report/make-one-species.R

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

setwd(here::here())
data_cache <- here::here("report", "data-cache-aug-2023")
build_dir <- file.path("report", "report-rmd")
dir.create(here::here("report", "data-cache"), showWarnings = FALSE)
dir.create(here::here(build_dir), showWarnings = FALSE)

# Set your species here:
this_spp <- "arrowtooth flounder"
this_spp <- "shortspine thornyhead"
this_spp_hyphens <- gsub(" ", "-", this_spp)

# Must be on PBS network:
gfdata::cache_pbs_data(
  species = this_spp,
  file_name = this_spp_hyphens,
  path = data_cache,
  unsorted_only = FALSE,
  historical_cpue = FALSE,
  survey_sets = TRUE,
  verbose = TRUE,
  compress = FALSE
)

# The last function call creates this data file:
dat <- readRDS(paste0(file.path(data_cache, this_spp_hyphens), ".rds"))
dat_iphc <- readRDS(paste0(file.path(data_cache, 'iphc', this_spp_hyphens), ".rds"))
hbll_bait_counts <- readRDS(file.path(data_cache, 'bait-counts.rds'))
iphc_hook_counts <- readRDS(file.path(data_cache, 'iphc', 'iphc-hook-counts.rds'))
# If you want to fit and plot the commercial CPUE indexes then run the following:
# (must be on PBS network; a lot of data + a bit slow)
# dat$cpue_index <- gfdata::get_cpue_index(gear = "bottom trawl", min_cpue_year = 1996)

get_max_yrs <- function(x, .grep) {
  dat$survey_sets %>%
    dplyr::filter(grepl(.grep, survey_abbrev)) %>%
    dplyr::group_by(survey_abbrev) %>%
    dplyr::summarize(max_year = max(year)) %>%
    split(x = .$max_year, f = .$survey_abbrev)
}

synoptic_max_survey_years <- get_max_yrs(dat$survey_sets, "^SYN")
hbll_out_max_survey_years <- get_max_yrs(dat$survey_sets, "^HBLL OUT")
age_comp_first_year <- lubridate::year(Sys.Date()) - 14

length_ticks <- readr::read_csv(here::here("report/length-axis-ticks.csv"),
      show_col_types = FALSE) |> as.data.frame()

gfsynopsis::make_pages(
  dat = dat,
  dat_iphc = dat_iphc, # note these figures do not include Andy's IPHC adjustments
  spp = this_spp,
  d_geostat_index = NULL, # geostatistical index standardization; NULL to skip
  french = FALSE,
  report_lang_folder = build_dir,
  resolution = 170, # balance size with resolution
  short_page_height_ratio = 0.85,
  png_format = TRUE, # vs. PDF
  save_gg_objects = TRUE, # save the ggplots to an .rds file?
  synoptic_max_survey_years = synoptic_max_survey_years,
  hbll_out_max_survey_years = hbll_out_max_survey_years,
  age_comp_first_year = age_comp_first_year,
  final_year_comm = 2022,
  final_year_surv = 2022,
  length_ticks = length_ticks[length_ticks$species_common_name == this_spp,],
  stitch_model_type = 'st-rw',
  grid_dir = file.path(data_cache, 'grids'),
  hbll_bait_counts = hbll_bait_counts,
  iphc_hook_counts = iphc_hook_counts
)

# Now go look in `report/report-rmd/figure-pages`
# and `report/report-rmd/ggplot-objects` if `save_gg_objects = TRUE`

gg_rds <- file.path(build_dir, "ggplot-objects", paste0(this_spp_hyphens, ".rds"))
if (file.exists(gg_rds)) {
  g <- readRDS(gg_rds)
  g$survey_index # for example
  names(g) # available plots
}