importWF: Import R Markdown file as workflow

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/linewise_utilities.R

Description

Import R Markdown file as workflow. Each R code chunk will be set as a step in the workflow. This operation requires a few extra settings on the R Markdown chunk options, to include a particular code chunk in the workflow analysis. Please check Details.

Usage

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importWF(sysargs, file_path, ignore_eval = TRUE, verbose = TRUE)

Arguments

sysargs

SYSargsList empty object. More information on Details.

file_path

string, file path of the workflow file.

ignore_eval

logical, treat all R chunks' eval option as TRUE in workflow Rmd file even if some chunks have eval=FALSE.

verbose

logical, print out verbose message while function running.

Details

To include a particular code chunk from the R Markdown file in the workflow analysis, please use the following code chunk options:

- spr = 'r': for code chunks with R code lines; - spr = 'sysargs': for code chunks with an 'SYSargsList' object; - spr.dep = <StepName>: for specify the previous dependency. If this options is not found, it will automaticly add the previous step.

For spr = 'sysargs', the last object assigned needs to be the SYSargsList. If the spr flag is not found, the R chunk will not be included in the workflow.

It is required to start a project using SPRproject() function, and use the object to populate the steps from R Markdown file.

Value

importWF will return an SYSargsList object.

Author(s)

Le Zhang and Daniela Cassol

See Also

SYSargsList

Examples

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file_path <- system.file("extdata/spr_simple_lw.Rmd", package="systemPipeR")
sal <- SPRproject(overwrite = TRUE)
sal <- importWF(sal, file_path)

tgirke/systemPipeR documentation built on July 20, 2021, 10:45 p.m.