotstatsBase$initialize()`](../../ClinicoPath/html/jjdotplotstatsBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
jjdotplotstatsClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Jjhistostats
### Description
'Wrapper Function for ggstatsplot::gghistostats and
ggstatsplot::grouped\_gghistostats to generate Histogram.'
### Usage
jjhistostats(
data,
dep,
grvar,
excl = TRUE,
typestatistics = "parametric",
centralityparameter = "mean",
changebinwidth = FALSE,
binwidth = 1.1,
barmeasure = "count",
usexlab = FALSE,
xlab = "",
useylab = FALSE,
ylab = "",
usetitle = FALSE,
title = "",
usesubtitle = FALSE,
subtitle = "",
useplotcaption = FALSE,
plotcaption = "",
usetitleprefix = FALSE,
titleprefix = "",
resultssubtitle = TRUE,
normalcurve = FALSE,
testvalueline = FALSE
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>grvar</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>typestatistics</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>centralityparameter</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>changebinwidth</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>binwidth</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>barmeasure</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>usexlab</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>xlab</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>useylab</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>ylab</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>usetitle</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>title</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>usesubtitle</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>subtitle</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>useplotcaption</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>plotcaption</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>usetitleprefix</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>titleprefix</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>resultssubtitle</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>normalcurve</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>testvalueline</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## JjhistostatsClass
### Description
Histogram
Histogram
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::jjhistostatsBase` ->
`jjhistostatsClass`
### Methods
#### Public methods
- [`jjhistostatsClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="jjhistostatsBase"
data-id="initialize"></span>
[`ClinicoPath::jjhistostatsBase$initialize()`](../../ClinicoPath/html/jjhistostatsBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
jjhistostatsClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Jjpiestats
### Description
Pie Charts
### Usage
jjpiestats(data, dep, group, grvar, excl = TRUE, originaltheme = FALSE)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>group</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>grvar</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>originaltheme</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot4</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot3</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## JjpiestatsClass
### Description
Pie Charts
Pie Charts
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::jjpiestatsBase` ->
`jjpiestatsClass`
### Methods
#### Public methods
- [`jjpiestatsClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="jjpiestatsBase"
data-id="initialize"></span>
[`ClinicoPath::jjpiestatsBase$initialize()`](../../ClinicoPath/html/jjpiestatsBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
jjpiestatsClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Jjscatterstats
### Description
Scatter Plot
### Usage
jjscatterstats(
data,
dep,
group,
grvar,
excl = TRUE,
typestatistics = "parametric",
originaltheme = FALSE
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>group</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>grvar</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>typestatistics</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>originaltheme</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## JjscatterstatsClass
### Description
Scatter Plot
Scatter Plot
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::jjscatterstatsBase` ->
`jjscatterstatsClass`
### Methods
#### Public methods
- [`jjscatterstatsClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="jjscatterstatsBase"
data-id="initialize"></span>
[`ClinicoPath::jjscatterstatsBase$initialize()`](../../ClinicoPath/html/jjscatterstatsBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
jjscatterstatsClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Jjstatsplot-package
### Description
`jjstatsplot` A wrapper for ggstatsplot: jjstatsplot help researchers to
generate plots in jamovi based on ggstatsplot package.
### Details
`jjstatsplot`
The main functions are-
- `jjhistostats` function to produce histogram.
<!-- -->
- `jjbarstats` function to produce Bar Graphs.
For more documentation, see the
[Website](https://sbalci.github.io/jjstatsplot/).
