postProcessReport {clinDataReview}

Convert clinical data Markdown files to HTML

Description

Convert clinical data Markdown files to HTML

Usage

postProcessReport(
  inputDir = ".",
  configDir = file.path(inputDir, "config"),
  indexPath = file.path(inputDir, "index.Rmd"),
  extraDirs = getExtraDirs(inputDir = inputDir, configDir = configDir),
  outputDir = "./report",
  intermediateDir = "./interim",
  mdFiles = NULL,
  nCores = 1,
  logFile = NULL,
  verbose = TRUE,
  ...
)

Arguments

inputDir

String with input directory, working directory by default.

configDir

String with directory with config files, by default a 'config' folder in inputDir.
It should contain a general 'config.yml' file and dedicated 'config-[X].yml' for each chapter. The order of each chapter is specified in the 'config' slot in the general general 'config.yml'.

indexPath

String with path to the index file, by default 'index.Rmd' in inputDir.

extraDirs

Character vector with extra directories required by the report, directory with external images. By default, the directories: 'figures', 'tables' and mentioned in the 'patientProfilePath' parameter of the general config file are included. All these folders should be available in inputDir.

outputDir

String with output directory, ('report' by default).

intermediateDir

String with intermediate directory ('interim' by default), where markdown files and rds file specifying Js libraries (with knit_meta) for each sub report are stored.

mdFiles

(optional) Path to the Markdown files that should be converted. If specified, the specified config files in configDir are ignored.

nCores

Integer containing the number of cores used to render the report (1 by default). If more than 1, two steps of the report creation are run in parallel across chapters:

• the rendering of the Rmarkdown file to Markdown

• the conversion from Markdown to HTML

logFile

(optional) String with path to a log file, where output (also error/messages/warnings) should be stored. If specified, the entire output is re-directed to this file.

verbose

Logical, if TRUE (FALSE by default) progress messages are printed during the report execution.

...

Any parameters passed to render, for expert use only.

Value

String with path to the front page of the report.

Author(s)

Laure Cougnaud

See Also

Other clinical data reporting: checkReportTitles(), forceParams(), getMdHeader(), getParamsFromConfig(), gitbook_clinDataReview_report(), html_clinDataReview_report(), knitPrintClinDataReview(), render_clinDataReviewReport()