NEWS.md
# ClinicoPath 0.0.2.0072
calculated cut-off groups in continuous survival can be added to data
# ClinicoPath 0.0.2.0069
optional padjustement to pairwise survival fixes: https://github.com/sbalci/ClinicoPathJamoviModule/issues/38
saving calculated variables to Data
# ClinicoPath 0.0.2.0064
- added ggvenn function
fixed https://github.com/yanlinlin82/ggvenn/issues/16
- deleted some functions, will add as updated
# ClinicoPath 0.0.2.0048
- started adding arguments of ggstatsplot
fixed: https://github.com/sbalci/jjstatsplot/issues/3
# ClinicoPath 0.0.2.0046
- use `x` and `y` instead of `main` and `condition` arguments for `ggpiestats` and `ggbarstats`
partially fixed: https://github.com/sbalci/jjstatsplot/issues/1
- add point.path argument in grouped_ggwithinstats
partially fixed: https://github.com/sbalci/jjstatsplot/issues/2
- waiting for update in jamovi mran version. current ggstatsplot dependencies are not up to date in jamovi's library
# ClinicoPath 0.0.2.0044
- fixed multivariate survival to work without continuous explanatory
# ClinicoPath 0.0.2.0043
- added jsurvival to linux
- added some functions of descriptives to linux
# ClinicoPath 0.0.2.0041
- updated jsurvival
- added more controls under collapse boxes
- advanced outcome: users can select more than one outcome level depending on their analysis (event free or overall survival). Competing risk survival will also be added in the future.
- advanced survival: users can use dates to calculate survival time. the date type should be defined. many variations for date types are given.
- Cumulative events, cumulative survival and KMunicate style Kaplan-Meier curves are added.
- A separate function for continuous explanatory variable is added. The optimal cut-off based on survival outcome is defined and after cut-off definition other univariate survival analysis are performed.
- under multivariate analysis users can now generate Kaplan-Meier curves upto two explanatory variables.
- an adjusted survival curve is also added, though it requires further management.
# ClinicoPath 0.0.2.0040
- separating univariate continuous survival from categorical
# ClinicoPath 0.0.2.0039
- added options to vartree
fixes: https://github.com/sbalci/ClinicoPathJamoviModule/issues/28
# ClinicoPath 0.0.2.0038
- fixes https://github.com/sbalci/ClinicoPathJamoviModule/issues/20
# ClinicoPath 0.0.2.0037
- added Survival Analysis for Continuous Explanatory
- added vtree package functions to vartree function
- fixes https://github.com/sbalci/ClinicoPathJamoviModule/issues/9
# ClinicoPath 0.0.2.0036
- added Benford Analysis
- added interactive size to jjbarstats
```
.init = function() {
deplen <- length(self$options$dep)
self$results$plot$setSize(400, deplen*300)
}
```
# ClinicoPath 0.0.2.0035
- meddecide has been added to jamovi library
https://github.com/sbalci/meddecide/
https://github.com/sbalci/meddecide/releases/
https://library.jamovi.org/win64/R3.6.3/meddecide-0.0.1.0005.jmo
https://library.jamovi.org/linux/R3.6.3/meddecide-0.0.1.0005.jmo
https://library.jamovi.org/macos/R3.6.3/meddecide-0.0.1.0005.jmo
# ClinicoPath 0.0.2.0034
- added metrics to survival functions
- updating survival options (continuous explanatory, cut-off, two categorical explanatory, multiple outcome options, elapsed time calculation from dates)
- added KMunicate type survival curve
- added Fagan's nomogram
# ClinicoPath 0.0.2.0027
- temporarily added many functions from various packages to update functions and arguments
# ClinicoPath 0.0.2.0026
- jsurvival has been added to jamovi library
https://github.com/sbalci/jsurvival
https://github.com/sbalci/jsurvival/releases/
https://library.jamovi.org/macos/R3.6.3/jsurvival-0.0.2.0026.jmo
https://library.jamovi.org/win64/R3.6.3/jsurvival-0.0.2.0026.jmo
# ClinicoPath 0.0.2.0025
- ClinicoPath as a combined module has been taken down from jamovi library.
- Users are adviced to install submodules.
