R/check_names.R

In cfree14/freeR: Miscellaneous functions in R

#' Check marine fish and invertebrate scientific names
#'
#' Checks marine fish and invertebrate scientific names against species in FishBase.
#'
#' @param species A character vector of species scientific names
#' @return A character vector of species scientific names not in FishBase
#' @examples
#' # Check species names (Gadus morhoa is incorrect)
#' species <- c("Gadus morhua", "Gadus morhoa")
#' check_names(species)
#' @export
check_names <- function(species){

  # FishBase taxa
  taxa_key_fb <- rfishbase::fishbase %>%
    as.data.frame() %>%
    dplyr::mutate(type="fish") %>%
    dplyr::select(type, everything()) %>%
    setNames(tolower(colnames(.))) %>%
    dplyr::mutate(sciname=paste(genus, species))

  # SeaLifeBase taxa
  taxa_key_slb <- rfishbase::sealifebase %>%
    as.data.frame() %>%
    dplyr::mutate(type="invert") %>%
    dplyr::select(type, everything()) %>%
    setNames(tolower(colnames(.))) %>%
    dplyr::mutate(sciname=paste(genus, species))

  # Merged taxa
  taxa_key <-  taxa_key_fb %>%
    bind_rows(taxa_key_slb) %>%
    setNames(tolower(names(.))) %>%
    dplyr::select(type, class, order, family, genus, species, sciname) %>%
    unique()

  # Check that species are in FB/SLB
  spp_wrong <- sort(unique(species[!species %in% taxa_key$sciname]))
  return(spp_wrong)

}