🐟 A reproducible data synopsis report for over 100 species of British Columbia groundfish
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
R
inst
man
report
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
README.md
gfsynopsis.Rproj
makefile

README.md

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

  1. Install gfsynopsis and csasdown:
# install.packages("devtools")
devtools::install_github("pbs-assess/gfsynopsis", dependencies = TRUE)
devtools::install_github("pbs-assess/csasdown")
  1. Clone or download the gfsynopsis GitHub repository.

  2. With the R working directory set to the root folder of the project (e.g. open the RStudio gfsynopsis.Rproj file), run:

source("report/make.R")
  1. 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.

  2. In RStudio, open gfsynopsis/report/report-rmd/index.Rmd and 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.