Accessible science for all is the motto of sa4ss and underpins the code in this R library that can be used to summarize output from Stock Synthesis in .pdf form.
sa4ss was created to ease some of the tedious overhead that comes with producing status updates of marine species for the Pacific Fishery Management Council. The package provides
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The package is intended for use by analysts within the Northwest and Southwest Fisheries Science Centers but the developers are happy to entertain ideas regarding future development scenarios that could facilitate adding additional templates that would be useful to others.
Regardless of your affiliation, please feel free to post any issues regarding the package to the GitHub issues page and any questions regarding how to use the package to the GitHub discussion board. Tags are available to mark your issue with an appropriate category. These categories are instrumental in providing guidance to the package maintainers regarding how to respond to your issue and to other users who follow this repository. Before you create an issue, please
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Below is a minimal example to familiarize yourself with using sa4ss. Before you can build a document it is wise to work through the following steps:
pak::pkg_install("rstudio/tinytex")
tinytex::install_tinytex(bundle = "TinyTeX-2")
packageVersion("tinytex")
to
determine which version you have and packageDate("tinytex")
to determine when
it was compiled. Use your best judgment to determine if you should update it or
not. I err on the side of updating too often.tinytex::reinstall_tinytex(bundle = "TinyTeX-2")
bundle
of "TinyTeX-1"
because then I know that I have all the
packages that I need. This is especially true for compiling documents that
are accessible to those with disabilities as the LaTeX 3 kernel is changing
daily. "TinyTeX-2"
will install all packages much like the
full distribution of TeXLive.rmarkdown::pandoc_available()
;TRUE
, you deserve a :trophy:; move on to the section on
rtools;FALSE
, try adding Pandoc to your path.
rmarkdown::pandoc_exec()
will show the path that needs to be added if
Pandoc is installed. You can 'edit environment variables for your account'
without needing IT.pkgbuild::rtools_path(); Sys.getenv("RTOOLS42_HOME")
*\rtools42\x86_64-w64-mingw32.static.posix\bin
is added to your path.tryCatch(expr = pkgload::unload("sa4ss"), error = function(x) "")
pak::pkg_install("pfmc-assessments/sa4ss")
sa4ss::session_test()
to ensure
that sa4ss works on your machine.draft()
once, but the call
to bookdown
will be your go-to function for compiling the document after you
update any of the files.
The resulting pdf (i.e., _main.pdf
) will be located within the directory doc
because I have set create_dir
to be TRUE
. If you set it to be FALSE
then
it will save the files to your current working directory._main.pdf
that includes the md, tex, and
pdf files.library(sa4ss)
sa4ss::draft(authors = "Kelli F. Johnson", create_dir = TRUE)
setwd("doc")
bookdown::render_book("00a.Rmd", clean = FALSE, output_dir = getwd())
setwd("..")
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The glossaries package on CTAN can help organize
acronyms. It works by using a master list of acronyms supplied in sa4ss
and \gls{}
, which will be the main function that you use in your text.
Glossaries will determine if the term should be abbreviated or if the long form
should be used, where it automatically will use the long form if it is the
first instance. This functionality is helpful when you have code split amongst
multiple files, you expect text to be moved around in the future, you want to
standardize the way things are written, your document has multiple authors.
For more information please see page 16 of the glossaries for beginners guide where each function for generating text is explained. In short,
gls{<label>}
: displays the long form in its first use and short form thereafter;glspl{<label>}
: displays the plural version;Gls{<label>}
: displays an uppercase version for the beginning of a sentence;Glspl{<label>}
: displays the plural form of the uppercase version;glsentryshort{<label>}
: displays the short version and can be used in a header; andglsentrylong{<label>}
: displays the long version and can be used in a header.Back to top
You can add a figure to your title page by including figure_title.png
in the
directory that stores all of your .Rmd files, which are typically called
doc(s)
. This figure will be centered, placed below your title, and will be
four inches wide. For those who do not want a figure on your title page, just
do nothing. The use of an if statement only includes the figure if it is
present and a default figure is not included in the package. Thanks to
stack exchange
for providing the code for the if statement.
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This project adheres to the National Marine Fisheries Service fish tools code of conduct. By contributing to this project, you agree to abide by its terms.
This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal laws. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation, or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.
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U.S. Department of Commerce | National Oceanographic and Atmospheric Administration | NOAA Fisheries