renderChapter: 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,
  ...
)

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.

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