Package: mlr3proba 0.7.0

John Zobolas

mlr3proba: Probabilistic Supervised Learning for 'mlr3'

Provides extensions for probabilistic supervised learning for 'mlr3'. This includes extending the regression task to probabilistic and interval regression, adding a survival task, and other specialized models, predictions, and measures.

Authors:Raphael Sonabend [aut], Franz Kiraly [aut], Michel Lang [aut], Nurul Ain Toha [ctb], Andreas Bender [ctb], John Zobolas [cre, aut], Lukas Burk [ctb], Philip Studener [aut], Maximilian Muecke [ctb]

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mlr3proba.pdf |mlr3proba.html✨
mlr3proba/json (API)
NEWS

# Install 'mlr3proba' in R:

install.packages('mlr3proba', repos = c('https://mlr-org.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mlr-org/mlr3proba/issues

Pkgdown:https://mlr3proba.mlr-org.com

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

actg - ACTG 320 Clinical Trial Dataset
gbcs - German Breast Cancer Study (GBCS) Dataset
grace - GRACE 1000 Dataset
whas - Worcester Heart Attack Study (WHAS) Dataset

On CRAN:

density-estimation machine-learning mlr3 probabilistic-regression probabilistic-supervised-learning supervised-learning survival-analysis

7.91 score 130 stars 276 scripts 213 downloads 1 mentions 74 exports 59 dependencies

Last updated 1 months agofrom:44fd50c331 (on v0.7.0). Checks:OK: 4 NOTE: 2 ERROR: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 21 2024
R-4.5-win-x86_64	NOTE	Nov 21 2024
R-4.5-linux-x86_64	NOTE	Nov 21 2024
R-4.4-win-x86_64	OK	Nov 21 2024
R-4.4-mac-x86_64	OK	Nov 21 2024
R-4.4-mac-aarch64	OK	Nov 21 2024
R-4.3-win-x86_64	ERROR	Nov 21 2024
R-4.3-mac-x86_64	ERROR	Nov 21 2024
R-4.3-mac-aarch64	ERROR	Nov 21 2024

Exports:.c_weight_survival_score .surv_return as_prediction_dens as_prediction_surv as_task_dens as_task_surv assert_surv assert_surv_matrix breslow get_mortality LearnerDens LearnerDensHistogram LearnerDensKDE LearnerSurv LearnerSurvCoxPH LearnerSurvKaplan LearnerSurvRpart MeasureDens MeasureDensLogloss MeasureRegrLogloss MeasureSurv MeasureSurvAUC MeasureSurvCalibrationAlpha MeasureSurvCalibrationBeta MeasureSurvChamblessAUC MeasureSurvCindex MeasureSurvDCalibration MeasureSurvGraf MeasureSurvHungAUC MeasureSurvIntLogloss MeasureSurvLogloss MeasureSurvMAE MeasureSurvMSE MeasureSurvNagelkR2 MeasureSurvOQuigleyR2 MeasureSurvRCLL MeasureSurvRMSE MeasureSurvSchmid MeasureSurvSongAUC MeasureSurvSongTNR MeasureSurvSongTPR MeasureSurvUnoAUC MeasureSurvUnoTNR MeasureSurvUnoTPR MeasureSurvXuR2 pecs pipeline_survtoclassif_disctime pipeline_survtoclassif_IPCW pipeline_survtoregr PipeOpBreslow PipeOpCrankCompositor PipeOpDistrCompositor PipeOpPredClassifSurvDiscTime PipeOpPredClassifSurvIPCW PipeOpPredRegrSurv PipeOpPredSurvRegr PipeOpPredTransformer PipeOpProbregr PipeOpResponseCompositor PipeOpSurvAvg PipeOpTaskRegrSurv PipeOpTaskSurvClassifDiscTime PipeOpTaskSurvClassifIPCW PipeOpTaskSurvRegr PipeOpTaskTransformer PipeOpTransformer plot_probregr PredictionDens PredictionSurv TaskDens TaskGeneratorCoxed TaskGeneratorSimdens TaskGeneratorSimsurv TaskSurv

