Hook functions are called when the corresponding chunk options are not
NULL to do additional jobs beside the R code in chunks. This package
provides a few useful hooks, which can also serve as examples of how to
define chunk hooks in knitr.
hook_pdfcrop(before, options, envir)hook_optipng(before, options, envir)
hook_pngquant(before, options, envir)
hook_mogrify(before, options, envir)
hook_plot_custom(before, options, envir)
hook_purl(before, options, envir)
See References below.
The function hook_pdfcrop() can use the program pdfcrop to
crop the extra white margin when the plot format is PDF to make better use of
the space in the output document, otherwise we often have to struggle with
par to set appropriate margins. Note
pdfcrop often comes with a LaTeX distribution such as MiKTeX or
TeXLive, and you may not need to install it separately (use
Sys.which('pdfcrop') to check it; if it not empty, you are able to use
it). Similarly, when the plot format is not PDF (e.g. PNG), the magick
package is used to crop the plot.
The function hook_optipng() calls the program optipng to
optimize PNG images. Note the chunk option optipng can be used to
provide additional parameters to the program optipng, e.g.
optipng = '-o7'.
The function hook_pngquant() calls the program pngquant to
optimize PNG images. Note the chunk option pngquant can be used to
provide additional parameters to the program pngquant, e.g.
pngquant = '--speed=1 --quality=0-50'.
The function hook_mogrify() calls the program mogrify. Note
the chunk option mogrify can be used to provide additional parameters
to the program mogrify (with default -trim to trim PNG
files).
When the plots are not recordable via recordPlot and
we save the plots to files manually via other functions (e.g. rgl
plots), we can use the chunk hook hook_plot_custom to help write code
for graphics output into the output document.
The hook hook_purl() can be used to write the code chunks to an R
script. It is an alternative approach to purl, and can be more
reliable when the code chunks depend on the execution of them (e.g.
read_chunk(), or opts_chunk$set(eval = FALSE)).
To enable this hook, it is recommended to associate it with the chunk option
purl, i.e. knit_hooks$set(purl = hook_purl). When this hook is
enabled, an R script will be written while the input document is being
knit. Currently the code chunks that are not R code or have the
chunk option purl=FALSE are ignored. Please note when the cache is
turned on (the chunk option cache = TRUE), no chunk hooks will be
executed, hence hook_purl() will not work, either. To solve this
problem, we need cache = 2 instead of TRUE (see
https://yihui.org/knitr/demo/cache/ for the meaning of cache =
2).
# NOT RUN {
if (require("rgl") && exists("hook_rgl")) knit_hooks$set(rgl = hook_rgl)
# then in code chunks, use the option rgl=TRUE
# }
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