Welcome to DateLife's reproducible manuscript GitHub repository!

To reproduce any version of this manuscript, you will need the R packages datelife, drake, knitr and rmarkdown.

To install them or update them, use the install_deps() function from the devtools package as:

devtools::install_deps()

From the manuscript directory, choose the version of the paper that you want to reproduce, for example manuscript-1st-submission.Rmd. You can open this in RStudio and hit the knit button. Or you can go to the R terminal and use rmarkdown::render("manuscript.Rmd", "all"), or straight from the terminal do:

cd manuscript/
R -e 'rmarkdown::render("manuscript-1st-submission.Rmd", "all")'
R -e 'rmarkdown::render("manuscript.Rmd", "all")'

Generate a differences file

To create a "differences.tex" file, use latexdiff (I installed latexdiff using brew with brew install latexdiff):

latexdiff manuscript-1st-submission.tex manuscript.tex > differences.tex
latexdiff manuscript-2nd-submission.tex manuscript.tex > differences.tex

Then I rendered the differences.tex file from terminal with R:

R -e 'tools::texi2pdf(file = "differences.tex", clean=TRUE)'

And moved it to the folder I want it to be in:

mv differences.pdf ../submission/manuscript-differences.pdf

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To render reviews:

R -e 'rmarkdown::render("review.Rmd", "all")'
R -e 'rmarkdown::render("review2.Rmd", "all")'