Updated almost all class tests for compatibility with the upcoming 4.…

…0.0 R version

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: virtualspecies
 Type: Package
 Title: Generation of Virtual Species Distributions
-Version: 1.5
-Date: 2019-04-30
+Version: 1.5.1
+Date: 2019-12-12
 Author: Boris Leroy [cre, aut], Christine N. Meynard [ctb], Celine Bellard [ctb], Franck Courchamp [ctb], Robin Delsol [ctb], Willson Gaul [ctb]
 Maintainer: Boris Leroy <[email protected]>
 Description: Provides a framework for generating virtual species distributions,

NEWS

@@ -1,3 +1,9 @@
+virtualspecies v1.5.1 (Release date: 2019-12-12)
+==============
+
+Changes:
+* Internal changes for compatibility with the upcoming R 4.0.0 version
+
 virtualspecies v1.5 (Release date: 2019-04-30)
 ==============
 

R/convertToPA.R

@@ -269,14 +269,14 @@ convertToPA <- function(x,
                         plot = TRUE)
 
 {
-  if("virtualspecies" %in% class(x))
+  if(inherits(x, "virtualspecies"))
   {
-    if("RasterLayer" %in% class(x$suitab.raster))
+    if(inherits(x$suitab.raster, "RasterLayer"))
     {
       sp.raster <- x$suitab.raster
     } else stop("x must be:\n- a raster layer object\nor\n- the output list from functions
                generateSpFromFun(), generateSpFromPCA() or generateRandomSp()")
-  } else if ("RasterLayer" %in% class(x))
+  } else if (inherits(x, "RasterLayer"))
   {
     sp.raster <- x
   } else stop("x must be:\n- a raster layer object\nor\n- the output list from functions
@@ -685,7 +685,7 @@ convertToPA <- function(x,
 
   species.prevalence <- cellStats(PA.raster, stat = "mean")
 
-  if("virtualspecies" %in% class(x))
+  if(inherits(x, "virtualspecies"))
   {
     if(PA.method == "threshold")
     {
@@ -729,7 +729,7 @@ convertToPA <- function(x,
                   main = c("Environmental suitability",
                            "Probability of occurrence", 
                            "Presence-absence"))
-  } else if ("RasterLayer" %in% class(x))
+  } else if (inherits(x, "RasterLayer"))
   {
     if(PA.method == "threshold")
     {

R/generateSpFromFun.R

@@ -153,7 +153,7 @@ generateSpFromFun <- function(raster.stack, parameters,
           names(parameters)[i], "'. See help(generateSpFromFun) for more details.",
           sep = "")}
     test <- tryCatch(match.fun(parameters[[i]]$fun), error = function(c) "error")
-    if(class(test) != "function")
+    if(!inherits(test, "function"))
     {
       stop(paste("The function ", parameters[[i]]$fun, " does not exist, please verify spelling.", sep = ""))
     }

R/limitDistribution.R

@@ -135,14 +135,14 @@ limitDistribution <- function(x,
 {
 
 
-  if("virtualspecies" %in% class(x))
+  if(inherits(x, "virtualspecies"))
   {
-    if("RasterLayer" %in% class(x$pa.raster))
+    if(inherits(x$pa.raster, "RasterLayer"))
     {
       sp.raster <- x$pa.raster
       results <- x
     } else stop("x must be:\n- a raster layer object\nor\n- the output list from function convertToPA(), generateSpFromFun(), generateSpFromPCA() or generateRandomSp()")
-  } else if ("RasterLayer" %in% class(x))
+  } else if (inherits(x, "RasterLayer"))
   {
     sp.raster <- x
     results <- list(sp.raster)
@@ -199,7 +199,7 @@ limitDistribution <- function(x,
     # This is especially important given that randomPoints weights samplings by the cell area (because cells closer to
     # the equator are larger)
   {
-    if(!(class(area) %in% c("SpatialPolygons", "SpatialPolygonsDataFrame")))
+    if(!(inherits(area, c("SpatialPolygons", "SpatialPolygonsDataFrame"))))
     {
       stop("If you choose geographical.limit = 'polygon', please provide a polygon of class SpatialPolygons or SpatialPolygonsDataFrame to argument area")
     }
@@ -208,15 +208,15 @@ limitDistribution <- function(x,
                                        area = area)
   } else if(geographical.limit == "extent")
   {
-    if(!(class(area) == "Extent"))
+    if(!(inherits(area, "Extent")))
     {
       message("No object of class extent (or wrong object) provided: click twice on the map to draw the extent in which presence points will be sampled")
       plot(sp.raster)
       area <- drawExtent(show = TRUE)      
     }
   } else if(geographical.limit == "raster")
   {
-    if (!("RasterLayer" %in% class(area)))
+    if (!(inherits(area, "RasterLayer")))
     {
       stop("If you choose to limit the distribution with a raster, please provide the raster to argument 'area'")    
     }