### Author(s)
**Maintainer**: Serdar Balci <drserdarbalci@gmail.com>
([ORCID](https://orcid.org/0000-0002-7852-3851))
### See Also
Useful links:
- <https://www.serdarbalci.com/ClinicoPathJamoviModule>
- <https://github.com/sbalci/ClinicoPathJamoviModule/>
- <https://github.com/sbalci/ClinicoPathDescriptives/>
- <https://github.com/sbalci/jsurvival>
- <https://github.com/sbalci/meddecide>
- <https://github.com/sbalci/jjstatsplot>
- <https://sbalci.github.io/ClinicoPathJamoviModule/>
- Report bugs at
<https://github.com/sbalci/ClinicoPathJamoviModule/issues/>
---
## Jjwithinstats
### Description
Violin Plots to Compare Within Groups
### Usage
jjwithinstats(
data,
dep,
group,
grvar,
typestatistics = "parametric",
originaltheme = FALSE,
pointpath = TRUE,
meanpath = TRUE
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>group</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>grvar</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>typestatistics</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>originaltheme</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>pointpath</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>meanpath</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## Jjwithinstats2
### Description
Violin Plots to Compare Within Groups for Wide Data Format
### Usage
jjwithinstats2(data, pairs, excl = TRUE, originaltheme = FALSE)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>pairs</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>originaltheme</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## Jjwithinstats2Class
### Description
Violin Plots to Compare Within Group for Wide Data Format
Violin Plots to Compare Within Group for Wide Data Format
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::jjwithinstats2Base` ->
`jjwithinstats2Class`
### Methods
#### Public methods
- [`jjwithinstats2Class$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="jjwithinstats2Base"
data-id="initialize"></span>
[`ClinicoPath::jjwithinstats2Base$initialize()`](../../ClinicoPath/html/jjwithinstats2Base.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
jjwithinstats2Class$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Jjwithinstats3
### Description
Violin Plots to Compare Repeated Measurements for Continuous Variables
### Usage
jjwithinstats3(data, dep, excl = TRUE, originaltheme = FALSE)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>originaltheme</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## Jjwithinstats3Class
### Description
Violin Plots to Compare Within Group for Wide Data Format 3
Violin Plots to Compare Within Group for Wide Data Format 3
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::jjwithinstats3Base` ->
`jjwithinstats3Class`
### Methods
#### Public methods
- [`jjwithinstats3Class$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="jjwithinstats3Base"
data-id="initialize"></span>
[`ClinicoPath::jjwithinstats3Base$initialize()`](../../ClinicoPath/html/jjwithinstats3Base.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
jjwithinstats3Class$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## JjwithinstatsClass
### Description
Violin Plots to Compare Within Group
Violin Plots to Compare Within Group
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::jjwithinstatsBase` ->
`jjwithinstatsClass`
### Methods
#### Public methods
- [`jjwithinstatsClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="jjwithinstatsBase"
data-id="initialize"></span>
[`ClinicoPath::jjwithinstatsBase$initialize()`](../../ClinicoPath/html/jjwithinstatsBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
jjwithinstatsClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Jviolin
### Description
Violin Plot
### Usage
jviolin(
data,
dep,
group,
col,
fill,
excl = TRUE,
flip = FALSE,
themex = "ipsum",
usexlabel = FALSE,
xlabel = "",
useylabel = FALSE,
ylabel = ""
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>group</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>col</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>fill</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>flip</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>themex</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>usexlabel</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>xlabel</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>useylabel</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>ylabel</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
---
## JviolinClass
### Description
Violin Plot
Violin Plot
### Value
Violin Plot
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::jviolinBase` -> `jviolinClass`
### Methods
#### Public methods
- [`jviolinClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="jviolinBase"
data-id="initialize"></span>
[`ClinicoPath::jviolinBase$initialize()`](../../ClinicoPath/html/jviolinBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
jviolinClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Linechart
### Description
Line Chart
### Usage
linechart(data, xvar, yvar)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>xvar</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>yvar</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
---
## Lollipop
### Description
Lollipop Chart
### Usage
lollipop(data, dep, group, highlight)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>group</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>highlight</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
---
## Multisurvival
### Description
Function for Multivariable Survival Analysis using Cox-regression.