- ClinicoPathDescriptives, jsurvival, and meddecide tables have been updated to look more jamovian :)
# ClinicoPath 0.0.2.0024
- ClinicoPathDescriptives functions are separately added to jamovi library under Exploration menu
ClinicoPathDescriptives module can be downloaded inside jamovi (click Modules and jamovi library)
https://library.jamovi.org/win64/R3.6.3/ClinicoPathDescriptives-0.0.2.0019.jmo
https://library.jamovi.org/linux/R3.6.3/ClinicoPathDescriptives-0.0.2.0019.jmo
https://library.jamovi.org/macos/R3.6.3/ClinicoPathDescriptives-0.0.2.0019.jmo
# ClinicoPath 0.0.2.0023
- added Age Pyramid
- survival status can be selected from levels
- WIP decisioncalculator
# ClinicoPath 0.0.2.0022
- GGStatsPlot functions are separately added to jamovi library under jjstatsplot menu
JJStastPlot module can be downloaded inside jamovi (click Modules and jamovi library)
https://library.jamovi.org/macos/R3.6.3/jjstatsplot-0.0.1.0001.jmo
https://library.jamovi.org/win64/R3.6.3/jjstatsplot-0.0.1.0001.jmo
https://library.jamovi.org/linux/R3.6.3/jjstatsplot-0.0.1.0001.jmo
# ClinicoPath 0.0.2.0021
- updating jjstatsplot for release
# ClinicoPath 0.0.2.0020
- made submodules:
- ClinicoPathDescriptives
https://github.com/sbalci/ClinicoPathDescriptives/
https://github.com/sbalci/ClinicoPathDescriptives/releases/
- JJStatsPlot:
https://github.com/sbalci/jjstatsplot
https://github.com/sbalci/jjstatsplot/releases/
- jsurvival:
https://github.com/sbalci/jsurvival
https://github.com/sbalci/jsurvival/releases/
- meddecide
https://github.com/sbalci/meddecide/
https://github.com/sbalci/meddecide/releases/
# ClinicoPath 0.0.2.0019
- rewrote summary of categorical values to decrease dependencies
# ClinicoPath 0.0.2.0018
- added cumulative events and cumulative hazard plots to survival
<https://rpkgs.datanovia.com/survminer/survminer_cheatsheet.pdf>
- added cox adjusted survival to multivariate survival
# ClinicoPath 0.0.2.0017
- added alluvial diagrams using easyalluvial package to Descriptives (under
Explore menu)\
<https://github.com/sbalci/ClinicoPathJamoviModule/issues/19>\
<https://github.com/erblast/easyalluvial/issues/19>
- added easyalluvial as an option to Graphs and Plots (under JJStatsPlot menu)
for repeated categorical measurements.
# ClinicoPath 0.0.2.0016
- See: <https://github.com/sbalci/jjstatsplot/releases/>
- See: <https://github.com/sbalci/ClinicoPath/releases/>
- crosstable function partially resolves
<https://github.com/jamovi/jamovi/issues/443>
- survival function resolves
<https://github.com/jonathon-love/deathwatch/issues/2>
- added export html to crosstables to bypass
<https://github.com/jamovi/jamovi/issues/892>
# ClinicoPath 0.0.2.0015
- Added tangram statistical results
- Added options to finalfit crosstables fixes:
<https://github.com/sbalci/ClinicoPathJamoviModule/issues/24> Partially
fixes: <https://github.com/jamovi/jamovi/issues/901> fixes:
<https://github.com/ewenharrison/finalfit/issues/52>
- Added experimental biblometrics functions
- includes experimental changes
# ClinicoPath 0.0.2.0014
- Added footnote to arsenal crosstable
# ClinicoPath 0.0.2.0012
- jjstatsplot is the wrapper functions for using ggstatsplot in jamovi.
- I thought it might be a nice separate module too. I have prepared it to ask
opinions.
- Use attached `.jmo`files to install via side load in jamovi.
- Requires latest jamovi \>=1.2.22 <https://www.jamovi.org/download.html>
- tangram error is fixed, but it does not reveal statistical test results.
- arsenal's footnote is not visible in Html output
# ClinicoPath 0.0.2.0004
Using `spgarbet/tangram@0.3.2` until the bug is fixed.
# ClinicoPath 0.0.2.0003
Added arsenal, finalfit, and gtsummary to crosstable function. gtsummary gives
different results, due to nonparametric tests. Should add options and
documentation. tangram still not functioning.
# ClinicoPath 0.0.2
- version 0.0.2 is released
- works with jamovi latest release (\>=1.2.18)
<https://www.jamovi.org/download.html>
{align="center"
width="75%"}
- The new version of \#ClinicoPath [@jamovistats] module is on the jamovi
library. Requires \#jamovi 1.2.18 \#rstats \#biostatistics \#pathology
\#pathologists
<https://twitter.com/serdarbalci/status/1261256107919642629>
- \#ClinicoPath \#jamovi module comes with example datasets as with other
\#jamovi modules. Use them as example to prepare your data.
