A review of biological samples collected from commercial groundfish fisheries in British Columbia, 1996-2022
This commercial biosampling compendium uses an automated workflow to generate figure and text summaries of groundfish commercial biosampling in British Columbia, Canada. Figure and text summaries are then formatted as a CSAS Technical Report using the R package csasdown. The content is nearing completion in July 2024.
Most packages can be installed from CRAN, but some need special installation:
# install.packages("remotes")
remotes::install_github("pbs-assess/gfdata")
remotes::install_github("pbs-assess/gfplot")
remotes::install_github("pbs-assess/csasdown")
All the .Rmd files used to create the tech report are found in the
report/report-rmd/ folder.
The make.R script (found in the report/ folder) contains all the code to create
the species specific pages. This script pulls data from the databases, creates
the figures (and writes them to the report/report-rmd/figs/ folder),
and generates the 05-plot-pages.Rmd file.
To render the report, open index.Rmd in RStudio and then click the knit button.
The csasdown package writes the tech report to the report/report-rmd/_book/
folder.
- Please note that "sample" should refer to the collection of specimens taken in a sampling event, while "specimen" should refer to an individual fish.