From af5c934763cd21dd7731b902fc37fc94e7ac2a3b Mon Sep 17 00:00:00 2001
From: Chantel Wetzel <chantel.wetzel@noaa.gov>
Date: Mon, 23 Sep 2024 12:54:08 -0700
Subject: [PATCH] delete file

rename file

update file
---
 R/GetSpp.fn.R | 145 --------------------------------------------------
 1 file changed, 145 deletions(-)
 delete mode 100644 R/GetSpp.fn.R

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)
-}