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+++ b/R/compClinvar.R
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+#' @name compClinvar
+#' @title Comparison of clinical variables
+#' @description Create a table summarizing all baseline variables (both continuous and categorical) stratifying by current identified Subtypes and performing statistical tests. The object gives a table that is easy to use in medical research papers.
+#' @param moic.res An object returned by `getMOIC()` with one specified algorithm or `get\%algorithm_name\%` or `getConsensusMOIC()` with a list of multiple algorithms.
+#' @param var2comp A data.frame of clinical variables that need to compare among current subtypes with rownames for samples and columns for variable names.
+#' @param strata A string value to indicate the stratifying variable. This function will generate an internal 'Subtype' variable which concatenates a string of 'CS' and values from 'clust' column of 'clust.res' in argument of `moic.res`. This argument is set as NULL by default and in this case using 'Subtype' variable as strata.
+#' @param factorVars A string vectors to indicate the categorical variables. If omitted, only factors are considered categorical variables.
+#' @param nonnormalVars A string vector to specify the variables for which the p-values should be those of nonparametric tests. By default all p-values are from normal assumption-based tests (oneway.test)., Default: NULL
+#' @param exactVars A string vector to specify the variables for which the p-values should be those of exact tests. By default all p-values are from large sample approximation tests (chisq.test)., Default: NULL
+#' @param includeNA A logic value to indicate if NA should be handled as a regular factor level rather than missing. NA is shown as the last factor level in the table if \code{includeNA = T}. Only effective for categorical variables., Default: FALSE
+#' @param doWord A logic value to indicate if transformating the .txt outfile to a .docx WORD file (.txt file will be also kept).
+#' @param tab.name A string value to indicate the name of the output table.
+#' @param res.path A string value to indicate the path for saving the table.
+#' @param ... Additionnal parameters pass to jstable::CreateTableOne2
+#' @importFrom jstable CreateTableOne2
+#' @importFrom dplyr %>%
+#' @importFrom officer read_docx body_add_par body_add_table body_add_par
+#' @export
+#' @return A summarizing table with stastitical testing results.
+#' @examples # There is no example and please refer to vignette.
+compClinvar <- function(moic.res      = NULL,
+                        var2comp      = NULL,
+                        strata        = NULL,
+                        factorVars    = NULL,
+                        nonnormalVars = NULL,
+                        exactVars     = NULL,
+                        includeNA     = FALSE,
+                        doWord        = TRUE,
+                        tab.name      = NULL,
+                        res.path      = getwd(),
+                        ...){
+
+  dat <- moic.res$clust.res
+  colnames(dat)[which(colnames(dat) == "clust")] <- "Subtype"
+  dat$Subtype <- paste0("CS", dat$Subtype)
+  com_sam <- intersect(dat$samID,rownames(var2comp))
+
+  # check data
+  if(length(com_sam) == nrow(dat)) {
+    message("--all samples matched.")
+  } else {
+    message(paste0("--",(nrow(dat)-length(com_sam))," samples mismatched from current subtypes."))
+  }
+  dat <- cbind.data.frame("Subtype" = dat[com_sam, "Subtype", drop = FALSE], var2comp[com_sam, , drop = FALSE])
+
+  # summarizing
+  if(is.null(strata)) {
+    strata <- "Subtype"
+  }
+  if(!is.element(strata, colnames(dat))) {
+    stop("fail to find this strata in var2comp. Consider using NULL by default.")
+  }
+
+  warn <- NULL
+  tryCatch(stabl <-
+             jstable::CreateTableOne2(vars = setdiff(colnames(dat), strata),
+                                     strata = strata,
+                                     data = dat,
+                                     factorVars = factorVars,
+                                     nonnormal = nonnormalVars,
+                                     exact = exactVars,
+                                     includeNA = includeNA,
+                                     showAllLevels = TRUE,
+                                     ...),
+           warning=function(w) {
+             warn <<- append(warn, conditionMessage(w))}
+           )
+  if(grepl("NA", warn, fixed = TRUE)) { # if get warning, probably due to the failure of computing exact p value in large data
+    set.seed(19991018)
+    stabl <- jstable::CreateTableOne2(vars = setdiff(colnames(dat), strata),
+                                      strata = strata,
+                                      data = dat,
+                                      factorVars = factorVars,
+                                      nonnormal = nonnormalVars,
+                                      exact = exactVars,
+                                      includeNA = includeNA,
+                                      showAllLevels = TRUE,
+                                      argsExact = list(simulate.p.value = T), # use simulated P values then
+                                      ...)
+  } else {
+    stabl <- jstable::CreateTableOne2(vars = setdiff(colnames(dat), strata),
+                                      strata = strata,
+                                      data = dat,
+                                      factorVars = factorVars,
+                                      nonnormal = nonnormalVars,
+                                      exact = exactVars,
+                                      includeNA = includeNA,
+                                      showAllLevels = TRUE,
+                                      ...)
+  }
+
+  # trim output
+  comtable <- as.data.frame(stabl)
+  comtable <- cbind.data.frame(var = rownames(stabl), comtable)
+  rownames(comtable) <- NULL; colnames(comtable)[1] <- " "
+  comtable[is.na(comtable)] <- ""
+  comtable <- comtable[,setdiff(colnames(comtable),"sig")] # remove significance
+  #print(comtable)
+
+  if(is.null(tab.name)) {
+    outFile <- "summarization of clinical variables stratified by current subtype.txt"
+  } else {
+    outFile <- paste0(tab.name,".txt")
+  }
+
+  write.table(stabl, file.path(res.path,outFile), sep = "\t", quote = FALSE)
+
+  # generate WORD format
+  if(doWord){
+    table_subtitle <- colnames(comtable)
+
+    title_name <- paste0("Table *. ", gsub(".txt", "", outFile, fixed = TRUE))
+    mynote <- "Note: ..."
+
+    my_doc <- officer::read_docx()
+    my_doc %>%
+      officer::body_add_par(value = title_name, style = "table title") %>%
+      officer::body_add_table(value = comtable, style = "table_template") %>%
+      officer::body_add_par(value = mynote) %>%
+      print(target = file.path(res.path,paste0("TABLE ", gsub(".txt", "", outFile, fixed = TRUE), ".docx")))
+  }
+  return(list(compTab = comtable))
+}