New Task*ST API, consolidate autoplot() (#199)

mlr-org · Jun 13, 2022 · aa5de5a · aa5de5a
1 parent cd52eed
commit aa5de5a
Show file tree

Hide file tree

Showing 165 changed files with 14,060 additions and 138,271 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -28,7 +28,6 @@ Imports:
     data.table,
     ggplot2,
     mlr3misc (>= 0.9.2),
-    mlr3spatial (> 0.1.2),
     paradox,
     R6,
     utils
@@ -44,6 +43,7 @@ Suggests:
     mlr3pipelines,
     mlr3tuning,
     patchwork,
+    here,
     plotly,
     raster,
     rgdal,
@@ -58,8 +58,6 @@ Suggests:
     withr
 VignetteBuilder:
     knitr
-Remotes:
-    mlr-org/mlr3spatial
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 Encoding: UTF-8

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,12 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(as_task_classif,TaskClassifST)
 S3method(as_task_classif_st,DataBackend)
 S3method(as_task_classif_st,TaskClassifST)
 S3method(as_task_classif_st,data.frame)
 S3method(as_task_classif_st,sf)
-S3method(as_task_regr,TaskRegrST)
 S3method(as_task_regr_st,DataBackend)
+S3method(as_task_regr_st,TaskClassifST)
 S3method(as_task_regr_st,TaskRegrST)
 S3method(as_task_regr_st,data.frame)
 S3method(as_task_regr_st,sf)
@@ -63,16 +62,23 @@ export(ResamplingSptCVCluto)
 export(ResamplingSptCVCstf)
 export(TaskClassifST)
 export(TaskRegrST)
-export(as_task_classif.TaskClassifST)
 export(as_task_classif_st)
+export(as_task_classif_st.DataBackend)
+export(as_task_classif_st.TaskClassifST)
+export(as_task_classif_st.data.frame)
+export(as_task_classif_st.sf)
 export(as_task_regr_st)
+export(as_task_regr_st.DataBackend)
+export(as_task_regr_st.TaskClassifST)
+export(as_task_regr_st.TaskRegrST)
+export(as_task_regr_st.data.frame)
+export(as_task_regr_st.sf)
 export(autoplot)
 import(checkmate)
 import(data.table, except = transpose)
 import(ggplot2)
 import(mlr3)
 import(mlr3misc)
-import(mlr3spatial)
 import(paradox)
 importFrom(R6,R6Class)
 importFrom(graphics,plot)

diff --git a/R/ResamplingRepeatedSpCVBlock.R b/R/ResamplingRepeatedSpCVBlock.R
@@ -167,8 +167,8 @@ ResamplingRepeatedSpCVBlock = R6Class("ResamplingRepeatedSpCVBlock",
       }
       instance = private$.sample(
         task$row_ids,
-        get_coordinates(task),
-        get_crs(task)
+        task$coordinates(),
+        task$crs
       )
 
       self$instance = instance

diff --git a/R/ResamplingRepeatedSpCVCoords.R b/R/ResamplingRepeatedSpCVCoords.R
@@ -84,7 +84,7 @@ ResamplingRepeatedSpCVCoords = R6Class("ResamplingRepeatedSpCVCoords",
         stopf("Grouping is not supported for spatial resampling methods.") # nocov
       }
 
-      instance = private$.sample(task$row_ids, get_coordinates(task))
+      instance = private$.sample(task$row_ids, task$coordinates())
 
       self$instance = instance
       self$task_hash = task$hash

diff --git a/R/ResamplingRepeatedSpCVDisc.R b/R/ResamplingRepeatedSpCVDisc.R
@@ -100,7 +100,7 @@ ResamplingRepeatedSpCVDisc = R6Class("ResamplingRepeatedSpCVDisc",
         function(x) private$.set_default_param_values(x)
       )
 
-      private$.sample(task$row_ids, get_coordinates(task))
+      private$.sample(task$row_ids, task$coordinates())
 
       self$task_hash = task$hash
       self$task_nrow = task$nrow

diff --git a/R/ResamplingRepeatedSpCVTiles.R b/R/ResamplingRepeatedSpCVTiles.R
@@ -131,7 +131,7 @@ ResamplingRepeatedSpCVTiles = R6Class("ResamplingRepeatedSpCVTiles",
         stopf("Grouping is not supported for spatial resampling methods")
       }
 
-      private$.sample(task$row_ids, get_coordinates(task))
+      private$.sample(task$row_ids, task$coordinates())
 
       self$task_hash = task$hash
       self$task_nrow = task$nrow

diff --git a/R/ResamplingRepeatedSptCVCluto.R b/R/ResamplingRepeatedSptCVCluto.R
@@ -127,10 +127,10 @@ ResamplingRepeatedSptCVCluto = R6Class("ResamplingRepeatedSptCVCluto",
         # time in seconds since 1/1/1970
         time_num = as.numeric(time)
 
