fix kaplan meier p val in cmp anal

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: jsmodule
 Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
-Version: 1.5.9
-Date: 2024-09-29
+Version: 1.5.10
+Date: 2024-12-11
 Authors@R: c(
   person("Jinseob", "Kim", email = "[email protected]", role = c("aut", "cre"),  comment = c(ORCID = "0000-0002-9403-605X")),
   person("Zarathu", role = c("cph", "fnd")),
@@ -10,7 +10,8 @@ Authors@R: c(
   person("Jinhwan", "Kim", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0009-0009-3217-2417")),
   person("Yoonkyoung", "Jeon", email = "[email protected]", role = c("aut")),
   person("Jaewoong", "Heo", email = "[email protected]", role = c("aut")),
-  person("Youngsun", "Park", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0009-0009-9336-2281")))
+  person("Youngsun", "Park", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0009-0009-9336-2281")),
+  person("Hyungwoo", "Jo", email = "[email protected]", role = c("aut")))
 Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
 Depends: R (>= 3.4.0)
 License: Apache License 2.0 

NEWS.md

@@ -1,3 +1,7 @@
+# jsmodule 1.5.10 
+## Update
+- Add competing risk analysis in subgroup, Kaplan-meier, regression tab.
+
 # jsmodule 1.5.9
 ## Bugfix:
 - `sav` file load in `FilePSInput.R`, `FileRepeatedInput.R`, `FileSurveyInput.R`

R/kaplan.R

@@ -495,14 +495,10 @@ kaplanModule <- function(input, output, session, data, data_label, data_varStruc
     data.km[[input$event_km]] <- as.numeric(as.vector(data.km[[input$event_km]]))
     if(input$cmp_risk_check){
       req(!is.null(input$cmp_event_km))
-      print(data.km %>% head())
-      print(input$event_km)
-      print('passing')
-      data.km[[input$cmp_event_km]]<- as.numeric(as.vector(data.km[[input$cmp_event_km]]))
+      data.km[[input$cmp_event_km]] <- as.numeric(as.vector(data.km[[input$cmp_event_km]]))
       data.km$cmpp_time <- with(data.km, ifelse(data.km[[input$event_km]]==0, data.km[[input$cmp_time_km]], data.km[[input$time_km]]))
       data.km$cmpp_event <- with(data.km, ifelse(data.km[[input$event_km]]==0, 2*data.km[[input$cmp_event_km]],  1))
-      print('passed')
-      print(data.km %>% head())
+      data.km$cmpp_event <- factor(data.km$cmpp_event, 0:2, labels=c("zero", "cmp", "cmprsk"))
     }
     if (input$subcheck == T) {
       validate(
@@ -691,19 +687,19 @@ kaplanModule <- function(input, output, session, data, data_label, data_varStruc
 
     if (is.null(design.survey)) {
       status_cmprsk <- NULL
-      print(res.km)
-      print(data.km %>% head(., n= 50))
       if (input$cmp_risk_check) {
-        status_cmprsk <- '1'
+        status_cmprsk <- 'cmp'
       }
       if (is.null(id.cluster)) {
+
+        if(input$cmp_risk_check){
         return(
           jskm::jskm(res.km,
             pval = input$pval, marks = input$marks, table = input$table, ylab = ylab, ystrataname = yst.name, ystratalabs = yst.lab, ci = input$ci, timeby = input$timeby, xlims = input$xlims, ylims = input$ylims,
             cumhaz = input$cumhaz, cluster.option = "None", cluster.var = NULL, data = data.km, pval.coord = pval.coord, legendposition = legend.p, linecols = pal, xlabs = text.x, dashed = dashed, cut.landmark = cut.landmark,
             showpercent = input$showpercent, surv.scale = surv.scale, status.cmprsk =  status_cmprsk
-          )
-        )
+          ))
+
       } else {
         return(
           jskm::jskm(res.km,