Merge pull request #94 from mlr-org/blockCV-rasterLayer-arg

DESCRIPTION

@@ -57,6 +57,7 @@ Suggests:
     mlr3tuning,
     patchwork,
     plotly,
+    raster,
     rmarkdown,
     rpart,
     sf,

R/ResamplingRepeatedSpCVBlock.R

@@ -14,7 +14,7 @@
 #'   # Instantiate Resampling
 #'   rrcv = rsmp("repeated_spcv_block",
 #'     folds = 3, repeats = 2,
-#'     range = c(5000, 10000))
+#'     range = c(5000L, 10000L))
 #'   rrcv$instantiate(task)
 #'
 #'   # Individual sets:
@@ -44,10 +44,17 @@ ResamplingRepeatedSpCVBlock = R6Class("ResamplingRepeatedSpCVBlock",
         ParamInt$new("repeats", lower = 1, default = 1L, tags = "required"),
         ParamInt$new("rows", lower = 1L),
         ParamInt$new("cols", lower = 1L),
-        ParamUty$new("range"),
+        ParamUty$new("range",
+          custom_check = function(x) checkmate::assert_integer(x)),
         ParamFct$new("selection", levels = c(
           "random", "systematic",
-          "checkerboard"), default = "random")
+          "checkerboard"), default = "random"),
+        ParamUty$new("rasterLayer",
+          default = NULL,
+          custom_check = function(x) {
+            checkmate::check_class(x, "RasterLayer",
+              null.ok = TRUE)
+          })
       ))
 
       ps$values = list(folds = 10L, repeats = 1L)

R/ResamplingSpCVBlock.R

@@ -12,7 +12,7 @@
 #'   task = tsk("ecuador")
 #'
 #'   # Instantiate Resampling
-#'   rcv = rsmp("spcv_block", range = 1000)
+#'   rcv = rsmp("spcv_block", range = 1000L)
 #'   rcv$instantiate(task)
 #'
 #'   # Individual sets:
@@ -36,10 +36,13 @@ ResamplingSpCVBlock = R6Class("ResamplingSpCVBlock",
         ParamInt$new("folds", lower = 1L, default = 10L, tags = "required"),
         ParamInt$new("rows", lower = 1L),
         ParamInt$new("cols", lower = 1L),
-        ParamInt$new("range", lower = 1L),
+        ParamInt$new("range"),
         ParamFct$new("selection", levels = c(
           "random", "systematic",
-          "checkerboard"), default = "random")
+          "checkerboard"), default = "random"),
+        ParamUty$new("rasterLayer",
+          default = NULL,
+          custom_check = function(x) checkmate::check_class(x, "RasterLayer", null.ok = TRUE))
       ))
       ps$values = list(folds = 10L)
       super$initialize(
@@ -79,6 +82,9 @@ ResamplingSpCVBlock = R6Class("ResamplingSpCVBlock",
       if (is.null(self$param_set$values$selection)) {
         self$param_set$values$selection = self$param_set$default[["selection"]]
       }
+      if (is.null(self$param_set$values$rasterLayer)) {
+        self$param_set$values$rasterLayer = self$param_set$default[["rasterLayer"]]
+      }
 
       # Check for valid combinations of rows, cols and folds
       if (!is.null(self$param_set$values$row) &&
@@ -128,6 +134,7 @@ ResamplingSpCVBlock = R6Class("ResamplingSpCVBlock",
           rows = self$param_set$values$rows,
           cols = self$param_set$values$cols,
           k = self$param_set$values$folds,
+          rasterLayer = self$param_set$values$rasterLayer,
           selection = self$param_set$values$selection,
           showBlocks = FALSE,
           progress = FALSE,

