Build vignettes:
rmarkdown::render('vignettes/simulation.Rmd', clean=FALSE, output_format='md_document')
Move files from vignettes directory to docs:
# delete old files
rm -rf simulation_files/
mv ../vignettes/simulation_files/ .
# overwrite old files
#mv ../vignettes/simulation.knit.md simulation.md
mv ../vignettes/simulation.md .
#mv ../vignettes/simulation.pdf .
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