AEDA: Automated Exploratory Data Analysis

#' Writes a rmd file for the Numeric Summary Report [WIP]
#'
#' @param report [\code{NumSumReport} Object]\cr
#'   The report Object which should be converted to an rmd file
#' @param sub.dir [\code{character(1)}]\cr
#'   the name of the (relative) sub-directory where the data report will be saved. Default is \code{Data_Report}
#' @param save.mode [\code{logical(1)}]\cr
#'   In Save mode its not possible to use an existing folder.
#'   To ensure no data is lost, a new folder will be created (if possible).
#' @param override [\code{logical(1)}]\cr
#'   override controls if the function is allowed to override
#'   an existing rmd-file
#'   Default is \code{TRUE}
#' @examples
#'  data("Aids2", package = "MASS")
#'  num.sum.task = makeNumSumTask(id = "AidsTask", data = Aids2,
#'    target = "sex")
#'  #get the numeric summary task object
#'  num.sum.result = makeNumSum(num.sum.task)
#'  #create the numeric summary report
#'  num.sum.report = makeReport(num.sum.result)
#'  #write the report
#'  writeReport(num.sum.report, save.mode = FALSE, override = TRUE)
#' @return Invisible NULL
#' @import checkmate
#' @export
writeReport.NumSumReport = function(report, sub.dir = "Data_Report", save.mode = TRUE, override = FALSE){
  report.env = new.env(parent = .GlobalEnv)
  assertClass(report, "NumSumReport")
  assertCharacter(sub.dir, len = 1L, min.chars = 1L)
  assertLogical(save.mode, len = 1L)
  # Create sub directory, save current wd and set new wd to the new directory
  origin.wd = createDir(sub.dir, save.mode)
  rmd.name = rmdName("NumSumReport")

  # TryCatch sets wd back and closes all open connections if an error occurs
  tryCatch({
    ##try part:
    #start the report file
    report.con = file(rmd.name, "w", encoding = rmdEncoding())

    writeLines("## Numeric Summary Report", con  = report.con)
    #Load object and libraries:
    writeLines(writeRChunkOptions(chunkname = "loadNumSumObj", id = getId(report)), con = report.con)
    rmdLibrary("knitr", file = report.con)
    rmdLibrary("kableExtra", file = report.con)
    rmdLibrary("DT", file = report.con)
    #writeLines("devtools::load_all() #temporary", con = report.con)
    # save object and write code to load it in the rmd-file
    saveLoadObj(report, getId(report), report.con, override = override)
    writeLines("```", con = report.con)

    ##Add generic text:
    writeLines("### Numeric Summary Results\n", con = report.con)
    writeLines("The following data frame shows summary statistics for numeric colums from the dataset:", con = report.con)
    #Show num.sum dataframe
    writeLines(writeRChunkOptions(chunkname = "showNumSumDF", id = getId(report)), con = report.con)
    #writeLines(paste0("kable(",report$report.id, "$num.sum.df[,c(5,6,4,7,8,10,12,13,14,16,21,22)])"), con = report.con)

    #Add colnames footer for kurtosis, skewness, l.bound and u.bound
    string1 = paste0("colnames(", report$report.id, "$num.sum.df[,c(5,6,4,7,8,10,12,13,14,16,21,22)])[1]")
    string1 = paste0(string1, " = paste0(colnames(", report$report.id, "$num.sum.df[,c(5,6,4,7,8,10,12,13,14,16,21,22)])[1], footnote_marker_alphabet(1))")
    writeLines(string1, con = report.con)
    writeLines("\n", con = report.con)

    string2 = paste0("colnames(", report$report.id, "$num.sum.df[,c(5,6,4,7,8,10,12,13,14,16,21,22)])[2]")
    string2 = paste0(string2, " = paste0(colnames(", report$report.id, "$num.sum.df[,c(5,6,4,7,8,10,12,13,14,16,21,22)])[2], footnote_marker_alphabet(2))")
    writeLines(string2, con = report.con)
    writeLines("\n", con = report.con)

    string3 = paste0("colnames(", report$report.id, "$num.sum.df[,c(5,6,4,7,8,10,12,13,14,16,21,22)])[11]")
    string3 = paste0(string3, " = paste0(colnames(", report$report.id, "$num.sum.df[,c(5,6,4,7,8,10,12,13,14,16,21,22)])[11], footnote_marker_alphabet(3))")
    writeLines(string3, con = report.con)
    writeLines("\n", con = report.con)

    string4 = paste0("colnames(", report$report.id, "$num.sum.df[,c(5,6,4,7,8,10,12,13,14,16,21,22)])[12]")
    string4 = paste0(string4, " = paste0(colnames(", report$report.id, "$num.sum.df[,c(5,6,4,7,8,10,12,13,14,16,21,22)])[12], footnote_marker_alphabet(4))")
    writeLines(string4, con = report.con)
    writeLines("\n", con = report.con)

    #plot kable table with styling
    writeLines(paste0("kable(", report$report.id, "$num.sum.df[,c(5,6,4,7,8,10,12,13,14,16,21,22)], caption = 'Numeric Summary', format = 'html', escape = FALSE) %>%
      kable_styling(full_width = F) %>%
      footnote(general = 'Following footnotes explain some measure from the table above ',
      alphabet = c('Kurtosis will be calculated via: $\\\\frac{\\\\sum_{i = 1}^{n}(x_i - \\\\bar{x})^4 / n}{s^4}$;', 'Skewness will be calculated via: $\\\\frac{\\\\sum_{i = 1}^{n}(x_i - \\\\bar{x})^3 / n}{s^3}$; ',
      'l.bound is defined as: $q_{0.25} - 1.5IQR$; ', 'u.bound is defined as: $q_{0.75} + 1.5IQR$; where $IQR$ is defined as $IQR:= q_{0.75} - q_{0.25}$'),
      general_title = 'General: ',
      alphabet_title = 'Explanation: ',
      footnote_as_chunk = T,
      escape = FALSE
      )"),
      con = report.con)

    #plot filterable datatable as option:
    writeLines(paste0("dt = DT::datatable(", report$report.id, "$num.sum.df[,c(5,6,4,7,8,10,12,13,14,16,21,22)], class = 'compact', filter = 'bottom', options = list(pageLength = 10),
      caption = htmltools::tags$caption(
      style = 'caption-side: bottom; text-align: center;',
      'Table : ', 'Numeric Summary'
      ))"), con = report.con)
    writeLines("#dt", con = report.con)
    writeLines(paste0("#", report$report.id, "$num.sum.var"), con = report.con)
    writeLines("```\n", con = report.con)

    ##Intro text:
    writeLines("### Numeric Summary Plots\n", con = report.con)
    writeLines("In the following for each numeric column a histogram and box plot will be shown:", con = report.con)
    ##show histogram and quantile plot
    writeLines(writeRChunkOptions(chunkname = "showPlots", id = getId(report),
      options = list(echo = FALSE, message = FALSE, warning = FALSE, out.width = "'50%'")), con = report.con)
    writeLines(paste0("invisible(lapply(", report$report.id, "$num.sum.var,", " FUN = function(x) {
    multiplot(plotlist = list(plot.hist = x[[3]], plot.box = x[[4]]), cols = 2)
    }))"), con = report.con)
    writeLines("```", con = report.con)

  }, finally = {
    setwd(origin.wd)
    close(report.con)
  })
  return(file.path(sub.dir, rmd.name))
}