R/autoplot.R

@@ -47,7 +47,7 @@
 #'   library(mlr3)
 #'   library(mlr3spatiotempcv)
 #'   task = tsk("ecuador")
-#'   resampling = rsmp("spcv_block", range = 1000)
+#'   resampling = rsmp("spcv_block", range = 1000L)
 #'   resampling$instantiate(task)
 #'
 #'   ## Visualize all partitions

codemeta.json

@@ -15,13 +15,13 @@
   ],
   "issueTracker": "https://github.com/mlr-org/mlr3spatiotempcv/issues",
   "license": "https://spdx.org/licenses/LGPL-3.0",
-  "version": "0.1.1.9000",
+  "version": "0.2.0.9001",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.0.3 Patched (2020-12-21 r79675)",
+  "runtimePlatform": "R version 4.0.4 Patched (2021-02-17 r80031)",
   "author": [
     {
       "@type": "Person",
@@ -223,6 +223,18 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=plotly"
     },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "raster",
+      "name": "raster",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=raster"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "rmarkdown",
@@ -369,7 +381,7 @@
       "@type": "SoftwareApplication",
       "identifier": "mlr3misc",
       "name": "mlr3misc",
-      "version": ">= 0.1.7",
+      "version": ">= 0.7.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -409,17 +421,18 @@
     }
   ],
   "releaseNotes": "https://github.com/mlr-org/mlr3spatiotempcv/blob/master/NEWS.md",
-  "readme": "https://github.com/mlr-org/mlr3spatiotempcv/blob/master/README.md",
-  "fileSize": "11481.001KB",
-  "contIntegration": "https://codecov.io/github/mlr-org/mlr3spatiotempcv?branch=master",
-  "developmentStatus": "https://www.tidyverse.org/lifecycle/#maturing",
+  "readme": "https://github.com/mlr-org/mlr3spatiotempcv/blob/main/README.md",
+  "fileSize": "13087.485KB",
+  "contIntegration": "https://codecov.io/github/mlr-org/mlr3spatiotempcv?branch=main",
+  "developmentStatus": "https://lifecycle.r-lib.org/articles/stages.html",
   "keywords": [
     "mlr3",
     "resampling",
     "spatial",
     "cross-validation",
     "temporal",
-    "resampling-methods"
+    "resampling-methods",
+    "r"
   ],
   "provider": {
     "@id": "https://cran.r-project.org",

tests/testthat/helper.R

@@ -156,7 +156,7 @@ test_make_blockCV_test_df = function() {
 
   data_sf = sf::st_as_sf(data,
     coords = c("x", "y"),
-    crs = "EPSG: 4326")
+    crs = "EPSG:4326")
 
   return(data_sf)
 

tests/testthat/test-1-autoplot.R

@@ -142,7 +142,7 @@ test_that("plot() works for 'repeated_spcv_block'", {
   set.seed(42)
 
   plots = prepare_autoplot("repeated_spcv_block",
-    folds = 4, range = c(2, 4), repeats = 2)
+    folds = 4, range = c(2L, 4L), repeats = 2)
 
   # autoplot() is used instead of plot() to prevent side-effect plotting
   p1 = autoplot(plots$rsp, plots$task, crs = 4326)

tests/testthat/test-ResamplingRepeatedSpCVBlock.R

@@ -1,22 +1,22 @@
 test_that("folds can be printed", {
   task = test_make_twoclass_task()
-  rsp = rsmp("repeated_spcv_block", folds = 3, repeats = 2, range = c(2, 4))
+  rsp = rsmp("repeated_spcv_block", folds = 3, repeats = 2, range = c(2L, 4L))
   rsp$instantiate(task)
 
   expect_equal(rsp$folds(1:6), c(1, 2, 1, 2, 1, 2))
 })
 
 test_that("reps can be printed", {
   task = test_make_twoclass_task()
-  rsp = rsmp("repeated_spcv_block", folds = 3, repeats = 2, range = c(2, 4))
+  rsp = rsmp("repeated_spcv_block", folds = 3, repeats = 2, range = c(2L, 4L))
   rsp$instantiate(task)
 
   expect_equal(rsp$repeats(1:9), c(1, 1, 1, 2, 2, 2, 3, 3, 3))
 })
 
 test_that("resampling iterations equals folds * repeats", {
   task = test_make_twoclass_task()
-  rsp = rsmp("repeated_spcv_block", folds = 3, repeats = 2, range = c(2, 4))
+  rsp = rsmp("repeated_spcv_block", folds = 3, repeats = 2, range = c(2L, 4L))
   rsp$instantiate(task)
 
   expect_equal(rsp$iters, 6)
@@ -32,7 +32,7 @@ test_that("error when neither cols & rows | range is specified", {
 
