analysis/VOCC/render-scrambled-years.R

In pbs-assess/gfranges: Groundfish Ranges

getwd()
setwd(here::here("/analysis/VOCC"))
env <- new.env() # parent = baseenv()

# dir.create(file.path("html/biomass-trends"))
list_species <- c(
  "Big Skate",
  "Longnose Skate",
  "Spotted Ratfish",
  "North Pacific Spiny Dogfish",
  # "Pacific Tomcod",
  "Walleye Pollock",
  "Pacific Cod",
  "Sablefish",
  "Lingcod",
  # "Pacific Hake",
  # "Rosethorn Rockfish",
  "Yellowmouth Rockfish",
  # "Harlequin Rockfish",
  "Canary Rockfish", # schooling, winter-birthing
  # "Copper Rockfish", # small sample
  "Darkblotched Rockfish",
  "Greenstriped Rockfish",
  "Pacific Ocean Perch", # schooling
  "Redbanded Rockfish",
  "Sharpchin Rockfish",
  #"Shortbelly Rockfish", # small sample
  "Silvergray Rockfish",
  "Splitnose Rockfish",
  "Yellowtail Rockfish", # schooling
  "Longspine Thornyhead",
  "Shortspine Thornyhead",
  "Arrowtooth Flounder",
  "Rex Sole",
  "Petrale Sole",
  "English Sole",
  "Dover Sole",
  "Southern Rock Sole",
  "Flathead Sole",
  "Curlfin Sole",
  # "Sand Sole",
  # "Slender Sole",
  # "Pacific Sanddab",
  "Pacific Halibut",
  "Redstripe Rockfish",
  "Rougheye/Blackspotted Rockfish Complex",
  "Widow Rockfish",
  "Quillback Rockfish",
  "Bocaccio",
  "Shortraker Rockfish",
  "Yelloweye Rockfish"
)

### build biotic gradients
list_regions <- c(
  "West Coast Vancouver Island",
  "West Coast Haida Gwaii",
  "both odd year surveys"
  #   "All synoptic surveys"
)


for (r_h in seq_along(list_regions)) {
  for (spp_i in seq_along(list_species)) {
    spp <- gsub(" ", "-", gsub("\\/", "-", tolower(list_species[spp_i])))
    covs <- "-tv-depth-only" # string describing model
    reg <- gsub(" ", "-", gsub("\\/", "-", tolower(list_regions[r_h])))
    try({
      rmarkdown::render("4-vocc-temp.Rmd",
        params = list(
          species = list_species[spp_i],
          # immature = TRUE,
          region = list_regions[r_h],
          covs = covs,
          scrambled_years = TRUE
        ),
        output_file = paste0(
          "html/VOCC-plots/scrambled-temp-gradients-", spp,
          # "-imm",
          covs, "-", reg, "-trim10.html"
        ),
        envir = env
      )
    })
  }
}