In pacific-hake/hake-assessment: Stock Assessment for Pacific Hake

# Extract YAML sections -------------------------------------------------------
proj_vars <- rmarkdown::metadata$project_variables
output <- rmarkdown::metadata$output$`hake_pdf`

if(!length(proj_vars)){
  stop("Document compilation not run properly. You must run this code ",
       "using the Bookdown/Rmarkdown system, by calling `hake::render()` ",
       "which is a simple wrapper for `bookdown::render_book()`")
}

# Globals for YAML tags -------------------------------------------------------
# Create a global variable for each item in the `project_variables` section
# of the YAML part of `000-launcher.rmd`
list2env(proj_vars, envir = globalenv())

# System info variables -------------------------------------------------------
sys_info <- Sys.info()
computer_name <- sys_info[["nodename"]]
os_name <- sys_info[["sysname"]]
user_name <- sys_info[["user"]]

# Model directories -----------------------------------------------------------
last_yr_models_dir <- file.path(models_dir,
                                last_assess_yr,
                                paste0(last_yr_model_version, "-version"))
models_dir <- file.path(models_dir,
                        assess_yr,
                        paste0(model_version, "-version"))

output_csv_dir <- here("doc", out_csv_path)
end_yr <- assess_yr

# Forecast years --------------------------------------------------------------
# `forecast_yrs` is a vector of years to forecast for. This is calculated from
# the number of `catch_year` columns in the forecast descriptions CSV file
# and always begins in the current assessment year (`assess_yr`)
fore_file <- here::here(doc_path, forecast_descriptions_fn)
if(!file.exists(fore_file)){
  stop("File `", fore_file, "` does not exist.")
}
fore_desc_df <- read_csv(fore_file, col_types = cols())
fore_num_yrs <- length(grep("catch_year" , names(fore_desc_df)))
if(!fore_num_yrs){
  stop("There are no column names containing `catch_year` in the forecast ",
       "definition file `", fore_file, "`")
}
forecast_yrs <- seq(assess_yr, (assess_yr + fore_num_yrs - 1))

# Figure margins  -------------------------------------------------------------
# `figure_margins` is special because it is an R expression in the YAML
# code and not just a plain value. It has to be parsed from a text string
# into an R expression using `eval(parse())`
yaml_check_margin_format(fig_margins)
fig_margins <- eval(parse(text = fig_margins))

# Document title --------------------------------------------------------------
# Extract document title for use in \\hypersetup in
# `post_process_modify_link_colors()`
doc_title <- rmarkdown::metadata$title
doc_title <- gsub(".*\\\\TitleFont\\{(.*)\\}.*$", "\\1", doc_title)
# Replace `r code` chunk with year (assuming it is year here)
doc_title <- gsub("(.*)`r\\s+.*`(.*)", paste0("\\1", assess_yr, "\\2"), doc_title)

# Document author -------------------------------------------------------------
# Extract document author for use in \\hypersetup in
# `post_process_modify_link_colors()`
doc_author <- gsub("\\\n", "", rmarkdown::metadata$author)
doc_author <- gsub("\\\\\\\\\\\\", "", doc_author)
doc_author <- gsub("\\s*$", "", doc_author)
doc_author <- gsub("\\\\", "\\\\\\\\", doc_author)

# Footer text  ----------------------------------------------------------------
# Evaluate the footer text from YAML inputs
footer_left <- extract_inline_rcode(
  output$footer_left)
footer_right <- extract_inline_rcode(
  output$footer_right)

# Theme set for ggplot --------------------------------------------------------
theme_set(hake_theme(ax_label_color = fig_label_color,
                     ax_title_font_size = fig_title_font_size,
                     ax_tick_font_size = fig_tick_font_size,
                     ax_title_font_face = fig_title_font_face,
                     ax_tick_font_face = fig_tick_font_face,
                     ax_tick_length_cm = fig_tick_length_cm,
                     margin_def = fig_margins))