R/import_species_list.R

In TrashBirdEcology/bbsAssistant: Download and Munge Data and Information from the North American Breeding Bird Survey

#' @title Import Species Metadata
#' @description Imports the file specieslist.txt. Is subsequently appended to the BBS dataset in \code{import_bbs_data()}
#'
#' @title Import the species list comprising names and numeric identifiers.
#' @param bbs_dir Directory for the ScienceBase (sb) item.
#' @importFrom dplyr left_join
#' @importFrom readr read_fwf
#' @export import_species_list
import_species_list <- function(bbs_dir){
    fn <- list.files(bbs_dir, full.names=TRUE, pattern="SpeciesList")
    species_list <- readr::read_fwf(fn, skip=c(9))## currently the best function for guessing the fixed widths...
    ## unfortunately, need to manually assign row 1 as header and remove the "line" row
    # names=as.vector(c(species_list[1,]))
    temp <- lapply(species_list[1, ], as.character)
    species_list <- species_list[-c(1:2),]

    colnames(species_list) <- temp

    species_list$AOU <- as.integer(as.character(species_list$AOU))

    ## Join this species list with the package data list
    species_list <- dplyr::left_join(species_list, bbsAssistant::species_list)

    return(species_list)
}