#' @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))

}