R/writeMDSAnalysisReport.R

In ptl93/AEDA: Automated Exploratory Data Analysis

#' Writes a rmd file for the Multidimensional Scaling Report [WIP]
#'
#' @param report [\code{MDSAnalysisReport} 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.\cr
#'   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
#'  mds.task = makeMDSTask(id = "swiss", data = swiss)
#'  mds.analysis.result = makeMDSAnalysis(mds.task)
#'  mds.analysis.report = makeReport(mds.analysis.result)
#'  #write the report
#'  writeReport(mds.analysis.report, save.mode = FALSE, override = TRUE)
#' @return Invisible NULL
#' @import checkmate
#' @export
writeReport.MDSAnalysisReport = function(report, sub.dir = "Data_Report",
  save.mode = TRUE, override = FALSE){
  report.env = new.env(parent = .GlobalEnv)
  assertClass(report, "MDSAnalysisReport")
  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("MDSAnalysisReport")

  # 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("## Multidimensional Scaling Summary Report",
      con  = report.con)
    #add generic text from vignette:
    writeLines("Multidimensional scaling (MDS) is a **visual representation of distances or dissimilarities
between sets of objects**. Objects can be colors, faces, map coordinates, political persuasion, or any kind
of real conceptual stimuli
<a href='https://books.google.de/books/about/Multidimensional_Scaling.html?id=ZzmIPcEXPf0C&redir_esc=y'
target='_blank'>(Kruskal and Wish, 1978)</a>.
Objects that are more similar (or have shorter distances) are closer together on the graph than objects that
are less similar (or have linger distances). As well as interpreting dissilarities as distances on a graph, MDS
can also serve as a dimension reduction technique for high-dimensional data.
An MDS algorithm aims to place each object in $K-$dimensional space such that the between-object distances are
preserved as well as possible. The approach of AEDA is to set $K = 2$ in order to create a two-dimensional
scatterplot to represent the objects.", con = report.con)
    #Load object and libraries:
    writeLines(writeRChunkOptions(chunkname = "loadMDSObj",
      id = getId(report)),
      con = 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("### Multidimensional Scaling Summary Results\n", con = report.con)
    writeLines("The following data frame shows the created dimensions for numeric columns from the dataset:",
      con = report.con)
    #Show result dataframe
    writeLines(writeRChunkOptions(chunkname = "showMDSdf", id = getId(report)), con = report.con)

    #plot filterable datatable as option:
    writeLines(paste0("dt = DT::datatable(", report$report.id,
      "$mds.analysis$mds.result.data, class = 'compact', filter = 'bottom', options = list(pageLength = 10),
      caption = htmltools::tags$caption(
      style = 'caption-side: bottom; text-align: center;',
      'Table : ', 'Multidimensional Scaling Result'
      ))"), con = report.con)
    writeLines("dt", con = report.con)
    writeLines("```\n", con = report.con)

    ##Intro text:
    writeLines("### Multidimensional Scaling Plot\n", con = report.con)
    writeLines("In the following the result of MDS will be shown:", con = report.con)
    writeLines(writeRChunkOptions(chunkname = "showMDSPlot", id = getId(report),
      options = list(echo = FALSE, message = FALSE, warning = FALSE, out.width = "'90%'")),
      con = report.con)
    writeLines(paste0(report$report.id, "$mds.analysis$mds.plot"), con = report.con)
    writeLines("```", con = report.con)

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