gfsynopsis: An R package for generating an annual data synopsis report for groundfish
This package uses the data extraction, data tidying, model fitting, and plotting functions from gfplot.
Building the document
- Install gfsynopsis and csasdown:
# install.packages("devtools") devtools::install_github("pbs-assess/gfsynopsis", dependencies = TRUE) devtools::install_github("pbs-assess/csasdown")
Clone or download the gfsynopsis GitHub repository.
With the R working directory set to the root folder of the project (e.g. open the RStudio
Wait for a long time for all the data to download, all the models to fit, and all the plots to generate. If you are starting from scratch then it may take a day or so to fit all the commercial CPUE index standardization models. If you already have these results cached, then it could take anywhere from ~10 minutes to a couple hours depending what needs to be built.
In RStudio, open
gfsynopsis/report/report-rmd/index.Rmdand click the "Knit" button, or in any R console run:
setwd("report/report-rmd") bookdown::render_book("index.Rmd") setwd("../../")
Problems? Sorry! File an issue.