analysis/VOCC/BACI/render-matches.R

In pbs-assess/gfranges: Groundfish Ranges

# Render matches for BACI

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

list_species <- c(
  "Bocaccio", # winter-birthing, overfished
  "Canary Rockfish", # schooling, winter-birthing
  "Copper Rockfish", # small sample
  "Darkblotched Rockfish",
  "Greenstriped Rockfish",
  "Pacific Ocean Perch", # schooling
  "Quillback Rockfish",
  "Redbanded Rockfish",
  "Rougheye/Blackspotted Rockfish Complex",
  "Sharpchin Rockfish",
  "Shortbelly Rockfish", # small sample
  "Silvergray Rockfish",
  "Splitnose Rockfish",
  "Widow Rockfish", # schooling
  "Yellowtail Rockfish", # schooling
  "Yelloweye Rockfish", # summer-birthing, overfished,
  "Longspine Thornyhead",
  "Shortspine Thornyhead"
)

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


list_species <- c(
  "Pacific Cod",
  #  "Lingcod",
  "Pacific Ocean Perch", # schooling
  # "Quillback Rockfish",
  "Redbanded Rockfish",
  # #"Rougheye/Blackspotted Rockfish Complex",
  # "Silvergray Rockfish",
  # "Splitnose Rockfish",
  "Petrale Sole",
  # "Arrowtooth Flounder",
  "Pacific Halibut"
)


list_regions <- c(
  "West Coast Vancouver Island",
 # "West Coast Haida Gwaii",
  "both odd year surveys"
)

ages <- c("mature") # , "imm"

render_matches <- function(climate, biomass_threshold, change_threshold){
 for (a in seq_along(ages)) {
  for (r_h in seq_along(list_regions)) {
    for (spp_i in seq_along(list_species)) {
      age <- ages[a]
      spp <- gsub(" ", "-", gsub("\\/", "-", tolower(list_species[spp_i])))
      reg <- gsub(" ", "-", gsub("\\/", "-", tolower(list_regions[r_h])))
      try({
        rmarkdown::render("4-vocc-BACI-multiyear.Rmd",
          params = list(
            species = list_species[spp_i],
            age = ages[a],
            region = list_regions[r_h],
            biomass_threshold = biomass_threshold,
            climate = climate,
            threshold = change_threshold
          ),
          output_file = paste0(
            "html/matches/match-", spp, "-", age, "-",
            climate, "-", biomass_threshold, "-", change_threshold, "-", reg, ".html"
          ), envir = env
        )
      })
    }
  }
 }
}

## DO matches
render_matches(climate = "do", biomass_threshold = "50", change_threshold = 0.25)


render_matches(climate = "do", biomass_threshold = "50", change_threshold = 0.5)
#render_matches(climate = "do", biomass_threshold = "25", change_threshold = 0.25)
#render_matches(climate = "do", biomass_threshold = "25", change_threshold = 0.5)

## Temperature matches
render_matches(climate = "temperature", biomass_threshold = "50", change_threshold = 0.25)
render_matches(climate = "temperature", biomass_threshold = "50", change_threshold = 0.5)
render_matches(climate = "temperature", biomass_threshold = "50", change_threshold = 0.75)
render_matches(climate = "temperature", biomass_threshold = "50", change_threshold = 1)
render_matches(climate = "temperature", biomass_threshold = "25", change_threshold = 0.25)
render_matches(climate = "temperature", biomass_threshold = "25", change_threshold = 0.5)
render_matches(climate = "temperature", biomass_threshold = "25", change_threshold = 0.75)
render_matches(climate = "temperature", biomass_threshold = "25", change_threshold = 1)