### Usage
multisurvival(
data,
elapsedtime,
tint = FALSE,
dxdate,
fudate,
outcome,
outcomeLevel,
dod,
dooc,
awd,
awod,
explanatory,
contexpl,
multievent = FALSE,
analysistype = "overall",
timetypedata = "ymd",
timetypeoutput = "months",
hr = FALSE,
sty = "t1",
km = FALSE,
ac = FALSE,
adjexplanatory,
endplot = 60,
byplot = 12,
ci95 = FALSE,
risktable = FALSE
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>elapsedtime</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>tint</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dxdate</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>fudate</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>outcome</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>outcomeLevel</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dod</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>dooc</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>awd</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>awod</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>explanatory</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>contexpl</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>multievent</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>analysistype</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>timetypedata</code></td>
<td><p>select the time type in data</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>timetypeoutput</code></td>
<td><p>select the time type in output</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>hr</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>sty</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>km</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>ac</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>adjexplanatory</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>endplot</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>byplot</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>ci95</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>risktable</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$text2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot3</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plotKM</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot7</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$calculatedtime</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an output</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$outcomeredifened</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an output</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## MultisurvivalClass
### Description
Multivariable Survival Analysis
Multivariable Survival Analysis
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::multisurvivalBase` ->
`multisurvivalClass`
### Methods
#### Public methods
- [`multisurvivalClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="multisurvivalBase"
data-id="initialize"></span>
[`ClinicoPath::multisurvivalBase$initialize()`](../../ClinicoPath/html/multisurvivalBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
multisurvivalClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Nomogram
### Description
Nomogram
### Usage
nomogram(data, dep, group, alt = "notequal", varEq = TRUE)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>group</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>alt</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>varEq</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
---
## Oddsratio
### Description
Function for Odds Ratio Table and Plot.
### Usage
oddsratio(data, explanatory, outcome)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>explanatory</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>outcome</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$text2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## OddsratioClass
### Description
Odds Ratio Table and Plot
Odds Ratio Table and Plot
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::oddsratioBase` -> `oddsratioClass`
### Methods
#### Public methods
- [`oddsratioClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="oddsratioBase"
data-id="initialize"></span>
[`ClinicoPath::oddsratioBase$initialize()`](../../ClinicoPath/html/oddsratioBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
oddsratioClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## OneSurvival
### Description
One Survival Outcome
### Usage
oneSurvival(data, times, status, ciyn = FALSE, timeunits = "None")
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>times</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>status</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>ciyn</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>timeunits</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$onesurvTable1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$onesurvPlot1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
Tables can be converted to data frames with `asDF` or `as.data.frame`.
For example:
`results$onesurvTable1$asDF`
`as.data.frame(results$onesurvTable1)`
---
## Pairchi2
### Description
Pairwise Chi-Square Test
### Usage
pairchi2(data, row, col)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>row</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>col</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$conftable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$chi2test</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$pairwise1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$pairwise2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$pairwise3</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
---
## Pairchi2Class
### Description
Title
Title
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::pairchi2Base` -> `pairchi2Class`
### Methods
#### Public methods
- [`pairchi2Class$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="pairchi2Base"
data-id="initialize"></span>
[`ClinicoPath::pairchi2Base$initialize()`](../../ClinicoPath/html/pairchi2Base.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
pairchi2Class$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Parallelplot
### Description
Parallel Plot
### Usage
parallelplot(data, dep, group, alt = "notequal", varEq = TRUE)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>group</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>alt</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>varEq</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
---
## Pipe
### Description
Pipe operator from
<https://github.com/poldham/covidlens/blob/master/R/utils-pipe.R> See
`magrittr::%>%` for details.
### Usage
lhs %>% rhs
---
## Ppv
### Description
Positive Predictive Value
### Usage
ppv(percTrue = 50, alpha = 0.05, power = 0.8, percHack = 0)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>percTrue</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>alpha</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>power</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>percHack</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$confusion</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table containing the true/false positives/negatives</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$ppv</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$dotPlot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
Tables can be converted to data frames with `asDF` or `as.data.frame`.
For example:
`results$confusion$asDF`
`as.data.frame(results$confusion)`
---
## Reportcat
### Description
Function for Generating Summaries for Categorical Variables.
