Updates to address the archiving of SDMTools. This packaged is moved …

…to suggests, tests that use it are skipped if it is not installed
zoonproject · Feb 10, 2020 · 4ccd34c · 4ccd34c · timcdlucas · Feb 10, 2020
1 parent 3ff8856
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: zoon
 Type: Package
 Title: Reproducible, Accessible & Shareable Species Distribution Modelling
-Version: 0.6.4
-Date: 2019-11-13
+Version: 0.6.5
+Date: 2012-02-10
 Authors@R: c(person("Tom", "August", role = c("aut", "cre"),
                     email = "[email protected]"),
              person("Tim", "Lucas", role = "aut", comment = c(ORCID = "0000-0003-4694-8107")),
@@ -24,15 +24,15 @@ Imports:
     rgdal,
     roxygen2,
     rworldmap,
-    SDMTools,
     sp,
     testthat
 Depends:
     raster (>= 2.4-20),
     R (>= 3.2.0)
 Suggests:
     knitr,
-    maxlike
+    maxlike,
+    SDMTools
 VignetteBuilder: knitr
 LazyData: TRUE
 URL: https://github.com/zoonproject/zoon

diff --git a/NAMESPACE b/NAMESPACE
@@ -45,8 +45,6 @@ import(sp)
 import(testthat)
 importFrom(RCurl,getURL)
 importFrom(RCurl,url.exists)
-importFrom(SDMTools,auc)
-importFrom(SDMTools,confusion.matrix)
 importFrom(grDevices,dev.off)
 importFrom(grDevices,grey)
 importFrom(grDevices,png)

diff --git a/R/test_outputs.R b/R/test_outputs.R
@@ -1,4 +1,3 @@
-#' @importFrom SDMTools auc confusion.matrix
 #' @import randomForest
 #'
 # A function for testing the outputs conform to the expected
@@ -171,36 +170,38 @@ test_occurrence_outputs <- function (roxy_parse, modulePath, en) {
                          "when chained in a workflow")
           )
 
-
-          # test list + crossvalidation
-          w <- tryCatchWorkflow(
-            expr = {
-              w <- workflow(
-                occurrence = list(
-                  OccurrenceModule,
-                  OccurrenceModule
-                ),
-                covariate = NaiveRandomRaster(
-                  extent = myExtent,
-                  res = 0.5,
-                  seed = 123
-                ),
-                process = BackgroundAndCrossvalid,
-                model = LogisticRegression,
-                output = PerformanceMeasures,
-                forceReproducible = FALSE
-              )
-            },
-            placeholder = "OccurrenceModule",
-            fun = roxy_parse$name
-          )
-          if (inherits(w, what = "moduleError")) stop(w)
-
-          expect_is(
-            w, "zoonWorkflow",
-            info = paste("The occurrence module did not work",
-                         "when listed in a workflow with crossvalidation")
-          )
+          SDMtools_check <- requireNamespace('SDMtools', quietly = TRUE)
+          if(SDMtools_check){
+            # test list + crossvalidation
+            w <- tryCatchWorkflow(
+              expr = {
+                w <- workflow(
+                  occurrence = list(
+                    OccurrenceModule,
+                    OccurrenceModule
+                  ),
+                  covariate = NaiveRandomRaster(
+                    extent = myExtent,
+                    res = 0.5,
+                    seed = 123
+                  ),
+                  process = BackgroundAndCrossvalid,
+                  model = LogisticRegression,
+                  output = PerformanceMeasures,
+                  forceReproducible = FALSE
+                )
+              },
+              placeholder = "OccurrenceModule",
+              fun = roxy_parse$name
+            )
+            if (inherits(w, what = "moduleError")) stop(w)
+
+            expect_is(
+              w, "zoonWorkflow",
+              info = paste("The occurrence module did not work",
+                           "when listed in a workflow with crossvalidation")
+            )
+          }
         } else if (data_type == "presence/absence") {
 
           # test normal
@@ -259,35 +260,39 @@ test_occurrence_outputs <- function (roxy_parse, modulePath, en) {
                          "when chained in a workflow")
           )
 
