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I found this option of rmd. This option is mentioned in the rmarkdown reference guide and in http://rmarkdown.rstudio.com/pdf_document_format.html#figure_options. However, neither of these two documents warn about the impairment to EPS figures.
The problem is that, when user use
For myself, I spent rather long time to find out why EPS figure is in low quality. Finally I found with
EPS vs PDF
When manager the figures under git. If you store figures in PDF, every time you render the rmd file, git will mark the figures as modified even there is no change in the figures. If the figures are stored in EPS format, there is no problem. git can read the figures and know the figures are not changed.
Perhaps this issue should be reported in rmarkdown repo?
I'm very sorry for wasting your time. I think we should definitely mention the problem with cropping eps figures in the rmarkdown documentation.
It is indeed tricky to deal with binary files in git. Usually I try to avoid committing binary files into git, such as images generated from R (I ignore them in