In pvrqualitasag/qgert: Qualitas Genetic Evaluation Routine Tools

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(qgert)

knitr::knit_hooks$set(hook_convert_odg = rmdhelp::hook_convert_odg)

Description

The function spin_sh() is the analoguous function to knitr::spin() but for bash scripts. That means the function spin_sh() takes a specially formatted bash script and converts it into a literate programming document. Normal text that contains the documentation of the bash script should be written after the roxygen comment (#') and code chunks should start with a code chunk option line which is written after #+.

The function spin_sh() separates the text from the code chunks and converts the bash script into a Rmarkdown (Rmd) document. When specified by the function parameter pb_knit, the Rmd is rendered into a static HTML page. In contrast to knitr::spin(), the bash code chunks must start with a chunk option line that starts with #+, otherwise code chunks are not recognized correctly. By default, the option eval=FALSE is set for every chunk, except the option is explicitly assigned with a given value.

Usage

The only argument that must be specified for spin_sh() is the name of a bash script that contains the special formatting described in the previous section.

spin_sh(ps_sh_hair = system.file('bash', 'spin_script.sh', package = 'qgert'))

The above function call takes the bash-script spin_script.sh converts it into a Rmarkdown file with the name spin_script.Rmd and then renders the Rmd source to a static HTML page stored in spin_script.html. The name of the output file can be specified with the argument ps_out_rmd. Options pb_knit and ps_out_rmd determine whether the Rmd source should be rendered to an HTML page and whether the Rmd source file should be kept or not.

Value

The result of calling spin_sh() as shown above is a static HTML page which shows documentation and code chunks together formatted in a way that users of the rmarkdown and the knitr packages are familiar with. A screenshot of the output file is shown below.

#rmdhelp::use_odg_graphic(ps_path = "odg/spin-sh-html-ouput.odg")
knitr::include_graphics(path = "odg/spin-sh-html-ouput.png")

Note

The original function knitr::spin() has many options and features which are not ported to spin_sh(). As an example, spin_sh() provides only two output format options (html and pdf) which can be determined with the additional parameter pobj_output_format which is directly passed to rmarkdown::render(). The functionality of spin_sh() can also be used from the bash script called spin_script.sh which is used in the test output above. The options required by spin_sh() are taken from commandline options where