emilymarkowitz-noaa / nmfsreports

Write smart R Markdown reports with these basic and easy functions!

Emily (Em) Markowitz

Research Fisheries Biologist

Alaska Fisheries Science Center

Groundfish Assessment Program's Eastern Bering Sea Survey Group

Learn more about me! Find my website here.

All work posted on this GitHub is subject to NOAA Fisheries' Standards

NOAA README

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 law. 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.

License

Software code created by U.S. Government employees is not subject to copyright in the United States (17 U.S.C. §105). The United States/Department of Commerce reserve all rights to seek and obtain copyright protection in countries other than the United States for Software authored in its entirety by the Department of Commerce. To this end, the Department of Commerce hereby grants to Recipient a royalty-free, nonexclusive license to use, copy, and create derivative works of the Software outside of the United States.

nmfsreports's Issues

Add a way to anchor figures, tables, and equations to table of contents

Maybe something like this?:
https://holtzy.github.io/Pimp-my-rmd/#internal_link
or
https://stackoverflow.com/questions/5319754/cross-reference-named-anchor-in-markdown

run.R doesn't run

1. It looks like I need to change, this line to TRUE to create the figures

https://github.com/RVerse-Tutorials/A_NMFSReport/blob/main/code/run.R#L45

3. But when I do that it says dir_out_ref does not exist. The other dirs_out's are defined in my environment but not that one.

https://github.com/RVerse-Tutorials/A_NMFSReport/blob/main/code/run.R#L49

Product feature wish list for V 0.0.1.2

To do:

• change header level of "references" and option so all references appear at the end of the document.
• add option so the code produces a word document (combined) and pdf (combined)
• add github actions for gh-pages
• center figures
• find way to change page to landscape for specific tables
• review required dependencies
• add figtab notes - write figures and tables before running documents
• #2
• fix how citation styles are used/how to use custom ones.

Packages missing in DESCRIPTION?

packrat, and RMarkReports included in the DESCRIPTION Imports?

And nmfspalette added to DESCRIPTION Remotes

For example:
When sourcing run.r an error arises:

Error in citation("nmfspalette") : 
  there is no package called ‘nmfspalette’