-          # test list + crossvalidation
-          w <- tryCatchWorkflow(
-            expr = {
-              w <- workflow(
-                occurrence = list(
-                  OccurrenceModule,
-                  OccurrenceModule
-                ),
-                covariate = NaiveRandomRaster(
-                  extent = myExtent,
-                  res = 0.5,
-                  seed = 123
-                ),
-                process = Crossvalidate,
-                model = LogisticRegression,
-                output = PerformanceMeasures,
-                forceReproducible = FALSE
-              )
-            },
-            placeholder = "OccurrenceModule",
-            fun = roxy_parse$name
-          )
-          if (inherits(w, what = "moduleError")) stop(w)
-
-          expect_is(
-            w, "zoonWorkflow",
-            info = paste("The occurrence module did not work",
-                         "when listed in a workflow with crossvalidation")
-          )
+          SDMtools_check <- requireNamespace('SDMtools', quietly = TRUE)
+          if(SDMtools_check){
+
+            # test list + crossvalidation
+            w <- tryCatchWorkflow(
+              expr = {
+                w <- workflow(
+                  occurrence = list(
+                    OccurrenceModule,
+                    OccurrenceModule
+                  ),
+                  covariate = NaiveRandomRaster(
+                    extent = myExtent,
+                    res = 0.5,
+                    seed = 123
+                  ),
+                  process = Crossvalidate,
+                  model = LogisticRegression,
+                  output = PerformanceMeasures,
+                  forceReproducible = FALSE
+                )
+              },
+              placeholder = "OccurrenceModule",
+              fun = roxy_parse$name
+            )
+            if (inherits(w, what = "moduleError")) stop(w)
+
+            expect_is(
+              w, "zoonWorkflow",
+              info = paste("The occurrence module did not work",
+                           "when listed in a workflow with crossvalidation")
+            )
+          }
         } ## Add tests for proportion and abundance ##
       }
     }
@@ -987,28 +992,32 @@ test_model_outputs <- function (roxy_parse, modulePath, en) {
                 info = "The model module did not work in a list workflow"
               )
 
-              # crossvalidate
-              w <- tryCatchWorkflow(
-                expr = {
-                  w <- workflow(
-                    occurrence = NaiveRandomPresenceAbsence(n = 1000,
-                                                            seed = 123),
-                    covariate = NaiveRandomRaster,
-                    process = Crossvalidate,
-                    model = list(ModelModule, ModelModule),
-                    output = PerformanceMeasures,
-                    forceReproducible = FALSE
-                  )
-                },
-                placeholder = "ModelModule",
-                fun = roxy_parse$name
-              )
-              if (inherits(w, what = "moduleError")) stop(w)
+              SDMtools_check <- requireNamespace('SDMtools', quietly = TRUE)
+              if(SDMtools_check){
 
-              expect_is(
-                w, "zoonWorkflow",
-                info = paste("The process module did not work in a",
-                             "crossvalidation workflow"))
+                # crossvalidate
+                w <- tryCatchWorkflow(
+                  expr = {
+                    w <- workflow(
+                      occurrence = NaiveRandomPresenceAbsence(n = 1000,
+                                                              seed = 123),
+                      covariate = NaiveRandomRaster,
+                      process = Crossvalidate,
+                      model = list(ModelModule, ModelModule),
+                      output = PerformanceMeasures,
+                      forceReproducible = FALSE
+                    )
+                  },
+                  placeholder = "ModelModule",
+                  fun = roxy_parse$name
+                )
+                if (inherits(w, what = "moduleError")) stop(w)
+
+                expect_is(
+                  w, "zoonWorkflow",
+                  info = paste("The process module did not work in a",
+                               "crossvalidation workflow"))
+              }
 
             } else if (data_type == "presence/background") {
 
@@ -1081,26 +1090,30 @@ test_model_outputs <- function (roxy_parse, modulePath, en) {
                 info = "The model module did not work in a list workflow"
               )
 