### Usage
reportcat(data, vars)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>the data as a data frame</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>vars</code></td>
<td><p>string naming the variables from <code>data</code> that contains the values used for the report.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## ReportcatClass
### Description
Summary of Categorical Variables
Summary of Categorical Variables
### Value
Text
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::reportcatBase` -> `reportcatClass`
### Methods
#### Public methods
- [`reportcatClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="reportcatBase"
data-id="initialize"></span>
[`ClinicoPath::reportcatBase$initialize()`](../../ClinicoPath/html/reportcatBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
reportcatClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Retracted
### Description
Find Retracted Papers from DOI
### Usage
retracted(data, doi)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>doi</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$text4</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text5</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
---
## RetractedClass
### Description
Find Retracted Papers from DOI
Find Retracted Papers from DOI
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::retractedBase` -> `retractedClass`
### Methods
#### Public methods
- [`retractedClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="retractedBase"
data-id="initialize"></span>
[`ClinicoPath::retractedBase$initialize()`](../../ClinicoPath/html/retractedBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
retractedClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Roc
### Description
Function for ROC Analysis.
### Usage
roc(
data,
measurement,
status,
excl = TRUE,
sty = FALSE,
quant = FALSE,
label = FALSE,
inter = FALSE
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>measurement</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>status</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>sty</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>quant</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>label</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>inter</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$textplot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## RocClass
### Description
ROC Analysis
ROC Analysis
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::rocBase` -> `rocClass`
### Methods
#### Public methods
- [`rocClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="rocBase"
data-id="initialize"></span>
[`ClinicoPath::rocBase$initialize()`](../../ClinicoPath/html/rocBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
rocClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Rocdata
### Description
Example data for ROC analysis
### Usage
data(rocdata)
### Format
A data frame
---
## Statsplot2
### Description
Function for Generating Plots and Graphs Based on Variable Types.
### Usage
statsplot2(
data,
dep,
group,
grvar,
direction = "independent",
distribution = "p",
alluvsty = "t1",
excl = TRUE,
originaltheme = FALSE
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dep</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>group</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>grvar</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>direction</code></td>
<td><p>select measurement type (repeated or independent)</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>distribution</code></td>
<td><p>select distribution type (parametric or nonparametric)</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>alluvsty</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>originaltheme</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text4</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## Statsplot2Class
### Description
Plots and Graphs Based on Variable Types
Plots and Graphs Based on Variable Types
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::statsplot2Base` ->
`statsplot2Class`
### Methods
#### Public methods
- [`statsplot2Class$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="statsplot2Base"
data-id="initialize"></span>
[`ClinicoPath::statsplot2Base$initialize()`](../../ClinicoPath/html/statsplot2Base.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
statsplot2Class$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Summarydata
### Description
Function for Generating Summaries for Continuous Variables.
### Usage
summarydata(data, vars)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>vars</code></td>
<td><p>a string naming the variables from <code>data</code> that contains the continuous values used for the report</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## SummarydataClass
### Description
Summary of Continuous Variables
Summary of Continuous Variables
### Value
Text
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::summarydataBase` ->
`summarydataClass`
### Methods
#### Public methods
- [`summarydataClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="summarydataBase"
data-id="initialize"></span>
[`ClinicoPath::summarydataBase$initialize()`](../../ClinicoPath/html/summarydataBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
summarydataClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Survival
### Description
Function for Generating Summaries for Survival Analysis.
### Usage
survival(
data,
elapsedtime,
tint = FALSE,
dxdate,
fudate,
explanatory,
outcome,
outcomeLevel,
dod,
dooc,
awd,
awod,
analysistype = "overall",
cutp = "12, 36, 60",
timetypedata = "ymd",
timetypeoutput = "months",
uselandmark = FALSE,
landmark = 3,
pw = FALSE,
padjustmethod = "holm",
sc = FALSE,
kmunicate = FALSE,
ce = FALSE,
ch = FALSE,
endplot = 60,
byplot = 12,
multievent = FALSE,
ci95 = FALSE,
risktable = FALSE,
censored = FALSE,
sas = FALSE
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>elapsedtime</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>tint</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dxdate</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>fudate</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>explanatory</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>outcome</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>outcomeLevel</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>dod</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dooc</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>awd</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>awod</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>analysistype</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>cutp</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>timetypedata</code></td>
<td><p>select the time type in data</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>timetypeoutput</code></td>
<td><p>select the time type in output</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>uselandmark</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>landmark</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>pw</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>padjustmethod</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>sc</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>kmunicate</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>ce</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>ch</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>endplot</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>byplot</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>multievent</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>ci95</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>risktable</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>censored</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>sas</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$medianSummary</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$medianTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$coxSummary</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$coxTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$tCoxtext2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$survTableSummary</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$survTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$pairwiseSummary</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$pairwiseTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot3</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot6</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$calculatedtime</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an output</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$outcomeredifened</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an output</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
Tables can be converted to data frames with `asDF` or `as.data.frame`.
