renderChapter {clinDataReview}

Render one chapter of a clinical report, based on a configuration file

Description

Render one chapter of a clinical report, based on a configuration file

Usage

renderChapter(
  configFile,
  configGeneralParams = getParamsFromConfig(configFile = "config.yml", configDir =
    configDir, inputDir = inputDir),
  configDir = file.path(inputDir, "config"),
  indexPath = file.path(inputDir, "index.Rmd"),
  inputDir = ".",
  intermediateDir = "./interim",
  logFile = NULL,
  verbose = TRUE,
  ...
)

Arguments

configFile

String with filename of the config file of interest in YAML format.

configGeneralParams

List with parameters from the general config file

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.

inputDir

String with input directory, working directory 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.

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.

...

options passed to renderFile

Value

No output file, the Markdown report for the chapter and the knit_meta object is available in the intermediateDir directory.
If the input parameters are not correctly extracted, NULL is returned.