clinDataReview (version 1.6.2)

clinDataReview-common-args-report: Common parameters for the clinical data reporting function

Description

Common parameters for the clinical data reporting function

Value

No return value, used for the documentation of the clinical data reporting functions of the package.

Arguments

indexPath

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

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'.

configFile

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

inputDir

String with input directory, working directory by default.

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.

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.

mdFile

String with path of the Markdown file

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.

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

verbose

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