knitr/rmarkdown/Latex: How to cross-reference figures and tables in 2 different pdf files?

问题

I'm trying to write a scientific article and the associated supplementary materials entirely in RStudio with rmarkdown.

It seems clear that book down is the way to go to cross-reference between files (https://stackoverflow.com/a/38884378/576684), but I also would like to be able to reference figures produced in one pdf in the other pdf.

Although my latex has got quite rusty with time, I imagine it could be achieved as follows:

compile the article tex and SuppMat tex a first time using rmarkdown::render()
compile these tex files from the command line in order to keep the corresponding .aux file with their references (missing references won't be resolved at this time)
recompile the 2 tex files from the command line another time where all references should now be resolved

Is it a reasonable way to do it? am I overlooking something simpler? In any case, it requires:

a different numbering of figures in each pdf file (covered by https://stackoverflow.com/a/51337664/576684)
to prevent rmarkdown from trashing the .aux files (it seems that pandoc doesn't allow this, hence the need to create the aux file using standalone latex)
to tell latex to use the additional .aux file if it is found (probably using header-includes: in the YAML header). how can I achieve that?

Thank you very much for your help!

回答1:

It turns out that the xr package is one way to go: https://texblog.org/2016/08/23/adding-references-from-an-external-file/

so this works from R:

rmarkdown::render("myarticle_ms.Rmd", 
                  bookdown::pdf_book(base_format=rticles::plos_article),
                  clean=FALSE)

rmarkdown::render("myarticle_SM.Rmd", 
                  bookdown::pdf_book(base_format=rticles::plos_article),
                  clean=FALSE)

tinytex::pdflatex("myarticle_ms.tex", clean=FALSE)
tinytex::pdflatex("myarticle_SM.tex", clean=FALSE)

tinytex::pdflatex("myarticle_ms.tex")
tinytex::pdflatex("myarticle_SM.tex")

with the following in the YAML header of myarticle_ms.Rmd (and the corresponding one the SuppMat file header):

header-includes:
  \usepackage{xr} \externaldocument{myarticle_SM}

Hope it makes life easier for a few others :)

来源：https://stackoverflow.com/questions/52531637/knitr-rmarkdown-latex-how-to-cross-reference-figures-and-tables-in-2-different

标签

latex

r-markdown

pandoc

bookdown