setup_MarkdownReports: setup_MarkdownReports
In vertesy/MarkdownReportsDev: Generate Scientific Figures and Reports Easily

Setup the markdown report file and the output directory, create a sub directory in "OutDir". Its name is stamped with the script name and the modification time. Create the "path_of_report" variable used by all log-writing and ~wplot functions.

setup_MarkdownReports(
  OutDir = getwd(),
  scriptname = basename(OutDir),
  title = "",
  setDir = TRUE,
  recursive.folder = TRUE,
  backupfolder = TRUE,
  append = FALSE,
  addTableOfContents = FALSE,
  saveSessionInfo = TRUE,
  saveParameterList = "p",
  b.defSize = c(def = 7, A4 = 8.27, `1col.nature` = 3.5, `2col.nature` = 7.2,
    `1col.cell` = 3.35, `1.5col.cell` = 4.49, `2col.cell` = 6.85)[1],
  b.defSize.fullpage = 8.27,
  b.usepng = FALSE,
  b.png4Github = FALSE,
  b.mdlink = TRUE,
  b.save.wplots = TRUE,
  b.def.color = "gold1"
)

`OutDir`	The output directory (absolute / full path).
`scriptname`	Name of the script file you are running. This filename is written in the title field of .pdf files, so that you know which script generated that file. Example: "GeneFilt.hist by MyFilteringScript".
`title`	Manually set the title of the report.
`setDir`	Set the working directory to OutDir? Default: TRUE
`recursive.folder`	Create output folder recursively, if parent folders do not exist. Parameter for dir.create(). Use continue_logging_markdown() if you return logging into an existing report. FALSE by default: rerunning the script overwrites the previous report. Archive reports manually into the timestamped subfolder within the OutDir.
`backupfolder`	Create a time-stamped backup folder inside the working directory (OutDir).
`append`	Set append to TRUE if you do not want to overwrite the previous report.
`addTableOfContents`	write 'TOC' below the header of the file, This is compiled to a proper Table Of Contents by, e.g. Typora.
`saveSessionInfo`	save 'sessioninfo::session_info()' results to '.session_info.DATE.txt.gz'
`saveParameterList`	save the list of parameters stored in the variable name provides ("p" by default) as a table in the markdown report. Uses the md.LogSettingsFromList() function. Set to FALSE to disable this option.
`b.defSize`	Default width of plot EXCEPT in pdfA4plot_on(), assuming h = w by default. c("def" = 7, "A4" = 8.27, "1col.nature" = 3.50, "2col.nature" = 7.20, "1col.cell" = 3.35, "1.5col.cell" = 4.49, "2col.cell" = 6.85)
`b.defSize.fullpage`	Default width of plot in pdfA4plot_on()A global background variable used by pdfA4plot_on.
`b.usepng`	A global background variable used by the plotting functions. If TRUE, a link to the .png versions of the saved plot will be created. The .png file itself is not created.
`b.png4Github`	A global background variable used by the plotting functions. If TRUE (default), the link to the .png versions of the saved plot will be created in a GitHub compatible format. That means, when you upload your markdown report and the .png images to your GitHub wiki under "Reports/" the links will correctly display the images online.
`b.mdlink`	A global background variable used by the plotting functions. If TRUE (default), all saved (.pdf) plots will be linked into your report.
`b.save.wplots`	A global background variable used by the plotting functions. If TRUE (default), plots will be saved to a .pdf file.
`b.def.color`	Set the default color for all wplot* functions.