unit tests & documentation for mask_userSDM

R/mask_userSDM.R

@@ -1,27 +1,59 @@
-#'
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+#
+# mask_userSDM.R
+# File author: Wallace EcoMod Dev Team. 2023.
+# --------------------------------------------------------------------------
+# This file is part of the Wallace EcoMod application
+# (hereafter “Wallace”).
+#
+# Wallace is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License,
+# or (at your option) any later version.
+#
+# Wallace is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Wallace. If not, see <http://www.gnu.org/licenses/>.
+# --------------------------------------------------------------------------
+#
 #' @title  mask_userSDM
 #' @description Upload user-specified SDM prediction
 #'
-#' @details
-#' See Examples.
+#' @details This function uploads a raster of a species' range prediction to be
+#' used in Wallace EcoMod. The file name needs to named in Genus_species format
+#' (Ex: Bassaricyon_neblina.tif) to have Wallace functionality. The raster can
+#' be binary or continuous, but may need to be binary for some further analyses
+#' in Wallace. This function returns a list of the range prediction raster as
+#' well as a spatial polygon of the extent of the range prediction.
 #'
-#' @param rasPath character of path to rasters, must be the full path including file name and extension.
+#' @param rasPath character of path to raster, must be the full path including file name and extension.
 #' Filename need to be name with genus_species format.
-#' @param rasName character vector of raster names to be assigned to loaded rasters
+#' @param rasName character vector of raster names to be assigned to loaded raster
 #' @param logger stores all notification messages to be displayed in the Log Window of Wallace GUI. insert the logger reactive list here for running in shiny,
 #'  otherwise leave the default NULL
 #' @param spN Species name
-# @keywords
-#'
-# @examples
 #'
+#' @examples
+#' \dontrun{
+#' ### Set parameters
+#' rasPath <- system.file("extdata/Bassaricyon_neblina.tif",package = "wallace")
+#' rasName <- "Bassaricyon_neblina.tif"
+#' ### Run function
+#' sdm <- mask_userSDM(rasPath, rasName, logger = NULL, spN = NULL)
+#' }
 #'
-# @return
+#' @return A list of two: the prediction rasterlayer and a spatialpolygon of the extent
 #' @author Gonzalo E. Pinilla-Buitrago <gpinillabuitrago@@gradcenter.cuny.edu>
 #' @author Jamie Kass <jkass@@gradcenter.cuny.edu>
+#' @author Bethany A. Johnson <bjohnso005@@citymail.cuny.edu>
+#'
+# @keywords
 # @note
-
-# @seealso
 # @references
 # @aliases - a list of additional topic names that will be mapped to
 # this documentation when the user looks them up from the command
@@ -43,15 +75,15 @@ mask_userSDM <- function(rasPath, rasName, logger = NULL, spN = NULL)  {
         'See guidance text in this module for more details.')
     return()
   }
-  smartProgress(logger, message = "Uploading user-specified SDM (**)...", {
+  smartProgress(logger, message = "Uploading user-specified SDM...", {
     r <- raster::trim(r)
     names(r) <- fileNameNoExt(rasName)
     extPoly <- raster::extent(r)
     if (extPoly@xmin < -180 | extPoly@xmax > 180 |
         extPoly@ymin < -90 | extPoly@ymax > 90) {
       logger %>%
         writeLog(
-          type = "error", "Wrong extent projection. '", rasName,"' cannot be uploaded. (**)")
+          type = "error", "Wrong extent projection. '", rasName,"' cannot be uploaded. ")
       return()
     }
     extPoly <- methods::as(extPoly, 'SpatialPolygons')

tests/testthat/test_mask_userSDM.R

@@ -0,0 +1,51 @@
+#### COMPONENT mask: Calculate Indicators
+#### MODULE: Upload user-specified SDM prediction
+context("userSDM")
+
+### Set parameters
+rasPath <- system.file("extdata/Bassaricyon_neblina.tif",package = "wallace")
+rasName <- "Bassaricyon_neblina.tif"
+
+### Run function
+sdm <- mask_userSDM(rasPath, rasName, logger = NULL, spN = NULL)
+
+# to test errors
+rasPath_error <- system.file("extdata/B_neblina_WCEA.tif",package = "wallace")
+#rasPath_error2 <- system.file("something with the wrong extent. see note below")
+
+################ Tests ####################################
+
+### test if the error messages appear when they are supposed to
+test_that("error checks", {
+  # unspecified CRS
+  expect_error(mask_userSDM(rasPath_error, rasName, logger = NULL, spN = NULL),
+               paste0("Input rasters have undefined coordinate reference system (CRS). Mapping functionality will not work. Please define their projections and upload again. See guidance text in this module for more details."),
+               fixed = TRUE)
+
+  # extents do not overlap
+  # BAJ 10/10/2024: need to upload a raster with xmax > 180 and xmin < -180 to get this error
+  # expect_error(mask_userSDM(rasPath_error2, rasName, logger = NULL, spN = NULL),
+  #              paste0("Wrong extent projection. '", rasName,"' cannot be uploaded. "))
+})
+
+
+### test if the warning messages appear when they are supposed to
+# No warning messages
+
+### test output features
+test_that("output checks", {
+  # list
+  expect_is(sdm, "list")
+  # list of 2
+  expect_equal(length(sdm),2)
+  # two items should be sdm$sdm & sdm$extSdm
+  expect_equal(names(sdm), c("sdm", "extSdm"))
+  # sdm$sdm should be a rasterlayer
+  expect_is(sdm$sdm, "RasterLayer")
+  # sdm$extSdm should be a spatialpolygon
+  expect_is(sdm$extSdm, "SpatialPolygons")
+  # same extents
+  expect_equal(raster::extent(sdm$sdm), raster::extent(sdm$extSdm))
+})
+
+### test function steps