Cleanup and various fixes

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mlr3proba
 Title: Probabilistic Supervised Learning for 'mlr3'
-Version: 0.5.8
+Version: 0.5.9
 Authors@R:
     c(person(given = "Raphael",
              family = "Sonabend",
@@ -79,12 +79,12 @@ Encoding: UTF-8
 LazyData: true
 NeedsCompilation: no
 Roxygen: list(markdown = TRUE, r6 = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1.9000
 Collate:
     'LearnerDens.R'
+    'zzz.R'
     'LearnerDensHistogram.R'
     'LearnerDensKDE.R'
-    'LearnerRegrGaussian.R'
     'LearnerSurv.R'
     'LearnerSurvCoxPH.R'
     'LearnerSurvKaplan.R'
@@ -135,11 +135,11 @@ Collate:
     'PredictionSurv.R'
     'RcppExports.R'
     'TaskDens.R'
-    'TaskDens_X.R'
+    'TaskDens_zzz.R'
     'TaskGeneratorSimdens.R'
     'TaskGeneratorSimsurv.R'
     'TaskSurv.R'
-    'TaskSurv_X.R'
+    'TaskSurv_zzz.R'
     'as_prediction_dens.R'
     'as_prediction_surv.R'
     'as_task_dens.R'
@@ -162,4 +162,3 @@ Collate:
     'scoring_rule_erv.R'
     'surv_measures.R'
     'surv_return.R'
-    'zzz.R'

NAMESPACE

@@ -93,8 +93,6 @@ export(as_task_dens)
 export(as_task_surv)
 export(assert_surv)
 export(breslow)
-export(crankcompositor)
-export(distrcompositor)
 export(pecs)
 export(pipeline_survtoregr)
 export(plot_probregr)

NEWS.md

@@ -1,3 +1,8 @@
+# mlr3proba 0.5.9
+
+* Fix several old issues (#348, #301, #281)
+* `distrcompositor` and `crankcompositor` deprecated functions were completely removed
+
 # mlr3proba 0.5.8
 
 * Fix Breslow issues (`phash` warning and `Inf` lp predictions)

R/LearnerDensHistogram.R

@@ -38,3 +38,6 @@ LearnerDensHistogram = R6::R6Class("LearnerDensHistogram",
     }
   )
 )
+
+#' @include zzz.R
+register_learner("dens.hist", LearnerDensHistogram)

R/LearnerDensKDE.R

@@ -1,7 +1,7 @@
 #' @template dens_learner
 #' @templateVar title Kernel
 #' @templateVar fullname LearnerDensKDE
-#' @templateVar caller kernels implemented in \CRANpkg{distr6}
+#' @templateVar caller kernels implemented in [distr6]
 #' @details The default bandwidth uses Silverman's rule-of-thumb for Gaussian kernels, however for
 #' non-Gaussian kernels it is recommended to use \CRANpkg{mlr3tuning} to tune the bandwidth with
 #' cross-validation. Other density learners can be used for automated bandwidth selection.
@@ -88,3 +88,5 @@ LearnerDensKDE = R6::R6Class("LearnerDensKDE",
     }
   )
 )
+
+register_learner("dens.kde", LearnerDensKDE)

R/LearnerSurv.R

@@ -7,7 +7,7 @@
 #' * Creates [Prediction]s of class [PredictionSurv].
 #' * Possible values for `predict_types` are:
 #'   - `"distr"`: Predicts a probability distribution for each observation in the test set,
-#'                uses \CRANpkg{distr6}.
+#'                uses [distr6].
 #'   - `"lp"`: Predicts a linear predictor for each observation in the test set.
 #'   - `"crank"`: Predicts a continuous ranking for each observation in the test set.
 #'   - `"response"`: Predicts a survival time for each observation in the test set.

R/LearnerSurvCoxPH.R

@@ -1,11 +1,10 @@
-#' @template surv_learner
 #' @templateVar title Cox Proportional Hazards
 #' @templateVar fullname LearnerSurvCoxPH
 #' @templateVar caller [survival::coxph()]
 #' @templateVar distr by [survival::survfit.coxph()]
 #' @templateVar lp by [survival::predict.coxph()]
-#' @description
-#'
+#' @templateVar id surv.coxph
+#' @template surv_learner
 #'
 #' @references
 #' `r format_bib("cox_1972")`
@@ -71,3 +70,5 @@ LearnerSurvCoxPH = R6Class("LearnerSurvCoxPH",
     }
   )
 )
+
+register_learner("surv.coxph", LearnerSurvCoxPH)

R/LearnerSurvKaplan.R

@@ -1,11 +1,9 @@
-#' @template surv_learner
 #' @templateVar title Kaplan-Meier Estimator
 #' @templateVar fullname LearnerSurvKaplan
 #' @templateVar caller [survival::survfit()]
 #' @templateVar distr by estimating the survival function with [survival::survfit()]
-#'
-#' @description
-#'
+#' @templateVar id surv.kaplan
+#' @template surv_learner
 #'
 #' @references
 #' `r format_bib("kaplan_1958")`
@@ -45,3 +43,5 @@ LearnerSurvKaplan = R6Class("LearnerSurvKaplan",
     }
   )
 )
+
+register_learner("surv.kaplan", LearnerSurvKaplan)

