In pbs-assess/gfsynopsis: Data Synopsis Reports for PBS Groundfish

knitr::opts_chunk$set(
  collapse = TRUE,
  warning = FALSE,
  message = FALSE,
  comment = "#>",
  fig.path = if (knitr:::is_latex_output()) "knitr-figs/" else "knitr-figs-docx/",
  cache.path = if (knitr:::is_latex_output()) "knitr-cache-tex/" else "knitr-cache-docx/",
  fig.asp = 0.618,
  fig.width = 9,
  out.width = "6in",
  echo = FALSE,
  autodep = TRUE,
  cache = TRUE,
  cache.comments = FALSE,
  dev = if (knitr:::is_latex_output()) "png" else "png",
  dpi = 200,
  fig.align = "center",
  fig.pos = "htb"
  # optipng = "-strip all"
)
# knitr::knit_hooks$set(optipng = knitr::hook_optipng) # must have optipng installed!


options(# Prevent xtable from adding a timestamp comment to the table code it produces
        xtable.comment = FALSE,
        # Don't allow kableExtra to load packages, we add them manually in csasdown
        kableExtra.latex.load_packages = FALSE,
        # Stop chunk output (echo) running into the margins
        width = 80,
        # Don't use scientific notation (stops tables from showing 1.2e3, etc.)
        scipen = 999
)

library(dplyr)
library(ggplot2)
library(gfsynopsis)
library(gfplot)
library(csasdown)
library(rosettafish)
ggplot2::theme_set(gfplot::theme_pbs())
french <- FALSE

meta <- rmarkdown::metadata$output
if (is.null(meta)) {
  # This knitr chunk has been run in R without running bookdown::render_book("index.Rmd")
  # so rmarkdown::metadata$output is not populated
  options(french = FALSE)
} else {
  if (length(grep("pdf", names(meta)))) {
    options(french = meta$`csasdown::sr_pdf`$french)
    prepub <- meta$`csasdown::sr_pdf`$prepub
  } else if (length(grep("word", names(meta)))) {
    options(french = meta$`csasdown::sr_word`$french)
    prepub <- meta$`csasdown::sr_word`$prepub
  }
}
csl <- "csl/csas.csl"
options(french = TRUE)
french <- TRUE
options(OutDec = ",")

if (is.null(getOption("french"))) {
  stop("`french` was not set up correctly in YAML header in index.Rmd. ",
       "It must be true or false",
       call. = FALSE)
}
if (getOption("french")) {
  csl <- "csl/csas-french.csl"
  options(OutDec = ",")
}

options(french = TRUE)
french <- TRUE
options(OutDec = ",")
csl <- "csl/csas-french.csl"