sbalci/ClinicoPathJamoviModule

---
title: "Use jsurvival in R"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Use jsurvival in R}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r setup}
library(ClinicoPath)
```


```{r data histopathology}
data("histopathology")
```

```{r}
#| glimpse histopathology

dplyr::glimpse(histopathology)
```


```{r}
ClinicoPath::survival(
    data = histopathology,
    elapsedtime = "OverallTime",
    tint = TRUE,
    dxdate = SurgeryDate,
    fudate = LastFollowUpDate,
    explanatory = LVI,
    outcome = Outcome,
    outcomeLevel = NULL,
    dod = NULL,
    dooc = NULL,
    awd = NULL,
    awod = NULL,
    timetypedata = "ymdhms",
    sc = TRUE,
    ce = TRUE,
    ch = TRUE
    )
```




```{r}
overall_survival <-
ClinicoPath::survival(
    data = histopathology,
    elapsedtime = "OverallTime",
    tint = TRUE,
    dxdate = SurgeryDate,
    fudate = LastFollowUpDate,
    explanatory = LVI,
    outcome = Outcome,
    outcomeLevel = NULL,
    dod = NULL,
    dooc = NULL,
    awd = NULL,
    awod = NULL,
    timetypedata = "ymdhms",
    sc = TRUE,
    ce = TRUE,
    ch = TRUE
    )
```


```{r}
ls(overall_survival)
```



```{r}
overall_survival$tCoxtext2
```


```{r}
overall_survival$survTableSummary
```


```{r}
overall_survival$survTable
```



```{r}
overall_survival$subtitle
```



```{r}
overall_survival$plot3
```



```{r}
overall_survival$plot2
```



```{r}
overall_survival$plot
```



```{r}
overall_survival$medianTable
```


```{r}
overall_survival$medianSummary
```



```{r}
overall_survival$coxTable
```



```{r}
overall_survival$coxTable$asDF
```




```{r}
overall_survival$coxSummary
```




```{r}
overall_survival$plot

```


```{r}
# overall_survival$plot$saveAs("overall_survival.png")
# 
# overall_survival <- png::readPNG("overall_survival.png")
# 
# tiff::writeTIFF(what = overall_survival, where = "overall_survival.tiff", compression = "none")
```
 
 



```{r}
# htmlTable::htmlTable(
#   kableExtra::kable(
#     overall_survival$coxTable$asDF
#     ))


```




All functions

histopathology
    

histopathology

jsurvival-package _PACKAGE jsurvival
    

jsurvival: Analysis for jsurvivalological Research

multisurvival()
    

Multivariable Survival Analysis

multisurvivalClass
    

Multivariable Survival Analysis

oddsratio()
    

Odds Ratio Table and Plot

oddsratioClass
    

Odds Ratio Table and Plot

singlearm()
    

Single Arm Survival

singlearmClass
    

Single Arm Survival

survival()
    

Survival Analysis

survivalClass
    

Survival Analysis

survivalcont()
    

Survival Analysis for Continuous Variable

survivalcontClass
    

Survival Analysis for Continuous Explanatory Variable
Contents

    Reference