For example:
`results$medianTable$asDF`
`as.data.frame(results$medianTable)`
### Examples
```r
# example will be added
```
---
## SurvivalClass
### Description
Survival Analysis
Survival Analysis
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::survivalBase` -> `survivalClass`
### Methods
#### Public methods
- [`survivalClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="survivalBase"
data-id="initialize"></span>
[`ClinicoPath::survivalBase$initialize()`](../../ClinicoPath/html/survivalBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
survivalClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Survivalcont
### Description
Survival Analysis for Continuous Variable
### Usage
survivalcont(
data,
elapsedtime,
tint = FALSE,
dxdate,
fudate,
contexpl,
outcome,
outcomeLevel,
dod,
dooc,
awd,
awod,
analysistype = "overall",
cutp = "12, 36, 60",
timetypedata = "ymd",
timetypeoutput = "months",
sc = FALSE,
kmunicate = FALSE,
ce = FALSE,
ch = FALSE,
endplot = 60,
byplot = 12,
findcut = FALSE,
multievent = FALSE,
ci95 = FALSE,
risktable = FALSE
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>elapsedtime</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>tint</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dxdate</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>fudate</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>contexpl</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>outcome</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>outcomeLevel</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>dod</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>dooc</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>awd</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>awod</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>analysistype</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>cutp</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>timetypedata</code></td>
<td><p>select the time type in data</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>timetypeoutput</code></td>
<td><p>select the time type in output</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>sc</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>kmunicate</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>ce</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>ch</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>endplot</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>byplot</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>findcut</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>multievent</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>ci95</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>risktable</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$coxSummary</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$coxTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$tCoxtext2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$rescutTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot4</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot5</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$medianSummary</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$medianTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$survTableSummary</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$survTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$plot3</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot6</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$calculatedtime</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an output</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$outcomeredifened</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an output</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$calculatedcutoff</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an output</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
Tables can be converted to data frames with `asDF` or `as.data.frame`.
For example:
`results$coxTable$asDF`
`as.data.frame(results$coxTable)`
---
## SurvivalcontClass
### Description
Survival Analysis for Continuous Explanatory Variable
Survival Analysis for Continuous Explanatory Variable
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::survivalcontBase` ->
`survivalcontClass`
### Methods
#### Public methods
- [`survivalcontClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="survivalcontBase"
data-id="initialize"></span>
[`ClinicoPath::survivalcontBase$initialize()`](../../ClinicoPath/html/survivalcontBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
survivalcontClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Tableone
### Description
Function for making Table One.
### Usage
tableone(data, vars, sty = "t1", excl = TRUE)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>vars</code></td>
<td><p>a string naming the variables from <code>data</code> that contains the values used for the Table One.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>sty</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$tablestyle1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$tablestyle2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$tablestyle3</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$tablestyle4</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
data('histopathology')
dat <- as.data.frame(histopathology)
ClinicoPath::tableone(
data = dat,
vars = vars(Sex, PreinvasiveComponent, LVI, PNI, Grade, Age),
sty = "t3",
excl = TRUE)
## End(Not run)
```
---
## TableoneClass
### Description
Table One
Table One
### Value
Table
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::tableoneBase` -> `tableoneClass`
### Methods
#### Public methods
- [`tableoneClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="tableoneBase"
data-id="initialize"></span>
[`ClinicoPath::tableoneBase$initialize()`](../../ClinicoPath/html/tableoneBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
tableoneClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Timeinterval
### Description
Time Interval
### Usage
timeinterval(data, explanatory, overalltime, outcome, outcomeLevel)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>explanatory</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>overalltime</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>outcome</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>outcomeLevel</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$text1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text1table</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$text1html</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$medianTable</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a table</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
Tables can be converted to data frames with `asDF` or `as.data.frame`.
