Merge pull request #441 from bjohnso005/dev_biomodelos

unit tests & documentation
wallaceEcoMod · Oct 23, 2024 · 9bf6eaf · 9bf6eaf
2 parents ba74553 + 5527f0d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: wallace
-Version: 2024.08.02
-Date: 2024-08-02
+Version: 2024.09.18
+Date: 2024-09-18
 Title: A Modular Platform for Reproducible Modeling of Species Niches 
     and Distributions
 Description: The 'shiny' application Wallace is a modular platform for 

diff --git a/R/indic_aoo.R b/R/indic_aoo.R
@@ -1,6 +1,33 @@
-##' @title  indic_aoo
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+#
+# indic_aoo.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  indic_aoo
 #' @description Calculate AOO.
 #'
+#' @details
+#' The function calculates the area of occupancy (AOO) from a thresholded
+#' prediction raster or a data.frame of occurrence records.
+#'
 #' @param r raster. Thresholded prediction raster. It could be NULL if occs provided.
 #' @param occs data.frame. Table with occurrences. It could be NULL if raster
 #' provided. If occs provided raster is ignored.
@@ -13,24 +40,57 @@
 #' @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
+#'
+#' @examples
+#'  \dontrun{
+#'  ### Set parameters
+#'  # binary raster
+#'  r <- terra::rast(system.file("extdata/Bassaricyon_neblina.tif",
+#'  package = "wallace"))
+#'  # occurrences
+#'
+#'  ### Run function
+#'  # aoo from raster
+#'  aoo_r <- indic_aoo(r,
+#'                     occs = NULL,
+#'                     lon = NULL,
+#'                     lat = NULL,
+#'                     wktFrom = getWKT("wgs84"),
+#'                     wktTo = getWKT("wcea"),
+#'                     logger = NULL)
+#'  # aoo from occs
+#'  aoo_occs <- indic_aoo(r <- NULL,
+#'                        occs,
+#'                        lon = "longitude",
+#'                        lat = "latitude",
+#'                        wktFrom = getWKT("wgs84"),
+#'                        wktTo = getWKT("wcea"),
+#'                        logger = NULL)
+#'  }
+#'
+#' @return A list of two elements: area and AOOraster. The first is the numeric
+#' value of the area (in km^2). The second is a RasterLayer of the extent
+#' (in WCEA & 2x2 km resolution).
+#'
 #' @author Gonzalo E. Pinilla-Buitrago <gpinillabuitrago@@gradcenter.cuny.edu>
+#' @author Bethany A. Johnson <bjohnso005@@citymail.cuny.edu>
 #' @export
 #'
 
 indic_aoo <- function(r = NULL, occs = NULL, lon = NULL, lat = NULL,
-                      wktFrom, wktTo, logger) {
+                      wktFrom, wktTo, logger = NULL) {
   if (!is.null(occs)) {
     if (is.null(lon) | is.null(lat)) {
-      logger %>% writeLog("No longitude and/or latitude name provided (**).")
+      logger %>% writeLog(type = 'error', "No longitude and/or latitude name provided.")
       return()
     } else {
       p.pts <- occs
       if (sum(c(lon, lat) %in% names(p.pts)) != 2) {
-        logger %>% writeLog("Longitude and/or latitude names not found (**).")
+        logger %>% writeLog(type = 'error', "Longitude and/or latitude names not found.")
         return()
       } else {
         p.pts <- p.pts %>%
-          dplyr::select(c(lon, lat)) %>%
+          dplyr::select(all_of(c(lon, lat))) %>% #BAJ
           terra::vect(geom = c(lon, lat))
         terra::crs(p.pts) <- wktFrom
         rast_temp <- terra::rast(terra::ext(terra::project(p.pts, wktTo)) + 10000,
@@ -44,7 +104,9 @@ indic_aoo <- function(r = NULL, occs = NULL, lon = NULL, lat = NULL,
       }
     }
   } else if (!is.null(r)) {
+    if ("RasterLayer" %in% class(r)) {
     r <- terra::rast(r)
+    }
     ## Unsuitable for NAs
     r[r == 0] <- NA
     p.poly <- terra::as.polygons(r)
@@ -56,8 +118,8 @@ indic_aoo <- function(r = NULL, occs = NULL, lon = NULL, lat = NULL,
       terra::trim()
     AOOarea <- terra::freq(AOOraster, value = 1)$count * 4
   } else {
-    logger %>% writeLog("Provide occurrences or raster (**).")
+    logger %>% writeLog(type = 'error', "Provide occurrences or raster.")
     return()
   }
-  return(list(area = AOOarea, AOOraster = methods::as(AOOraster, "Raster")))
+  return(list(area = AOOarea, AOOraster = raster::raster(AOOraster)))
 }
diff --git a/R/indic_area.R b/R/indic_area.R
@@ -1,18 +1,53 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+#
+# indic_area.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  indic_area
 #' @description Calculate Range size in square kilometers.
+#' @details Calculate the geographic range size of a thresholded raster. The units are in square kilometers.
 #'
 #' @param r raster. Thresholded prediction raster. It could be NULL if occs provided.
 #' @param wkt character. Well-known text representation of coordinate reference systems
 #'  to calculate area.
 #' @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
+#'
+#' @examples
+#' \dontrun{
+#' r <- terra::rast(system.file("extdata/Bassaricyon_neblina.tif",package = "wallace"))
+#' wkt <- getWKT("wcea")
+#' areaRange <- indic_area(r, wkt, logger = NULL)
+#' }
+#' @return Numeric value
 #' @author Gonzalo E. Pinilla-Buitrago <gpinillabuitrago@@gradcenter.cuny.edu>
+#' @author Bethany A. Johnson <bjohnso005@@citymail.cuny.edu>
 #' @export
 #'
 
