R/get-spp-names.R

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

#' Get spp. names
#'
#' @export
get_spp_names <- function() {
  file <- system.file("extdata", "spp-of-interest.csv", package = "gfsynopsis")
  spp <- utils::read.csv(file, strip.white = TRUE, stringsAsFactors = FALSE,
    comment.char = "#")
  spp <- dplyr::filter(spp, !is.na(species_code))
  spp$species_code <- sprintf(paste0("%0", 3L, "d"), spp$species_code)
  spp$species_common_name <- tolower(gsub(" $", "", spp$species_common_name))
  # Not in databases at all:
  spp <- spp[!duplicated(spp), , drop = FALSE]
  spp$spp_w_hyphens <- gsub("/", "-", gsub(" ", "-", spp$species_common_name))
  stopifnot(sum(duplicated(spp$species_common_name)) == 0)
  tibble::as_tibble(spp)
}

# Add the worms ID:
# species <- gfplot::get_species()
# species <- species[!is.na(species$species_science_name), ]
# species <- species[!is.na(species$lsid), ]
# file <- "inst/extdata/spp-of-interest.csv"
# spp <- utils::read.csv(file, strip.white = TRUE, stringsAsFactors = FALSE)
# spp <- dplyr::filter(spp, !is.na(species_code))
# spp$species_code <- sprintf(paste0("%0", 3L, "d"), spp$species_code)
# spp <- left_join(spp, select(species, species_code, lsid))
# spp <- spp %>% rename(worms_id = lsid) %>%
#   mutate(worms_id = gsub("urn:lsid:marinespecies.org:taxname:", "", worms_id))
# readr::write_csv(spp, file)