Raw geomeans captions updated to clarify that the number of years in the wild geomeans could be different than for the total geomeans because there may be years with missing fraction wild.
Altered productivity_fig.R to output the data for the figure as a csv file.
Raw geomeans captions have been updated to clarify how 0s in the data are dealt with. They are replaced with NA. The methods vignette has been updated to include a section on how 0s are dealt with and misspellings corrected.
I revamped how to customize plots and palettes. I no longer use nwctrends.palette. Instead I use pkg_globals in the package environment. The user passes in nwctrends.options as a list with any of the plot options that they want to update (e.g. line color or line type or point type). See the new onLoad.R file and the nwctrends_options.R file. Note .onLoad() is run whether the package is loaded via library() or via NWCTrends::.
Added some examples to NWCTrends_report.R.
I was overloading the inst/doc folder with non-vignette material. I moved the needed report files (Rmd and tex) to inst/report_files and the demo data to inst/extdata. The inst/doc folder now only has the two vignettes and the documentation PDFs.
I also updated the vignettes folder such that if install_local() or install_github() with build_vignettes=TRUE is used, the inst/doc created will match that on GitHub. Note, the user would have to accept inst/doc will be delected. It doesn't delete the files in the repo, just re-creates inst/doc in the installed version in the user library.
I added a file local_build_instructions.txt to the repo to remind me how to build the vignettes and how to deal with devtools::check() deleting the inst/doc folder.
Added a data object nwctrends.pallete with red, blue, black, green and white defined (in a list). To change the colors, the user a new palette list to NWCTrends()
Added show.all.fracwild to NWCTrends_report() so that that can be changed from the main function.
This is the version used in the 2020 NWFSC PNW Salmonid Viability Report.
Add more meta data: Method (Survey, Model), Citation, and Contributor. A metadata.csv file is added to each Output folder.
pkgname.R Roxygen2 code.NEWS.md fileThis is the version used in the 2015 NWFSC PNW Salmonid Viability Report.