 test_that("error when length(range) != length(repeats)", {
   task = test_make_twoclass_task()
-  rsp = rsmp("repeated_spcv_block", repeats = 2, range = 5)
+  rsp = rsmp("repeated_spcv_block", repeats = 2, range = 5L)
   expect_error(
     rsp$instantiate(task),
     ".*to be the same length as 'range'."
@@ -41,13 +41,13 @@ test_that("error when length(range) != length(repeats)", {
 
 test_that("no error when length(range) == repeats", {
   task = test_make_twoclass_task()
-  rsp = rsmp("repeated_spcv_block", folds = 3, repeats = 2, range = c(2, 4))
+  rsp = rsmp("repeated_spcv_block", folds = 3, repeats = 2, range = c(2L, 4L))
   expect_silent(rsp$instantiate(task))
 })
 
 test_that("error when number of desired folds is larger than number possible blocks", {
   task = test_make_twoclass_task()
-  rsp = rsmp("repeated_spcv_block", folds = 10, repeats = 2, range = c(2, 4))
+  rsp = rsmp("repeated_spcv_block", folds = 10, repeats = 2, range = c(2L, 4L))
   expect_error(rsp$instantiate(task))
 })
 

tests/testthat/test-ResamplingSpCVBlock.R

@@ -1,14 +1,14 @@
 test_that("resampling iterations equals folds", {
   task = test_make_twoclass_task()
-  rsp = rsmp("spcv_block", folds = 2, range = 2)
+  rsp = rsmp("spcv_block", folds = 2, range = 2L)
   rsp$instantiate(task)
 
   expect_equal(rsp$iters, 2)
 })
 
 test_that("error when number of desired folds is larger than number possible blocks", {
   task = test_make_twoclass_task()
-  rsp = rsmp("spcv_block", folds = 10, range = 4)
+  rsp = rsmp("spcv_block", folds = 10, range = 4L)
 
   expect_error(rsp$instantiate(task))
 })
@@ -33,7 +33,7 @@ test_that("error when only one of rows or cols is set", {
 })
 
 test_that("Error when length(range) >= 2", {
-  expect_error(rsmp("spcv_block", range = c(500, 1000)))
+  expect_error(rsmp("spcv_block", range = c(500L, 1000L)))
 })
 
 
@@ -44,7 +44,7 @@ test_that("mlr3spatiotempcv indices are the same as blockCV indices: selection =
   task = test_make_blockCV_test_task()
 
   rsmp <- rsmp("spcv_block",
-    range = 50000,
+    range = 50000L,
     selection = "checkerboard")
   rsmp$instantiate(task)
 
@@ -53,7 +53,7 @@ test_that("mlr3spatiotempcv indices are the same as blockCV indices: selection =
   capture.output(testBlock <- suppressMessages(
     suppressWarnings(blockCV::spatialBlock(
       speciesData = testSF,
-      theRange = 50000,
+      theRange = 50000L,
       selection = "checkerboard",
       showBlocks = FALSE)
   )))
@@ -87,3 +87,34 @@ test_that("mlr3spatiotempcv indices are the same as blockCV indices: cols and ro
 
   expect_equal(rsmp$instance$fold, testBlock$foldID)
 })
+
+test_that("mlr3spatiotempcv indices are the same as blockCV indices: rasterLayer", {
+  set.seed(42)
+
+  task = test_make_blockCV_test_task()
+  testSF = test_make_blockCV_test_df()
+
+  r <- raster::raster(raster::extent(testSF), crs = "EPSG:4326")
+  r[] <- 10
+
+  rsmp <- rsmp("spcv_block",
+    range = 50000L,
+    selection = "checkerboard",
+    rasterLayer = r)
+  rsmp$instantiate(task)
+
+
+  # blockCV
+  capture.output(testBlock <- suppressMessages(
+    blockCV::spatialBlock(
+      speciesData = testSF,
+      theRange = 50000L,
+      selection = "checkerboard",
+      rasterLayer = r,
+      showBlocks = FALSE,
+      verbose = FALSE,
+      progress = FALSE)
+  ))
+
+  expect_equal(rsmp$instance$fold, testBlock$foldID)
+})