Merge pull request #253 from danlwarren/develop

Many small bug fixes

.gitignore

@@ -28,3 +28,5 @@ benchmarks/*
 wc5/*
 docs
 inst/doc
+
+wc10/

DESCRIPTION

@@ -2,7 +2,7 @@ Package: ENMTools
 Type: Package
 Title: Analysis of Niche Evolution using Niche and Distribution Models
 Version: 1.1.1
-Date: 2023-04-11
+Date: 2024-01-10
 Encoding: UTF-8
 Authors@R: c(person(given = "Dan", family = "Warren", role = c("aut", "cre"), email = "dan.l.warren@gmail.com", comment = c(ORCID = "0000-0002-8747-2451")),
 	      	person(given = "Russell", family = "Dinnage", role = "aut", email = "r.dinnage@gmail.com", comment = c(ORCID = "0000-0003-0846-2819")))

R/check.species.R

@@ -39,20 +39,20 @@ check.species <- function(this.species, env = NA, trim.dupes = FALSE){
   }
 
 
-  if(!is.logical(this.species$presence.points) || !is.na(this.species$presence.points)){
+  if(!is.logical(this.species$presence.points) || !all(is.na(this.species$presence.points))){
     this.species$presence.points <- check.points(this.species$presence.points, "presence.points")
   }
   if(!inherits(this.species$presence.points, "SpatVector")){
-    if(!is.na(this.species$presence.points)){
+    if(!all(is.na(this.species$presence.points))){
       "Species presence points require an object of or coercible to class SpatVector"
     }
   }
 
-  if(!is.logical(this.species$background.points) || !is.na(this.species$background.points)){
+  if(!is.logical(this.species$background.points) || !all(is.na(this.species$background.points))){
     this.species$background.points <- check.points(this.species$background.points, "background.points")
   }
   if(!inherits(this.species$background.points, "SpatVector")){
-    if(!is.na(this.species$background.points)){
+    if(!all(is.na(this.species$background.points))){
       "Species background points require an object of or coercible to class SpatVector"
     }
   }

R/enmtools.ecospat.bg.R

@@ -29,7 +29,7 @@
 #' }
 #' }
 
-enmtools.ecospat.bg <- function(species.1, species.2, env, nreps = 99, layers = NULL, test.type = "asymmetric", th.sp=0, th.env=0, R=100, nback = 1000, bg.source = "default", verbose = FALSE, ...){
+enmtools.ecospat.bg <- function(species.1, species.2, env, nreps = 99, layers = NULL, test.type = "symmetric", th.sp=0, th.env=0, R=100, nback = 1000, bg.source = "default", verbose = FALSE, ...){
 
   assert.extras.this.fun()
 

R/enmtools.species.R

@@ -25,9 +25,14 @@ enmtools.species <- function(range = NA, presence.points = NA, background.points
     }
   }
 
+  # We were thinking to require this to be done by hand, but it can still
+  # be super convenient to do this on the fly when species.from.file is called
+  if(inherits(presence.points, "data.frame")){
+    presence.points <- check.points(presence.points)
+  }
 
   if(!inherits(presence.points, "SpatVector")){
-    if(!is.na(presence.points)){
+    if(!all(is.na(presence.points))){
       stop("Argument presence.points requires an object of class SpatVector")
     }
   }

R/interactive.plot.enmtools.species.R

@@ -28,22 +28,24 @@ interactive.plot.enmtools.species <- function(x, map.provider = "Esri.WorldPhysi
   labels <- NULL
   colors <- NULL
 