<https://twitter.com/serdarbalci/status/1261639212664840192>
- You can easily make 'Table One' for reports/manuscripts via \#ClinicoPath
[@jamovistats] module. Uses \#tableone, \#arsenal, \#gtsummary, and
\#janitor packages. \#rstats \#biostatistics \#pathology \#pathologists
<https://twitter.com/serdarbalci/status/1262083972328230912>
- \#jamovi has very nice tables. Sometimes I prefer to read the tables
automatically via \#ClinicoPath [@jamovistats] module. Using \#easystats
\#report package. \#naturallanguage \#data \#summary \#rstats
\#biostatistics \#pathology \#pathologists
<https://twitter.com/serdarbalci/status/1262354990787694599>
- With \#ClinicoPath [@jamovistats] module it is easy to make crosstables.
uses \#tangram package \#rstats \#biostatistics \#pathology \#pathologists
<https://twitter.com/serdarbalci/status/1262691784574017536>
- You can make different plots based on variable type via \#jamovi
\#ClinicoPath module. Using \#rstats [@jamovistats] \#ggstatsplot
\#ggalluvial \#easyalluvial packages \#pathology \#pathologists
\#datavisualisation
<https://www.youtube.com/watch?v=m3uInetiC8w>
<https://twitter.com/serdarbalci/status/1263191858454413312>
- Some examples of survival analysis via [@jamovistats] \#ClinicoPath module.
Using \#rstats \#finalfit by [@ewenharrison] \#survival \#survminer
\#ggstatsplot in \#jamovi \#biostatistics \#pathology \#pathologists
<https://www.youtube.com/watch?v=gIPf4xIKAOU>
<https://www.linkedin.com/pulse/survival-analysis-via-jamovi-clinicopath-module-serdar-balc%25C4%25B1>
\#datavisualisation \#datascience \#patoloji \#analysis \#datascientist \#data
\#clinicaltrials \#clinicalstudies \#clinicaltrial \#clinicalresearch
<https://twitter.com/serdarbalci/status/1264153665386004480>
It is generating natural language summaries to make easy to read the tables:
"Median Survival: When LVI is Absent, median survival is 26 [20.1 - 32.3,"95%
CI] months. When LVI is Present, median survival is 9.3 [8.8 - 10.6, 95% CI]
months."
<https://twitter.com/serdarbalci/status/1264153686508478465>
"Hazard: When LVI is Present, there is 2.55 (1.85-3.51, p\<0.001) times risk
than when LVI is Absent."
<https://twitter.com/serdarbalci/status/1264153695715053568>
"1, 3, 5-yr Survival: When LVI Absent, 12 month survival is 70.9% [63.36%-79.3%,
95% CI]. When LVI Absent, 24 month survival is 54.2% [45.85%-64.1%, When LVI
Present, 12 month survival is 28.4% [20.03%-40.3%, 95% CI]. When LVI Present, 24
month survival is 14.4% ..."
<https://twitter.com/serdarbalci/status/1264153698764312577>
"pairwise comparison of Grade: The comparison between Grade 2 and Grade 1 has a
p-value of 0.87." Note for myself: The wording should be better.
<https://twitter.com/serdarbalci/status/1264153700114862080>
You can do multivariate survival analysis
<https://twitter.com/serdarbalci/status/1264153711087140864>
And also make Odds Ratio Tables and Plots. When you change the order of
variables in jamovi data, the analysis also changes.
<https://twitter.com/serdarbalci/status/1264153752015122432>
<https://github.com/sbalci/ClinicoPathJamoviModule>
<iframe width="560" height="315" src="https://www.youtube.com/embed/videoseries?list=PLxRBOaoEoP4JfAMi7aIbkRXPXGUEwzTNv" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen>
</iframe>
# ClinicoPath 0.0.1.0001
Added multivariate survival, and comparison plots.
# ClinicoPath v0.0.1
A jamovi module that contains main analysis used in clinicopathological
research. ClinicoPath help researchers to generate natural language summaries of
their dataset, generate cross tables with statistical tests, and survival
analysis with survival tables, survival curves, and natural language summaries.
You may install using side load: windows:
<https://library.jamovi.org/win64/R3.6.1/ClinicoPath-0.0.1.jmo> macOS:
<https://library.jamovi.org/macos/R3.6.1/ClinicoPath-0.0.1.jmo>
<https://github.com/sbalci/ClinicoPathJamoviModule>
<https://github.com/sbalci/ClinicoPathJamoviModule/releases/tag/v0.0.1>
# ClinicoPath 0.0.1.1001
- removed 'frequencies'
- Documentations are being added.
- CI are being added.
- Badges, README are updated.
# ClinicoPath 0.0.1.1000
## Functions work as defaults
- Divided module into 2 windows: ClinicoPath1 and ClinicoPath2
- Removed unnecessary outputs.
- Added ToDo section and a warning that still in development
- Updated Readme file
- Currently functions are working. But only in defaults.
### For descriptive analysis:
- TableOne
- WriteSummary
- Report General Features
- Frequencies
### For comparing variables:
- CrossTable
- GGStatsPlot2
### For survival analysis
- FinalFit
- FinalFit Multivariate Survival
### For medical decision tests:
- Medical Decision
- Decision Calculator
### For correlation analysis:
- Correlation
### For inter and intra observer agreement
- Interrater Intrarater Reliability
### Decision tree and cluster analysis sections.
- Not active yet.
# ClinicoPath 0.0.1-beta
- First Pre-release
- <https://github.com/sbalci/ClinicoPathJamoviModule/releases/tag/0.0.1-beta>