diff --git a/R/GetSpp.fn.R b/R/GetSpp.fn.R deleted file mode 100644 index 7f7f60c..0000000 --- a/R/GetSpp.fn.R +++ /dev/null @@ -1,145 +0,0 @@ -#' Get Species Information -#' -#' @details -#' Get the scientific name, common name, and strata group for -#' a vector of species. -#' -#' @param species A vector of species names. The words can be separated -#' using spaces or underscores. Full names are not required but they will -#' increase the consistency of the results should partial matches return -#' multiple matches. -#' @param unident A logical entry with the default value of \code{FALSE}, -#' to match historical output that did not include unidentified groups. -#' -#' @export -#' @return A data frame with the -#' scientific name in the latin column and in the scientific_name column -#' that has spaces replaced with underscores; -#' common name in the common column and in the common_name column -#' that has spaces replaced with underscores; -#' species values used as input in the input column; and -#' strata used to assess its status in the strata column. -#' @seealso See -#' \code{\link{PullSpp.fn}} for information on common and scientific names; -#' and \code{\link{GetStrata.fn}} for the different stratifications. -#' @author Kelli Faye Johnson -#' @examples -#' GetSpp.fn(c("sablefish", "petrale")) -#' # Expect a warning because vermilion doesn't have an strata assigned to it -#' testthat::expect_warning( -#' GetSpp.fn(c("vermilion")) -#' ) -#' # Dusky returns multiple entries -#' testthat::expect_warning( -#' GetSpp.fn(c("dusky")) -#' ) -#' -GetSpp.fn <- function(species, unident = FALSE) { - - lifecycle::deprecate_soft( - when = "2.5", - what = "nwfscSurvey::GetSpp.n()", - details = "Please switch to get_species_info()." - ) - - # background information - sppnames <- nwfscSurvey::PullSpp.fn() - if (!unident) { - sppnames <- sppnames[!grepl("unident", sppnames[["common"]]), ] - } - - spplist <- t(data.frame( - c("coast", "arrowtooth_flounder"), - c("coast", "aurora_rockfish"), - c("coast", "big_skate"), - c("ca", "blackgill_rockfish"), - c("north_south", "bocaccio"), - c("coast", "canary_rockfish"), - c("north_south", "chilipepper"), - c("coast", "curlfin_sole"), - c("coast", "darkblotched_rockfish"), - c("coast", "dover_sole"), - c("coast", "english_sole"), - c("wa_or", "flathead_sole"), - c("coast", "greenspotted_rockfish"), - c("coast", "greenstriped_rockfish"), - c("coast", "lingcod"), - c("coast", "longnose_skate"), - c("coast", "longspine_thornyhead"), - c("wa_or", "pacific_cod"), - c("north_south", "pacific_ocean_perch"), - c("coast", "pacific_sanddab"), - c("coast", "pacific_spiny_dogfish"), - c("coast", "petrale_sole"), - c("coast", "redbanded_rockfish"), - c("coast", "rex_sole"), - c("coast", "rosethorn_rockfish"), - c("coast", "rougheye_rockfish"), - c("sablefish", "sablefish"), - c("coast", "sharpchin_rockfish"), - c("north_south", "shortbelly_rockfish"), - c("coast", "shortspine_thornyhead"), - c("north_south", "splitnose_rockfish"), - c("coast", "stripetail_rockfish"), - c("coast", "widow_rockfish"), - c("coast", "yelloweye_rockfish"), - c("north_south", "yellowtail_rockfish") - )) - row.names(spplist) <- NULL - - # Match species name - index <- lapply(species, function(y) { - out <- which(apply(apply(sppnames, 1, grepl, pattern = y, ignore.case = TRUE), 2, any)) - names(out) <- NULL - return(out) - }) - - if (any(lapply(index, length) == 0)) { - bad <- which(lapply(index, length) == 0) - warning("The following species were not found in the look up table\n", - "generated from the data warehouse (webapps.nwfsc.noaa.gov)\n", - "and only information for species in the table will be returned:\n", - paste(species[bad], collapse = ", "), - call. = FALSE - ) - species <- species[-1 * bad] - index <- index[-1 * bad] - } - - if (length(species) == 0) { - stop("No matches were found for your input species.") - } - out <- sppnames[unlist(index), ] - out[, "input"] <- rep(species, times = vapply(index, length, FUN.VALUE = 1L)) - - # Match strata - index <- match(tolower(out[, "common_name"]), tolower(spplist[, 2])) - if (any(is.na(index))) { - bad <- which(is.na(index)) - if (length(index) == 1) { - warning("The following species were not found in the look up table\n", - "stored in GetSpp for default strata, please self-assign strata:\n", - paste(unique(out[bad, "input"]), collapse = ", "), - call. = FALSE - ) - } - - if (length(index) != 1) { - warning("Multiple matches were found for the input species in the look up table\n", - "stored in GetSpp. Only one match is returned. The common_name for the removed match is:\n", - paste(unique(out[bad, "common_name"]), collapse = ", "), - call. = FALSE - ) - } - out <- out[!is.na(index), ] - index <- index[!is.na(index)] - } - - out[, "strata"] <- ifelse( - test = is.na(index), - yes = "coast", - no = spplist[index, 1] - ) - - return(out) -}