Reproducible CSAS Reports with R Markdown
csasdown is an R package for generating Canadian Science Advisory Secretariat (CSAS) documents in PDF or Word format using R Markdown and bookdown.
Check the NEWS file for information on what has changed recently.
Check the Wiki for hints and FAQs.
Have a problem? If it's a bug or feature request, please post it as a GitHub Issue. If it's a question on csasdown use, we encourage you to use the new GitHub discussion board. Questions that are emailed or sent on MS Teams may be (anonymously and without data or screenshots) copied to the discussion board and answered there. Let us know if you don't want that to happen. For quick back-and-forth questions, you can catch us on DFO MS Teams.
If you use csasdown to write a report, please let us know so we can add it to the list of publications known to have used the package. This helps us justify spending our work time on its development. You can post to the discussion board, send us a quick email (contact details here), or find us on DFO MS Teams.
To compile PDF documents using R, you need to have Pandoc, LaTeX, and several related packages installed. If you have a recent version of RStudio, then you already have Pandoc.
-
You will need to install LaTeX if you do not have it already. Read this Wiki page for a detailed description of this procedure. Most likely you will want to use the R package tinytex.
-
If using tinytex, some tinytex versions will require you to install these packages manually:
tinytex::tlmgr_install('babel-french')
tinytex::tlmgr_install('babel-english')- Install the csasdown package:
install.packages("remotes")
remotes::install_github("pbs-assess/csasdown", dependencies = TRUE)-
If you already have a folder (or subfolder) you'd like your report to be kept in,
setwd()to your folder in R and continue on. Add the argumentcreate_rstudio_file = FALSEto the belowdraft()calls (or manually delete the RStudio project file that gets auto created). If you are starting a new project and want all the files to be in the root folder, create that new folder,setwd()to that folder in R, and then continue the steps below. -
Run this line in your R console to create a new Research Document from the built-in template in whatever your working directory is:
csasdown::draft("resdoc")or for an advanced Research Document with bilingual features (in development, you likely want to use the main "resdoc" above for now):
csasdown::draft("resdoc-b")You can do the same for a Technical Report:
csasdown::draft("techreport")a Manuscript Report:
csasdown::draft("manureport")or for a Science Response:
csasdown::draft("sr")or a Fisheries Science Advisory Report (FSAR):
csasdown::draft("fsar")Note that the techreport and manureport examples contain a lot of information on getting started with R Markdown and should be the first one you render if you are new to csasdown. The resdoc example contains other examples.
The resdoc-b contains examples and guidance on setting up chunks to hold both English and French Rmarkdown, and explanations of the features introduced in version 0.1.0 (see the NEWS file).
-
Render the document right away to make sure everything works by opening the file index.Rmd and clicking the knit button in RStudio. Once completed, a preview pane showing the PDF document will appear. The location of the PDF is in the _book directory. See the Rendering section below for more information. You can also render on the command line by
setwd()to the folder that containsindex.Rmdand_bookdown.ymland runningcsasdown::render(). See the Rendering section below. -
Read the output PDF carefully and compare with what is written in the .Rmd files. This will help you understand more quickly how the document is put together and how you might want to structure your document.
-
(Optional but recommended) Create a blank repository on GitHub, commit your changes, and push to GitHub. New to Git? Start with https://happygitwithr.com/.
-
Need to make an English and French version? csasdown has support for both. Also see csasdown's sibling package rosettafish, which can help with translating text in figures.
A list of the publications can be found on this wiki page.
You need to edit the individual chapter R Markdown files to write your report. While writing, you should git commit your work frequently. For a gentle novice-friendly guide to getting starting with using Git with R and RStudio, see http://happygitwithr.com/.
Rendering using the knit button
To render your report into a PDF or Word document, open index.Rmd in RStudio and then click the knit button:
A message will appear telling you which language and document type is being rendered.
Every time you add something new, you should render the document to make sure you didn't break the build. It is much easier to find the problem when only one small known change was made since the last time it was rendered.
To change the output formats between PDF and Word find the following chunk of code in index.Rmd and change it to either pdf or word.
Like this:
output:
csasdown::resdoc_pdf:
french: false
or this:
output:
csasdown::resdoc_word:
french: false
Rendering using the console
You can also render from the console if you're not using RStudio or to allow debugging of your code.
To do this, you must have your working directory (see getwd()) be the one with the index.Rmd file and _bookdown.yml files in it. Use setwd(). Then run:
csasdown::render()or, for a detailed explanation of each step in the rendering process:
csasdown::render(verbose = TRUE)This method of rendering allows you to debug your code by inserting browser() calls which stops compilation at specific places.
Note that you'll need to run sink() in the console once it stops on your browser() calls to see any variable values.
It also does not open a preview viewer once finished like the knit button method does, so you will have to navigate to the _book/ directory and open it up manually.
The rendered PDF or Word file of your report will be deposited in the _book/ directory.
Project structure in the Bookdown document:
The following components are ones you should edit to customize your report:
This is the main configuration file for your report. It determines what .Rmd files are included in the output, and in what order. Arrange the order of your chapters in this file and ensure that the names match the names in your folders. If you add new .Rmd files, add them here. You may comment out some files while working on others by placing a # in front of them. This will stop compilation of those files, reducing the time to compile while working on another file.
A temporary copy of this file is created when running render(). It is the file that is actually used in the rendering process.
If you want to see what it holds, render with this command: render(keep_files = TRUE) to keep it around after rendering.
This file contains all the meta information that goes at the beginning of your document. You'll need to edit this to put your name on the first page, add the title of your report, etc. The name of this file cannot be changed.
A temporary copy of this file is created when running render(). It is the file that is actually used in the rendering process.
If you want to see what it holds, render with this command: render(keep_files = TRUE) to keep it around after rendering.
These are the .Rmd files for each chapter/section of your report. Write your report in these. You can delete any or all of these and create as many of your own as you wish, but if you do you must change the _bookdown.yml file accordingly.
Temporary copies of these file are created when running render(). They are the files that are actually used in the rendering process.
If you want to see what they hold, render with this command: render(keep_files = TRUE) to keep them around after rendering.
Store your bibliography (as BibTeX files) here. You might look at the citr addin and Zotero to efficiently manage and insert citations.
Style files for bibliographies should be stored here. You will want to use the included csas.csl, which is based on the CJFAS (Canadian Journal of Fisheries and Aquatic Sciences) .csl file.
Store pre-made figures and data here and reference them in your R Markdown files. See the bookdown book for details on cross-referencing items using R Markdown.
This contains any .docx or .tex files that are need to compile the documents. With the exception of the title page file, you shouldn't have to edit any of these files.
This project has drawn directly on code and ideas from the following:
NAFOdown is a derivative of csasdown for rendering NAFO (Northwest Atlantic Fisheries Organization) reports.
If you would like to contribute to this project, please start by reading our Guide to Contributing. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.