inst/requests/trevor.R

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

library(dplyr)

dc <- file.path("report", "data-cache")
if (!file.exists(file.path(dc, "pacific-ocean-perch.rds"))) { # a random check
  gfsynopsis::get_data(type = "A", path = dc)
}
spp <- gfsynopsis:::get_spp_names() %>% filter(type == "A")
spp <- filter(spp, species_common_name != "pacific hake")

out <- list()
for (i in seq_along(spp$species_common_name)) {
  dat <- readRDS(paste0(file.path(dc, spp$spp_w_hyphens[i]), ".rds"))
  d <- dat$survey_index
  out[[i]] <- d
}

dat <- bind_rows(out)
dat <- filter(dat, survey_abbrev %in%
  c("HBLL OUT N", "HBLL OUT S", "SYN WCHG", "SYN WCVI",
    "SYN HS", "HBLL INS N", "HBLL INS S", "SYN QCS"
  )) %>%
  arrange(survey_abbrev, species_common_name, year) %>%
  select(-survey_series_id)
glimpse(dat)

readr::write_csv(dat, "pbs-gf-trawl-hbll.csv")