convertMdToHtml: Convert clinical data Markdown files to HTML

Description Usage Arguments Value Author(s) See Also

View source: R/reporting-render_clinDataReviewReport.R

Description

This consists of:

  1. importing the general config file ('config'.yml) to identify each report of interest ('config' tag)

  2. for each report of interest: checking if the associated Markdown and rds file (list of Js dependencies) are available in intermediateDir

  3. combining all Rmarkdown reports to a single document: main.md

  4. converting main.md to an HTML document

Usage

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convertMdToHtml(
  outputDir = "./report",
  inputDir = ".",
  configDir = file.path(inputDir, "config"),
  indexPath = file.path(inputDir, "index.Rmd"),
  intermediateDir = "./interim",
  mdFiles = NULL
)

Arguments

outputDir

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

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.

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.

Value

String with path to the front page of the clinical data report.

Author(s)

Laure Cougnaud

See Also

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


clinDataReview documentation built on July 14, 2021, 5:08 p.m.