R/plotSuitabilityToProba.R

@@ -60,7 +60,7 @@
 
 plotSuitabilityToProba <- function(sp, add = FALSE, ...)
 {
-  if("virtualspecies" %in% class(sp))
+  if(inherits(sp, "virtualspecies"))
   {
     if(!("PA.conversion" %in% names(sp)))
     {

R/sampleOccurrences.R

@@ -306,18 +306,18 @@ sampleOccurrences <- function(x, n,
   attr(results, "seed") <- .Random.seed
 
 
-  if("virtualspecies" %in% class(x))
+  if(inherits(x, "virtualspecies"))
   {
-    if("RasterLayer" %in% class(x$occupied.area))
+    if(inherits(x$occupied.area, "RasterLayer"))
     {
       sp.raster <- x$occupied.area
-    } else if("RasterLayer" %in% class(x$pa.raster))
+    } else if(inherits(x$pa.raster, "RasterLayer"))
     {
       sp.raster <- x$pa.raster
     } else stop("x must be:\n- a raster layer object\nor\n- the output list from
                 functions generateRandomSp(), convertToPA() or 
                 limitDistribution()")
-  } else if ("RasterLayer" %in% class(x))
+  } else if (inherits(x, "RasterLayer"))
   {
     sp.raster <- x
     if(extract.probability)
@@ -361,9 +361,9 @@ sampleOccurrences <- function(x, n,
         worldmap@data$SOVEREIGNT %in% sampling.area | 
           worldmap@data$REGION %in% sampling.area |
           worldmap@data$continent %in% sampling.area), ]
-    } else if(!(class(sampling.area) %in% c("SpatialPolygons",
-                                            "SpatialPolygonsDataFrame", 
-                                            "Extent")))
+    } else if(!(inherits(sampling.area, c("SpatialPolygons",
+                                          "SpatialPolygonsDataFrame", 
+                                          "Extent"))))
     {
       stop("Please provide to sampling.area either \n
            - the names of countries, region and/or continents in which to sample\n
@@ -383,7 +383,7 @@ sampleOccurrences <- function(x, n,
 
   if(correct.by.suitability)
   {
-    if(!("virtualspecies" %in% class(x)) | !("suitab.raster" %in% names(x)))
+    if(!(inherits(x, "virtualspecies")) | !("suitab.raster" %in% names(x)))
     {
       stop("If you choose to weight the probability of detection by the suitability of the species (i.e., correct.by.suitability = TRUE),
            then you need to provide an appropriate virtual species containing a suitability raster to x.")
@@ -469,8 +469,8 @@ sampleOccurrences <- function(x, n,
     # This is especially important given that randomPoints weights samplings by 
     # the cell area (because cells closer to the equator are larger)
   {
-    if(!(class(bias.area) %in% c("SpatialPolygons", 
-                                 "SpatialPolygonsDataFrame")))
+    if(!(inherits(bias.area, c("SpatialPolygons", 
+                               "SpatialPolygonsDataFrame"))))
     {
       stop("If you choose bias = 'polygon', please provide a polygon of class 
            SpatialPolygons or SpatialPolygonsDataFrame to argument bias.area")
@@ -503,7 +503,7 @@ sampleOccurrences <- function(x, n,
 
   if (bias == "manual")
   {
-    if(!("RasterLayer" %in% class(weights)))
+    if(!(inherits(weights, "RasterLayer")))
     {
       stop("You must provide a raster layer of weights (to argument weights) 
            if you choose bias == 'manual'")
@@ -546,7 +546,7 @@ sampleOccurrences <- function(x, n,
     bias.raster <- bias.raster * bias.raster1
   } else if(bias == "extent")
   {
-    if(!(class(bias.area) == "Extent"))
+    if(!(inherits(bias.area, "Extent")))
     {
       message("No object of class extent provided: click twice on the map to draw the extent in which presence points will be sampled")
       plot(sp.raster)

R/utilityFunctions.R

@@ -65,7 +65,7 @@
     }
   }
 
-  if (class(ext)=='character') {
+  if (inherits(ext, 'character')) {
     if (! ext %in% c('points')) { 
       stop("if ext is a character variable it should be 'points'") 
     } else if (missing(p)) { 
@@ -92,7 +92,7 @@
     stopifnot(hasValues(mask))
     cells <- crop(mask, mask2)
     cells <- try( stats::na.omit(cbind(1:ncell(cells), getValues(cells))))
-    if (class(cells) == 'try-error') {
+    if (inherits(cells, 'try-error')) {
       stop("the raster is too large to be used with 'prob=TRUE'")
     }
     prob <- cells[,2]