 indic_area <- function(r, wkt, logger = NULL) {
+  if ("RasterLayer" %in% class(r)) {
   r <- terra::rast(r)
+  }
   ## Unsuitable for NAs
   r[r == 0] <- NA
   ## Raster to polygon

diff --git a/R/indic_eoo.R b/R/indic_eoo.R
@@ -1,5 +1,29 @@
+# Wallace EcoMod: a flexible platform for reproducible modeling of
+# species niches and distributions.
+#
+# indic_eoo.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  indic_eoo
 #' @description Calculate EOO.
+#' @details Calculate extent of occurrence (EOO) based on a binary raster or occurrence points.
 #'
 #' @param r raster. Thresholded prediction raster. It could be NULL if occs provided.
 #' @param occs data.frame. Table with occurrences. It could be NULL if raster
@@ -11,34 +35,55 @@
 #' @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
+#'
+#' @examples
+#' \dontrun{
+#' # binary raster
+#' r <- terra::rast(system.file("extdata/Bassaricyon_neblina.tif",package = "wallace"))
+#' # occurrences
+#' occs <- read.csv(system.file("extdata/Bassaricyon_neblina.csv",package = "wallace"))
+#' # wcea
+#' wkt <- getWKT("wcea")
+#'
+#' eoo_r <- indic_eoo(r, occs = NULL, lon = NULL, lat = NULL, wkt, logger = NULL)
+#' eoo_o <- indic_eoo(r = NULL, occs, lon = "longitude", lat = "latitude", wkt, logger = NULL)
+#' }
+#'
+#' @return A list of two elements: area and eooPoly. area is a numeric value and eooPoly is a SpatialPolygon.
 #' @author Andrea Paz <paz.andreita@@gmail.com>
 #' @author Gonzalo E. Pinilla-Buitrago <gpinillabuitrago@@gradcenter.cuny.edu>
+#' @author Bethany A. Johnson <bjohnso005@@citymail.cuny.edu>
 #' @export
 #'
 
 indic_eoo <- function(r = NULL, occs = NULL, lon = NULL, lat = NULL,
-                      wkt, logger) {
+                      wkt, logger=NULL) {
   if (!is.null(occs)) {
     if (is.null(lon) | is.null(lat)) {
-      logger %>% writeLog("No longitude and/or latitude name provided (**).")
+      logger %>% writeLog(type = 'error',
+                          "No longitude and/or latitude name provided.")
       return()
     } else {
       p.pts <- occs
       if (sum(c(lon, lat) %in% names(p.pts)) != 2) {
-        logger %>% writeLog("Longitude and/or latitude names not found (**).")
+        logger %>% writeLog(type = 'error',
+                            "Longitude and/or latitude names not found.")
         return()
       } else {
-        p.pts <- p.pts %>% dplyr::select(c(lon, lat))
+        p.pts <- p.pts %>% dplyr::select(all_of(c(lon, lat)))
       }
     }
   } else if (!is.null(r)) {
+    if ("RasterLayer" %in% class(r)) {
     r <- terra::rast(r)
+    }
     r[r == 0] <- NA
     p.pts <- terra::as.points(r) %>%
       terra::geom() %>% data.frame() %>%
       dplyr::select(tidyselect::all_of(c("x", "y")))
   } else {
-    logger %>% writeLog("Provide occurrences or raster (**).")
+    logger %>% writeLog(type = 'error',
+      "Provide occurrences or raster.")
     return()
   }
   wgs84 <- "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"