-              # crossvalidate
-              w <- tryCatchWorkflow(
-                expr = {
-                  w <- workflow(
-                    occurrence = UKAnophelesPlumbeus,
-                    covariate = UKAir,
-                    process = Chain(Background(n = 70), Crossvalidate),
-                    model = ModelModule,
-                    output = PerformanceMeasures,
-                    forceReproducible = FALSE
-                  )
-                },
-                placeholder = "ModelModule",
-                fun = roxy_parse$name
-              )
-              if (inherits(w, what = "moduleError")) stop(w)
-
-              expect_is(w, "zoonWorkflow",
-                        info = paste("The model module did not work",
-                                     "in a crossvalidation workflow"))
+              SDMtools_check <- requireNamespace('SDMtools', quietly = TRUE)
+              if(SDMtools_check){
+
+                # crossvalidate
+                w <- tryCatchWorkflow(
+                  expr = {
+                    w <- workflow(
+                      occurrence = UKAnophelesPlumbeus,
+                      covariate = UKAir,
+                      process = Chain(Background(n = 70), Crossvalidate),
+                      model = ModelModule,
+                      output = PerformanceMeasures,
+                      forceReproducible = FALSE
+                    )
+                  },
+                  placeholder = "ModelModule",
+                  fun = roxy_parse$name
+                )
+                if (inherits(w, what = "moduleError")) stop(w)
+
+                expect_is(w, "zoonWorkflow",
+                          info = paste("The model module did not work",
+                                       "in a crossvalidation workflow"))
+              }
             }
           }
         }

diff --git a/tests/testthat/testChangeWorkflow.R b/tests/testthat/testChangeWorkflow.R
@@ -65,29 +65,31 @@ test_that("Basic ChangeWorkflow works", {
           "output = PrintMap, forceReproducible = FALSE)")
   ))
 
-
+  
   # Change Process, model and output
-  set.seed(1)
-  w4 <- workflow(
-    UKAnophelesPlumbeus,
-    UKAir,
-    BackgroundAndCrossvalid(k = 2),
-    RandomForest,
-    PerformanceMeasures
-  )
-
-  set.seed(1)
-  w5 <- ChangeWorkflow(
-    w4,
-    process = Background(n = 70),
-    model = LogisticRegression,
-    output = PrintMap
-  )
-  expect_true(all.equal(
-    w1[!names(w1) %in% "session.info"],
-    w5[!names(w5) %in% "session.info"]
-  ))
-
+  suppressWarnings({SDMtools_check <- requireNamespace('SDMtools', quietly = TRUE)})
+  if(SDMtools_check){
+    set.seed(1)
+    w4 <- workflow(
+      UKAnophelesPlumbeus,
+      UKAir,
+      BackgroundAndCrossvalid(k = 2),
+      RandomForest,
+      PerformanceMeasures
+    )
+
+    set.seed(1)
+    w5 <- ChangeWorkflow(
+      w4,
+      process = Background(n = 70),
+      model = LogisticRegression,
+      output = PrintMap
+    )
+    expect_true(all.equal(
+      w1[!names(w1) %in% "session.info"],
+      w5[!names(w5) %in% "session.info"]
+    ))
+  }
 
   # Change occurrence and covariate
   set.seed(1)
@@ -125,23 +127,26 @@ test_that("Basic ChangeWorkflow works", {
 
   # Only change output
   # Change Process, model and output
-  set.seed(1)
-  w7a <- workflow(
-    UKAnophelesPlumbeus,
-    UKAir,
-    Background(n = 70),
-    LogisticRegression,
-    PerformanceMeasures
-  )
-  set.seed(1)
-  w7b <- ChangeWorkflow(
-    w7a,
-    output = PrintMap
-  )
-  expect_true(all.equal(
-    w1[!names(w1) %in% "session.info"],
-    w7b[!names(w7b) %in% "session.info"]
-  ))
+  suppressWarnings({SDMtools_check <- requireNamespace('SDMtools', quietly = TRUE)})
+  if(SDMtools_check){
+    set.seed(1)
+    w7a <- workflow(
+      UKAnophelesPlumbeus,
+      UKAir,
+      Background(n = 70),
+      LogisticRegression,
+      PerformanceMeasures
+    )
+    set.seed(1)
+    w7b <- ChangeWorkflow(
+      w7a,
+      output = PrintMap
+    )
+    expect_true(all.equal(
+      w1[!names(w1) %in% "session.info"],
+      w7b[!names(w7b) %in% "session.info"]
+    ))
+  }
 })
 
 test_that("ChangeWorkflow - Chains", {

diff --git a/tests/testthat/testcall_path.R b/tests/testthat/testcall_path.R
@@ -491,6 +491,9 @@ test_that("Test call_path in a large number of variations", {
     )
   )
 
+  suppressWarnings({SDMtools_check <- requireNamespace('SDMtools', quietly = TRUE)})
+  if(!SDMtools_check) skip('Some tests require SDMtools - install it first')
+
   CP_work4 <- workflow(
     occurrence = UKAnophelesPlumbeus,
     covariate = UKAir,