Physcraper manuscript

To render the revised BMC Bioinformatics version:

First create the "differences.tex" file using latexdiff (I installed latexdiff using brew with brew install latexdiff):

latexdiff sources/bmc_template_submission/bmc_article_submission_2021-01-08.tex sources/bmc_template_submission/bmc_article.tex > sources/bmc_template_submission/differences.tex

Then I rendered the differences.tex file with R:

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

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

mv differences.pdf docs/submission-bmc-2021-01-08-reviews.pdf

To render the BMC Bioinformatics template version:

tools::texi2pdf(file = "sources/bmc_template_submission/bmc_article.tex", clean=TRUE)

but I have not found a way to assign name and location to output.

so I just renamed it with mv:

mv bmc_article.pdf docs/submission-bmc-2020-12-28.pdf

#output = paste0("docs/submission-bmc-", Sys.Date(), ".pdf")

A previous try to bmc format that failed:

rmarkdown::render(input = "sources/2pdf-bmc.Rmd", output_file = paste0("../docs/try-submission-bmc", Sys.Date(), ".pdf"))

How to render other versions of this ms.

rmarkdown::render(input = "physcraper_ms.Rmd", output_file = paste("physcraper_ms-", Sys.Date(), ".pdf"))


rmarkdown::render(input = "render2-word.Rmd", output_file = paste0("docs/word-", Sys.Date(), ".docx"))
rmarkdown::render(input = "render2-sysbio.Rmd", output_file = paste0("docs/submission-sysbio-", Sys.Date(), ".pdf"))
rmarkdown::render(input = "render2-mee.Rmd", output_file = paste0("docs/submission-mee-", Sys.Date(), ".pdf"))
rmarkdown::render(input = "render2-mee.Rmd", output_file = paste0("docs/submission-mee-", Sys.Date(), ".doc"), output_format = "word_document")

The following will render the ms on various outputs specified in the yaml. This does not work with different outputs from the rticles package.

rmarkdown::render(input = "physcraper_ms.Rmd", output_format= "all")

Trying output_yaml worked. You just have to use the yaml params that are common to different formats in the main document, and add the extra ones on the extra yaml file. If there are any overlapping params, it will take the ones from the yaml specified in output_yaml:

rmarkdown::render(input = "physcraper_ms.Rmd", output_yaml= "joss.yaml")
rmarkdown::draft("ams_submission", template = "ams_article", package = "rticles")

rmarkdown::render(input = "physcraper_ms.Rmd", output_file= paste("ams_submission.pdf"), output_yaml= "ams.yaml")

To compile a .tex file to pdf I simply use the compile pdf button from RStudio, which I think uses tools::texi2pdf(output, clean=clean); tip taken from this RStudio community thread

To get the relevant figures from the physcraperex package:

curl -o docs/figs/ilex-updated-tree.png https://raw.githubusercontent.com/McTavishLab/physcraperex/master/docs/articles/ilex_files/figure-html/plot-tips-and-branches-1.png