-  if(inherits(raster::raster(x$range), "RasterLayer")){
-    m <- m %>%
-      leaflet::addRasterImage(raster::raster(x$range), function(y) ifelse(is.na(y), "#00000000", "#00000090"),
-                     group = "Range", maxBytes = max.bytes)
-    overlays <- c(overlays, "Range")
-    labels <- c(labels, "Range raster")
-    colors <- c(colors, "black")
+  if(!isTRUE(is.na(x$range))){
+    if(inherits(raster::raster(x$range), "RasterLayer")){
+      m <- m %>%
+        leaflet::addRasterImage(raster::raster(x$range), function(y) ifelse(is.na(y), "#00000000", "#00000090"),
+                                group = "Range", maxBytes = max.bytes)
+      overlays <- c(overlays, "Range")
+      labels <- c(labels, "Range raster")
+      colors <- c(colors, "black")
+    }
   }
 
 
   if(class(x$background.points) %in% c("SpatVector")){
     background.points <- terra::as.data.frame(x$background.points, geom = "XY")
     m <- m %>%
       leaflet::addCircleMarkers(~x, ~y, color = "red",
-                       data = background.points, stroke = FALSE, fillOpacity = 0.5,
-                       radius = 8, group = "Background points")
+                                data = background.points, stroke = FALSE, fillOpacity = 0.5,
+                                radius = 8, group = "Background points")
     overlays <- c(overlays, "Background points")
     labels <- c(labels, "Background points")
     colors <- c(colors, "red")
@@ -54,14 +56,14 @@ interactive.plot.enmtools.species <- function(x, map.provider = "Esri.WorldPhysi
     if(cluster.points) {
       m <- m %>%
         leaflet::addCircleMarkers(~x, ~y, color = "green",
-                         stroke = FALSE, fillOpacity = 0.5, radius = 8,
-                         data = presence.points, clusterOptions = leaflet::markerClusterOptions(),
-                         group = "Occurrence points")
+                                  stroke = FALSE, fillOpacity = 0.5, radius = 8,
+                                  data = presence.points, clusterOptions = leaflet::markerClusterOptions(),
+                                  group = "Occurrence points")
     } else {
       m <- m %>%
         leaflet::addCircleMarkers(~x, ~y, color = "green",
-                         data = presence.points, stroke = FALSE, fillOpacity = 0.5,
-                         radius = 8, group = "Occurrence points")
+                                  data = presence.points, stroke = FALSE, fillOpacity = 0.5,
+                                  radius = 8, group = "Occurrence points")
     }
     overlays <- c(overlays, "Occurrence points")
     labels <- c(labels, "Occurrence points")
@@ -77,7 +79,7 @@ interactive.plot.enmtools.species <- function(x, map.provider = "Esri.WorldPhysi
 
   m <- m %>%
     leaflet::addLegend("bottomright", colors = colors,
-              labels = labels)
+                       labels = labels)
 
   m
 

R/raster.standardize.R

@@ -25,5 +25,12 @@ raster.standardize <- function(x, verbose=FALSE){
     print(paste("Starting standardize on", x, "at", Sys.time()))
   }
 
+  minval <- terra::minmax(x)[1]
+
+  if(minval < 0){
+    x <- x - minval + 1e-20
+  }
+
+
   return(x/as.numeric(terra::global(x, "sum", na.rm = TRUE)))
 }

R/species.from.file.R

@@ -30,6 +30,7 @@ species.from.file <- function(filename, species.col = "species"){
 
     # More than one species in the file, create and return a list of enmtools.species objects
     for(i in sp.names){
+      print(i)
       this.species <- enmtools.species(species.name = i,
                                        presence.points = input.df[input.df[,species.col] == i,])
       this.species <- check.species(this.species)

R/utils.R

@@ -36,6 +36,7 @@ check.points <- function(pts, name = "input") {
     warning(sprintf('%s are not the expected SpatVector class (instead, it is of class %s). ENMTools will attempt to coerce using terra::vect(as.matrix(...), crs = "EPSG:4326"), but we cannot guaranteed the correctness of the result. Please consider using SpatVector format directly in the future, to minimize unexpected results.',
             name,
             cls))
+    pts <- format.latlon(pts)
     pts <- terra::vect(as.matrix(pts), crs = "EPSG:4326")
   }
   pts