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Knit Rmd or spin R files without the typical pain of working directories

Source: R/core.R
ezknitr_core.Rd

ezknitr is an extension of knitr that adds flexibility in several ways. One common source of frustration with knitr is that it assumes the directory where the source file lives should be the working directory, which is often not true. ezknitr addresses this problem by giving you complete control over where all the inputs and outputs are, and adds several other convenient features. The two main functions are ezknit and ezspin, which are wrappers around knitr's knit and spin, used to make rendering markdown/HTML documents easier.

Usage

ezspin(
  file,
  wd,
  out_dir,
  fig_dir,
  out_suffix,
  params = list(),
  verbose = FALSE,
  chunk_opts = list(tidy = FALSE),
  keep_rmd = FALSE,
  keep_md = TRUE,
  keep_html = TRUE,
  move_intermediate_file = TRUE,
  ...
)

ezknit(
  file,
  wd,
  out_dir,
  fig_dir,
  out_suffix,
  params = list(),
  verbose = FALSE,
  chunk_opts = list(tidy = FALSE),
  keep_md = TRUE,
  keep_html = TRUE
)

Arguments

file

The path to the input file (.Rmd file if using ezknit or .R script if using ezspin). If wd is provided, then this path is relative to wd.

wd

The working directory to be used in the Rmd/R script. Defaults to the current working directory (note that this is not the same behaviour as knitr). See the 'Detailed Arguments' section for more details.

out_dir

The output directory for the rendered markdown or HTML files (if wd is provided, then this path is relative to wd). Defaults to the directory containing the input file.

fig_dir

The name (or path) of the directory where figures should be generated. See the 'Detailed Arguments' section for more details.

out_suffix

A suffix to add to the output files. Can be used to differentiate outputs from runs with different parameters. The name of the output files is the name of the input file appended by out_suffix, separated by a dash.

params

A named list of parameters to be passed to use in the input Rmd/R file. For example, if the script to execute assumes that there is a variable named DATASET_NAME, then you can use params = list('DATASET_NAME' = 'oct10dat').

verbose

If TRUE, then show the progress of knitting the document.

chunk_opts

List of knitr chunk options to use. See ?knitr::opts_chunk for a list of available chunk options.

keep_rmd, keep_md

Should intermediate Rmd or md files be kept (TRUE) or deleted (FALSE)?

keep_html

Should the final html file be kept (TRUE) or deleted (FALSE)?

move_intermediate_file

Should the intermediate Rmd file be moved to the output folder (TRUE) or stay in the same folder as the source R file (FALSE)?

...

Any extra parameters that should be passed to knitr::spin.

Value

The path to the output directory (invisibly).

Details

If you have a very simple project with a flat directory structure, then knitr works great. But even something as simple as trying to knit a document that reads a file from a different directory or placing the output rendered files in a different folder cannot be easily done with knitr.

ezknitr improves basic knitr functionality in a few ways. You get to decide:

  • What the working directory of the source file is

  • Where the output files will go

  • Where the figures used in the markdown will go

  • Any parameters to pass to the source file

Detailed Arguments

All paths given in the arguments can be either absolute or relative.

The wd argument is very important and is set to the current working directory by default. The path of the input file and the path of the output directory are both relative to wd (unless they are absolute paths). Moreover, any code in the R script that reads or writes files will use wd as the working directory.

The fig_dir argument is relative to the output directory, since the figures accompanying a markdown file should be placed in the same directory. It is recommended to either leave fig_dir as default or set it to a different name but not to a different directory. Because of the way knitr works, there are a few known minor issues if fig_dir is set to a different directory.

Difference between ezknit and ezspin

ezknit is a wrapper around knitr::knit while ezspin is a wrapper around ezspin. The two functions are very similar. knit is the more popular and well-known function. It is used to render a markdown/HTML document from an Rmarkdown source. spin takes an R script as its input, produces an Rmarkdown document from the R script, and then calls knit on it.

See also

open_output_dir setup_ezknit_test setup_ezspin_test set_default_params knit spin

Examples

if (FALSE) { # \dontrun{
   tmp <- setup_ezknit_test()
   ezknit("R/ezknit_test.Rmd", wd = "ezknitr_test")
   ezknit("R/ezknit_test.Rmd", wd = "ezknitr_test",
          out_dir = "output", fig_dir = "coolplots",
          params = list(numPoints = 50))
   open_output_dir()
   unlink(tmp, recursive = TRUE, force = TRUE)
 
   tmp <- setup_ezspin_test()
   ezspin("R/ezspin_test.R", wd = "ezknitr_test")
   ezspin("R/ezspin_test.R", wd = "ezknitr_test",
          out_dir = "output", fig_dir = "coolplots",
          params = list(numPoints = 50), keep_rmd = TRUE)
   open_output_dir()
   unlink(tmp, recursive = TRUE, force = TRUE)
} # }