R/LearnerSurvRpart.R

@@ -1,12 +1,14 @@
-#' @template surv_learner
 #' @templateVar title Rpart Survival Trees
 #' @templateVar fullname LearnerSurvRpart
 #' @templateVar caller [rpart::rpart()]
 #' @templateVar crank using [rpart::predict.rpart()]
+#' @templateVar id surv.rpart
+#' @template surv_learner
 #'
-#' @description
-#' Parameter `xval` is set to 0 in order to save some computation time.
-#' Parameter `model` has been renamed to `keep_model`.
+#' @section Initial parameter values:
+#'
+#' - `xval` is set to 0 in order to save some computation time.
+#' - `model` has been renamed to `keep_model`.
 #'
 #' @references
 #' `r format_bib("breiman_1984")`
@@ -87,3 +89,5 @@ LearnerSurvRpart = R6Class("LearnerSurvRpart",
     }
   )
 )
+
+register_learner("surv.rpart", LearnerSurvRpart)

R/MeasureDensLogloss.R

@@ -47,3 +47,5 @@ MeasureDensLogloss = R6::R6Class("MeasureDensLogloss",
     }
   )
 )
+
+register_measure("dens.logloss", MeasureDensLogloss)

R/MeasureRegrLogloss.R

@@ -54,3 +54,5 @@ MeasureRegrLogloss = R6::R6Class("MeasureRegrLogloss",
     }
   )
 )
+
+register_measure("regr.logloss", MeasureRegrLogloss)

R/MeasureSurvCalibrationAlpha.R

@@ -64,3 +64,5 @@ MeasureSurvCalibrationAlpha = R6Class("MeasureSurvCalibrationAlpha",
     }
   )
 )
+
+register_measure("surv.calib_alpha", MeasureSurvCalibrationAlpha)

R/MeasureSurvCalibrationBeta.R

@@ -59,3 +59,5 @@ MeasureSurvCalibrationBeta = R6Class("MeasureSurvCalibrationBeta",
     }
   )
 )
+
+register_measure("surv.calib_beta", MeasureSurvCalibrationBeta)

R/MeasureSurvChamblessAUC.R

@@ -63,3 +63,5 @@ MeasureSurvChamblessAUC = R6Class("MeasureSurvChamblessAUC",
     }
   )
 )
+
+register_measure("surv.chambless_auc", MeasureSurvChamblessAUC)

R/MeasureSurvCindex.R

@@ -95,3 +95,5 @@ gonen = function(crank, tiex) {
 
   c_gonen(sort(crank), tiex)
 }
+
+register_measure("surv.cindex", MeasureSurvCindex)

R/MeasureSurvDCalibration.R

@@ -132,3 +132,5 @@ MeasureSurvDCalibration = R6Class("MeasureSurvDCalibration",
     }
   )
 )
+
+register_measure("surv.dcalib", MeasureSurvDCalibration)

R/MeasureSurvGraf.R

@@ -125,3 +125,6 @@ MeasureSurvGraf = R6::R6Class("MeasureSurvGraf",
     }
   )
 )
+
+register_measure("surv.graf", MeasureSurvGraf)
+register_measure("surv.brier", MeasureSurvGraf)

R/MeasureSurvHungAUC.R

@@ -59,3 +59,5 @@ MeasureSurvHungAUC = R6Class("MeasureSurvHungAUC",
     }
   )
 )
+
+register_measure("surv.hung_auc", MeasureSurvHungAUC)

R/MeasureSurvIntLogloss.R

@@ -115,3 +115,5 @@ MeasureSurvIntLogloss = R6::R6Class("MeasureSurvIntLogloss",
     }
   )
 )
+
+register_measure("surv.intlogloss", MeasureSurvIntLogloss)

R/MeasureSurvLogloss.R

@@ -88,3 +88,5 @@ MeasureSurvLogloss = R6::R6Class("MeasureSurvLogloss",
     }
   )
 )
+
+register_measure("surv.logloss", MeasureSurvLogloss)

R/MeasureSurvMAE.R

@@ -47,3 +47,5 @@ MeasureSurvMAE = R6::R6Class("MeasureSurvMAE",
     }
   )
 )
+
+register_measure("surv.mae", MeasureSurvMAE)

R/MeasureSurvMSE.R

@@ -47,3 +47,5 @@ MeasureSurvMSE = R6::R6Class("MeasureSurvMSE",
     }
   )
 )
+
+register_measure("surv.mse", MeasureSurvMSE)

R/MeasureSurvNagelkR2.R

@@ -40,3 +40,5 @@ MeasureSurvNagelkR2 = R6Class("MeasureSurvNagelkR2",
     }
   )
 )
+
+register_measure("surv.nagelk_r2", MeasureSurvNagelkR2)