For example:
`results$medianTable$asDF`
`as.data.frame(results$medianTable)`
---
## Tree
### Description
Function for making Decision Trees.
### Usage
tree(
data,
vars,
facs,
target,
targetLevel,
train,
trainLevel,
showPlot = FALSE
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>vars</code></td>
<td><p>continuous explanatory variables</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>facs</code></td>
<td><p>categorical explanatory variables</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>target</code></td>
<td><p>target variable</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>targetLevel</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>train</code></td>
<td><p>Variable containing Test/Train information</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>trainLevel</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>showPlot</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$text2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text2a</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$text2b</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text3</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$text4</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## TreeClass
### Description
Decision Tree
Decision Tree
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::treeBase` -> `treeClass`
### Methods
#### Public methods
- [`treeClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="treeBase"
data-id="initialize"></span>
[`ClinicoPath::treeBase$initialize()`](../../ClinicoPath/html/treeBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
treeClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Vartree
### Description
Function for Generating Tree Summaries of Variables.
### Usage
vartree(
data,
vars,
percvar,
percvarLevel,
summaryvar,
prunebelow,
pruneLevel1,
pruneLevel2,
follow,
followLevel1,
followLevel2,
excl = TRUE,
vp = TRUE,
horizontal = FALSE,
sline = TRUE,
varnames = FALSE,
nodelabel = TRUE,
pct = FALSE,
showcount = TRUE,
legend = FALSE,
pattern = FALSE,
sequence = FALSE,
ptable = FALSE,
mytitle = "",
useprunesmaller = FALSE,
prunesmaller = 5,
summarylocation = "leafonly"
)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>vars</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>percvar</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>percvarLevel</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>summaryvar</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>prunebelow</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>pruneLevel1</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>pruneLevel2</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>follow</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>followLevel1</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>followLevel2</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>excl</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>vp</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>horizontal</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>sline</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>varnames</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>nodelabel</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>pct</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>showcount</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>legend</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>pattern</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>sequence</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>ptable</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>mytitle</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>useprunesmaller</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>prunesmaller</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>summarylocation</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$text1</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="odd">
<td style="text-align: left;"><code>results$text2</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a preformatted</td>
</tr>
<tr class="even">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
### Examples
```r
## Not run:
# example will be added
## End(Not run)
```
---
## VartreeClass
### Description
Variable Tree
Variable Tree
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::vartreeBase` -> `vartreeClass`
### Methods
#### Public methods
- [`vartreeClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="vartreeBase"
data-id="initialize"></span>
[`ClinicoPath::vartreeBase$initialize()`](../../ClinicoPath/html/vartreeBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
vartreeClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---
## Venn
### Description
Venn Diagram
### Usage
venn(data, var1, var1true, var2, var2true, var3, var3true, var4, var4true)
### Arguments
<table data-summary="R argblock">
<tbody>
<tr class="odd" data-valign="top">
<td><code>data</code></td>
<td><p>The data as a data frame.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>var1</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>var1true</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>var2</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>var2true</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>var3</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>var3true</code></td>
<td><p>.</p></td>
</tr>
<tr class="even" data-valign="top">
<td><code>var4</code></td>
