fixed snow issue by removing raster::clusteR and simplified tests

sylvainschmitt · Oct 24, 2023 · cf59b06 · cf59b06
1 parent 58f669b
commit cf59b06
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Showing 10 changed files with 24 additions and 95 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -77,12 +77,9 @@ importFrom(raster,"values<-")
 importFrom(raster,Which)
 importFrom(raster,aggregate)
 importFrom(raster,as.factor)
-importFrom(raster,beginCluster)
 importFrom(raster,calc)
-importFrom(raster,clusterR)
 importFrom(raster,crop)
 importFrom(raster,crs)
-importFrom(raster,endCluster)
 importFrom(raster,extent)
 importFrom(raster,extract)
 importFrom(raster,layerStats)

diff --git a/R/ensemble.R b/R/ensemble.R
@@ -1,5 +1,5 @@
 #' @include Algorithm.SDM.R checkargs.R
-#' @importFrom raster raster stack reclassify beginCluster clusterR endCluster
+#' @importFrom raster raster stack reclassify
 NULL
 
 #'Methods to assemble multiple algorithms in an ensemble SDM
@@ -247,14 +247,7 @@ setMethod("ensemble", "Algorithm.SDM", function(x, ..., name = NULL, ensemble.me
         if (verbose) {
           cat("uncertainty mapping...")
         }
-        if(cores>0){
-          beginCluster(cores)
-          esdm@uncertainty <- clusterR(projections, fun=function(x) calc(x, var))
-          endCluster()
-        }
-        else{
-          esdm@uncertainty <- calc(projections, var)
-        }
+        esdm@uncertainty <- calc(projections, var)
         names(esdm@uncertainty) <- "uncertainty map"
         if (verbose) {
           cat("   done \n")

diff --git a/tests/testthat/test_ensemble_modelling.R b/tests/testthat/test_ensemble_modelling.R
@@ -2,8 +2,15 @@ test_that('ensemble modelling function', {
   data(Env)
   data(Occurrences)
   Occurrences <- subset(Occurrences, Occurrences$SPECIES == 'elliptica')
+  # parrallel
   ESDM <- ensemble_modelling(c('CTA', 'MARS'), Occurrences, Env, rep = 1,
                             Xcol = 'LONGITUDE', Ycol = 'LATITUDE',
-                            ensemble.thresh = c(0), verbose = FALSE)
+                            ensemble.thresh = c(0), verbose = FALSE,
+                            cores = 2, tmp = TRUE)
   expect_is(ESDM, 'Ensemble.SDM')
+  # projection
+  Env_new <- stack(Env[[1]]-1,Env[[2]],Env[[3]])
+  ESDM_proj <- project(ESDM,Env_new,output.format='model')
+  expect_is(ESDM_proj, 'Ensemble.SDM')
+  expect_false(all(is.na(values(ESDM_proj@projection))))
 })
diff --git a/tests/testthat/test_modelling.R b/tests/testthat/test_modelling.R
@@ -4,8 +4,12 @@ test_that('modelling function', {
   Occurrences <- subset(Occurrences, Occurrences$SPECIES == 'elliptica')
   available.algo <- available.algo <- c("GLM", "GAM", "MARS", "GBM", "CTA", "RF", "ANN", "SVM")
   for(i in available.algo){
-    # cat(paste("testing", i, "...\n"))
     show_failure(SDM <- modelling(i, Occurrences, Env, Xcol = 'LONGITUDE', Ycol = 'LATITUDE', verbose = F))
     expect_is(SDM, paste0(i,'.SDM'))
   }
+  # projection
+  Env_new <- stack(Env[[1]]-1,Env[[2]],Env[[3]])
+  SDM_proj <- project(SDM, Env_new, output.format='model')
+  expect_is(SDM_proj, 'SVM.SDM')
+  expect_false(all(is.na(values(SDM_proj@projection))))
 })
diff --git a/tests/testthat/test_parallel_ESDM.R b/tests/testthat/test_parallel_ESDM.R
diff --git a/tests/testthat/test_parallel_SSDM.R b/tests/testthat/test_parallel_SSDM.R
diff --git a/tests/testthat/test_project_ESDM.R b/tests/testthat/test_project_ESDM.R
diff --git a/tests/testthat/test_project_SDM.R b/tests/testthat/test_project_SDM.R
diff --git a/tests/testthat/test_project_SSDM.R b/tests/testthat/test_project_SSDM.R
diff --git a/tests/testthat/test_stack_modelling.R b/tests/testthat/test_stack_modelling.R
@@ -1,9 +1,17 @@
 test_that('stack modelling function', {
   data(Env)
   data(Occurrences)
+  # parrallel
+  i <- "species" # 'algorithms' and 'replicates' missing
   SSDM <- stack_modelling(c('CTA', 'SVM'), Occurrences, Env, rep = 1,
                          Xcol = 'LONGITUDE', Ycol = 'LATITUDE',
                          Spcol = 'SPECIES', ensemble.thresh = 0,
-                         verbose = FALSE, cores = 0)
+                         verbose = FALSE,
+                         cores = 2, parmode = i , tmp = FALSE)
   expect_is(SSDM, 'Stacked.SDM')
+  # projection
+  Env_new <- stack(Env[[1]]-0.3,Env[[2]],Env[[3]])
+  SSDM_proj <- project(SSDM,Env_new,output.format='model')
+  expect_is(SSDM_proj, 'Stacked.SDM')
+  expect_false(all(is.na(values(SSDM_proj@diversity.map))))
 })