R/MeasureSurvOQuigleyR2.R

@@ -40,3 +40,5 @@ MeasureSurvOQuigleyR2 = R6Class("MeasureSurvOQuigleyR2",
     }
   )
 )
+
+register_measure("surv.oquigley_r2", MeasureSurvOQuigleyR2)

R/MeasureSurvRCLL.R

@@ -136,3 +136,5 @@ MeasureSurvRCLL = R6::R6Class("MeasureSurvRCLL",
     }
   )
 )
+
+register_measure("surv.rcll", MeasureSurvRCLL)

R/MeasureSurvRMSE.R

@@ -48,3 +48,5 @@ MeasureSurvRMSE = R6::R6Class("MeasureSurvRMSE",
     }
   )
 )
+
+register_measure("surv.rmse", MeasureSurvRMSE)

R/MeasureSurvSchmid.R

@@ -114,3 +114,5 @@ MeasureSurvSchmid = R6::R6Class("MeasureSurvSchmid",
     }
   )
 )
+
+register_measure("surv.schmid", MeasureSurvSchmid)

R/MeasureSurvSongAUC.R

@@ -67,3 +67,5 @@ MeasureSurvSongAUC = R6Class("MeasureSurvSongAUC",
     }
   )
 )
+
+register_measure("surv.song_auc", MeasureSurvSongAUC)

R/MeasureSurvSongTNR.R

@@ -60,3 +60,5 @@ MeasureSurvSongTNR = R6Class("MeasureSurvSongTNR",
     }
   )
 )
+
+register_measure("surv.song_tnr", MeasureSurvSongTNR)

R/MeasureSurvSongTPR.R

@@ -63,3 +63,5 @@ MeasureSurvSongTPR = R6Class("MeasureSurvSongTPR",
     }
   )
 )
+
+register_measure("surv.song_tpr", MeasureSurvSongTPR)

R/MeasureSurvUnoAUC.R

@@ -65,3 +65,5 @@ MeasureSurvUnoAUC = R6Class("MeasureSurvUnoAUC",
     }
   )
 )
+
+register_measure("surv.uno_auc", MeasureSurvUnoAUC)

R/MeasureSurvUnoTNR.R

@@ -57,3 +57,5 @@ MeasureSurvUnoTNR = R6Class("MeasureSurvUnoTNR",
     }
   )
 )
+
+register_measure("surv.uno_tnr", MeasureSurvUnoTNR)

R/MeasureSurvUnoTPR.R

@@ -58,3 +58,5 @@ MeasureSurvUnoTPR = R6Class("MeasureSurvUnoTPR",
     }
   )
 )
+
+register_measure("surv.uno_tpr", MeasureSurvUnoTPR)

R/MeasureSurvXuR2.R

@@ -40,3 +40,5 @@ MeasureSurvXuR2 = R6Class("MeasureSurvXuR2",
     }
   )
 )
+
+register_measure("surv.xu_r2", MeasureSurvXuR2)

R/PipeOpCrankCompositor.R

@@ -1,5 +1,5 @@
 #' @title PipeOpCrankCompositor
-#' @name mlr_pipeops_compose_crank
+#' @name mlr_pipeops_crankcompose
 #' @template param_pipelines
 #'
 #' @description
@@ -47,7 +47,7 @@
 #'
 #' @section Internals:
 #' The `median`, `mode`, or `mean` will use analytical expressions if possible but if not they are
-#' calculated using methods from \CRANpkg{distr6}. `mean` requires \CRANpkg{cubature}.
+#' calculated using methods from [distr6]. `mean` requires \CRANpkg{cubature}.
 #'
 #' @seealso [pipeline_crankcompositor]
 #' @family survival compositors
@@ -75,20 +75,20 @@ PipeOpCrankCompositor = R6Class("PipeOpCrankCompositor",
   public = list(
     #' @description
     #' Creates a new instance of this [R6][R6::R6Class] class.
-    initialize = function(id = "compose_crank", param_vals = list(
-      method = "sum_haz", response = FALSE, overwrite = FALSE)) {
-      ps = ps(
+    initialize = function(id = "crankcompose", param_vals = list()) {
+      param_set = ps(
         method = p_fct(default = "sum_haz", levels = c("sum_haz", "mean", "median", "mode"),
           tags = "predict"),
         which = p_int(default = 1, lower = 1, tags = "predict"),
         response = p_lgl(default = FALSE, tags = "predict"),
         overwrite = p_lgl(default = FALSE, tags = "predict")
       )
-      ps$add_dep("which", "method", CondEqual$new("mode"))
+      param_set$add_dep("which", "method", CondEqual$new("mode"))
+      param_set$values = list(method = "sum_haz", response = FALSE, overwrite = FALSE)
 
       super$initialize(
         id = id,
-        param_set = ps,
+        param_set = param_set,
         param_vals = param_vals,
         input = data.table(name = "input", train = "NULL", predict = "PredictionSurv"),
         output = data.table(name = "output", train = "NULL", predict = "PredictionSurv"),
@@ -185,3 +185,5 @@ PipeOpCrankCompositor = R6Class("PipeOpCrankCompositor",
     }
   )
 )
+
+register_pipeop("crankcompose", PipeOpCrankCompositor)