<td><p>.</p></td>
</tr>
<tr class="odd" data-valign="top">
<td><code>var4true</code></td>
<td><p>.</p></td>
</tr>
</tbody>
</table>
### Value
A results object containing:
<table data-summary="Rd table">
<tbody>
<tr class="odd">
<td style="text-align: left;"><code>results$todo</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">a html</td>
</tr>
<tr class="even">
<td style="text-align: left;"><code>results$plot</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">an image</td>
</tr>
<tr class="odd">
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
<td style="text-align: left;"></td>
</tr>
</tbody>
</table>
---
## VennClass
### Description
Venn Diagram
Venn Diagram
### Super classes
`jmvcore::Analysis` -> `ClinicoPath::vennBase` -> `vennClass`
### Methods
#### Public methods
- [`vennClass$clone()`](#method-clone)
Inherited methods
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImage"></span>
[`jmvcore::Analysis$.createImage()`](../../jmvcore/html/Analysis.html#method-.createImage)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createImages"></span>
[`jmvcore::Analysis$.createImages()`](../../jmvcore/html/Analysis.html#method-.createImages)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".createPlotObject"></span>
[`jmvcore::Analysis$.createPlotObject()`](../../jmvcore/html/Analysis.html#method-.createPlotObject)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".load"></span>
[`jmvcore::Analysis$.load()`](../../jmvcore/html/Analysis.html#method-.load)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".render"></span>
[`jmvcore::Analysis$.render()`](../../jmvcore/html/Analysis.html#method-.render)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".save"></span>
[`jmvcore::Analysis$.save()`](../../jmvcore/html/Analysis.html#method-.save)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".savePart"></span>
[`jmvcore::Analysis$.savePart()`](../../jmvcore/html/Analysis.html#method-.savePart)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setCheckpoint"></span>
[`jmvcore::Analysis$.setCheckpoint()`](../../jmvcore/html/Analysis.html#method-.setCheckpoint)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setParent"></span>
[`jmvcore::Analysis$.setParent()`](../../jmvcore/html/Analysis.html#method-.setParent)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetHeaderSource"></span>
[`jmvcore::Analysis$.setReadDatasetHeaderSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setReadDatasetSource"></span>
[`jmvcore::Analysis$.setReadDatasetSource()`](../../jmvcore/html/Analysis.html#method-.setReadDatasetSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setResourcesPathSource"></span>
[`jmvcore::Analysis$.setResourcesPathSource()`](../../jmvcore/html/Analysis.html#method-.setResourcesPathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id=".setStatePathSource"></span>
[`jmvcore::Analysis$.setStatePathSource()`](../../jmvcore/html/Analysis.html#method-.setStatePathSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="addAddon"></span>
[`jmvcore::Analysis$addAddon()`](../../jmvcore/html/Analysis.html#method-addAddon)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asProtoBuf"></span>
[`jmvcore::Analysis$asProtoBuf()`](../../jmvcore/html/Analysis.html#method-asProtoBuf)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="asSource"></span>
[`jmvcore::Analysis$asSource()`](../../jmvcore/html/Analysis.html#method-asSource)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="check"></span>
[`jmvcore::Analysis$check()`](../../jmvcore/html/Analysis.html#method-check)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="init"></span>
[`jmvcore::Analysis$init()`](../../jmvcore/html/Analysis.html#method-init)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="optionsChangedHandler"></span>
[`jmvcore::Analysis$optionsChangedHandler()`](../../jmvcore/html/Analysis.html#method-optionsChangedHandler)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="postInit"></span>
[`jmvcore::Analysis$postInit()`](../../jmvcore/html/Analysis.html#method-postInit)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="print"></span>
[`jmvcore::Analysis$print()`](../../jmvcore/html/Analysis.html#method-print)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="readDataset"></span>
[`jmvcore::Analysis$readDataset()`](../../jmvcore/html/Analysis.html#method-readDataset)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="run"></span>
[`jmvcore::Analysis$run()`](../../jmvcore/html/Analysis.html#method-run)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="serialize"></span>
[`jmvcore::Analysis$serialize()`](../../jmvcore/html/Analysis.html#method-serialize)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setError"></span>
[`jmvcore::Analysis$setError()`](../../jmvcore/html/Analysis.html#method-setError)
- <span class="pkg-link" pkg="jmvcore" topic="Analysis"
data-id="setStatus"></span>
[`jmvcore::Analysis$setStatus()`](../../jmvcore/html/Analysis.html#method-setStatus)
- <span class="pkg-link" pkg="ClinicoPath" topic="vennBase"
data-id="initialize"></span>
[`ClinicoPath::vennBase$initialize()`](../../ClinicoPath/html/vennBase.html#method-initialize)
------------------------------------------------------------------------
<span id="method-clone"></span>
#### Method `clone()`
The objects of this class are cloneable with this method.
##### Usage
vennClass$clone(deep = FALSE)
##### Arguments
`deep`
Whether to make a deep clone.
---