-        data_matrix = data.matrix(data.frame(get_coordinates(task), time_num))
+        data_matrix = data.matrix(data.frame(task$coordinates(), time_num))
         colnames(data_matrix) = c("x", "y", "z")
       } else {
-        data_matrix = data.matrix(data.frame(get_coordinates(task)))
+        data_matrix = data.matrix(data.frame(task$coordinates()))
 
         colnames(data_matrix) = c("x", "y")
       }

diff --git a/R/ResamplingRepeatedSptCVCstf.R b/R/ResamplingRepeatedSptCVCstf.R
@@ -36,9 +36,6 @@ ResamplingRepeatedSptCVCstf = R6Class("ResamplingRepeatedSptCVCstf",
 
     #' @description
     #' Create a "Spacetime Folds" resampling instance.
-    #'
-    #' For a list of available arguments, please see
-    #' [CAST::CreateSpacetimeFolds].
     #' @param id `character(1)`\cr
     #'   Identifier for the resampling strategy.
     initialize = function(id = "repeated_sptcv_cstf") {

diff --git a/R/ResamplingSpCVBlock.R b/R/ResamplingSpCVBlock.R
@@ -127,8 +127,8 @@ ResamplingSpCVBlock = R6Class("ResamplingSpCVBlock",
       }
       instance = private$.sample(
         task$row_ids,
-        get_coordinates(task),
-        get_crs(task)
+        task$coordinates(),
+        task$crs
       )
 
       self$instance = instance

diff --git a/R/ResamplingSpCVBuffer.R b/R/ResamplingSpCVBuffer.R
@@ -69,9 +69,9 @@ ResamplingSpCVBuffer = R6Class("ResamplingSpCVBuffer",
       instance = private$.sample(
         task$row_ids,
         task$data()[[task$target_names]],
-        get_coordinates(task),
-        task$extra_args$positive,
-        get_crs(task),
+        task$coordinates(),
+        task$positive,
+        task$crs,
         task$properties)
 
       self$instance = instance

diff --git a/R/ResamplingSpCVCoords.R b/R/ResamplingSpCVCoords.R
@@ -60,7 +60,7 @@ ResamplingSpCVCoords = R6Class("ResamplingSpCVCoords",
         stopf("Grouping is not supported for spatial resampling methods")
       }
 
-      instance = private$.sample(task$row_ids, get_coordinates(task))
+      instance = private$.sample(task$row_ids, task$coordinates())
 
       self$instance = instance
       self$task_hash = task$hash

diff --git a/R/ResamplingSpCVDisc.R b/R/ResamplingSpCVDisc.R
@@ -76,7 +76,7 @@ ResamplingSpCVDisc = R6Class("ResamplingSpCVDisc",
         stopf("Grouping is not supported for spatial resampling methods")
       }
 
-      private$.sample(task$row_ids, get_coordinates(task))
+      private$.sample(task$row_ids, task$coordinates())
 
       self$task_hash = task$hash
       self$task_nrow = task$nrow

diff --git a/R/ResamplingSpCVTiles.R b/R/ResamplingSpCVTiles.R
@@ -88,7 +88,7 @@ ResamplingSpCVTiles = R6Class("ResamplingSpCVTiles",
         stopf("Grouping is not supported for spatial resampling methods")
       }
 
-      private$.sample(task$row_ids, get_coordinates(task))
+      private$.sample(task$row_ids, task$coordinates())
 
       self$task_hash = task$hash
       self$task_nrow = task$nrow

diff --git a/R/ResamplingSptCVCluto.R b/R/ResamplingSptCVCluto.R
@@ -109,10 +109,10 @@ ResamplingSptCVCluto = R6Class("ResamplingSptCVCluto",
         # time in seconds since 1/1/1970
         time_num = as.numeric(time)
 
-        data_matrix = data.matrix(data.frame(get_coordinates(task), time_num))
+        data_matrix = data.matrix(data.frame(task$coordinates(), time_num))
         colnames(data_matrix) = c("x", "y", "z")
       } else {
-        data_matrix = data.matrix(data.frame(get_coordinates(task)))
+        data_matrix = data.matrix(data.frame(task$coordinates()))
 
         colnames(data_matrix) = c("x", "y")
       }

diff --git a/R/ResamplingSptCVCstf.R b/R/ResamplingSptCVCstf.R
@@ -31,9 +31,6 @@ ResamplingSptCVCstf = R6Class("ResamplingSptCVCstf",
 
     #' @description
     #' Create a "Spacetime Folds" resampling instance.
-    #'
-    #' For a list of available arguments, please see
-    #' [CAST::CreateSpacetimeFolds].
     #' @param id `character(1)`\cr
     #'   Identifier for the resampling strategy.
     initialize = function(id = "sptcv_cstf") {