Dependencies:backports checkmate cli codetools colorspace data.table dictionar6 digest distr6 evaluate fansi farver future future.apply ggplot2 globals glue gridExtra gtable isoband labeling lattice lgr lifecycle listenv magrittr MASS Matrix mgcv mlbench mlr3 mlr3measures mlr3misc mlr3pipelines mlr3viz munsell nlme ooplah palmerpenguins paradox parallelly param6 pillar pkgconfig PRROC R6 RColorBrewer Rcpp rlang scales set6 survival tibble utf8 uuid vctrs viridis viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
mlr3proba: Probabilistic Supervised Learning for 'mlr3'	mlr3proba-package mlr3proba
Get Survival Predict Types	.surv_return
ACTG 320 Clinical Trial Dataset	actg
Convert to a Density Prediction	as_prediction_dens as_prediction_dens.data.frame as_prediction_dens.PredictionDens
Convert to a Survival Prediction	as_prediction_surv as_prediction_surv.data.frame as_prediction_surv.PredictionSurv
Convert to a Density Task	as_task_dens as_task_dens.data.frame as_task_dens.DataBackend as_task_dens.TaskDens
Convert to a Survival Task	as_task_surv as_task_surv.data.frame as_task_surv.DataBackend as_task_surv.formula as_task_surv.TaskSurv
Assert survival object	assert_surv
Assert survival matrix	assert_surv_matrix
Plot for PredictionSurv	autoplot.PredictionSurv
Plot for Density Tasks	autoplot.TaskDens
Plot for Survival Tasks	autoplot.TaskSurv
Survival probabilities using Breslow's estimator	breslow
German Breast Cancer Study (GBCS) Dataset	gbcs
Calculate the expected mortality risks from a survival matrix	get_mortality
GRACE 1000 Dataset	grace
Density Learner	LearnerDens
Survival Learner	LearnerSurv
Density Measure	MeasureDens
Survival Measure	MeasureSurv
Abstract Class for survAUC Measures	MeasureSurvAUC
Estimate Survival crank Predict Type Pipeline	mlr_graphs_crankcompositor pipeline_crankcompositor
Estimate Survival distr Predict Type Pipeline	mlr_graphs_distrcompositor pipeline_distrcompositor
Estimate Regression distr Predict Type Pipeline	mlr_graphs_probregr pipeline_probregr
Estimate Survival Time/Response Predict Type Pipeline	mlr_graphs_responsecompositor pipeline_responsecompositor
Survival Prediction Averaging Pipeline	mlr_graphs_survaverager pipeline_survaverager
Survival Prediction Averaging Pipeline	mlr_graphs_survbagging pipeline_survbagging
Survival to Classification Reduction using Discrete Time Pipeline	mlr_graphs_survtoclassif_disctime pipeline_survtoclassif_disctime
Survival to Classification Reduction using IPCW Pipeline	mlr_graphs_survtoclassif_IPCW pipeline_survtoclassif_IPCW
Survival to Regression Reduction Pipeline	mlr_graphs_survtoregr pipeline_survtoregr
Histogram Density Estimator	LearnerDensHistogram mlr_learners_dens.hist
Kernel Density Estimator	LearnerDensKDE mlr_learners_dens.kde
Cox Proportional Hazards Survival Learner	LearnerSurvCoxPH mlr_learners_surv.coxph
Kaplan-Meier Estimator Survival Learner	LearnerSurvKaplan mlr_learners_surv.kaplan
Rpart Survival Trees Survival Learner	LearnerSurvRpart mlr_learners_surv.rpart
Log Loss Density Measure	MeasureDensLogloss mlr_measures_dens.logloss
Log Loss Regression Measure	MeasureRegrLogloss mlr_measures_regr.logloss
Van Houwelingen's Calibration Alpha Survival Measure	MeasureSurvCalibrationAlpha mlr_measures_surv.calib_alpha
Van Houwelingen's Calibration Beta Survival Measure	MeasureSurvCalibrationBeta mlr_measures_surv.calib_beta
Chambless and Diao's AUC Survival Measure	MeasureSurvChamblessAUC mlr_measures_surv.chambless_auc
Concordance Statistics Survival Measure	MeasureSurvCindex mlr_measures_surv.cindex
D-Calibration Survival Measure	MeasureSurvDCalibration mlr_measures_surv.dcalib
Integrated Brier Score Survival Measure	MeasureSurvBrier MeasureSurvGraf mlr_measures_surv.brier mlr_measures_surv.graf
Hung and Chiang's AUC Survival Measure	MeasureSurvHungAUC mlr_measures_surv.hung_auc
Integrated Log-Likelihood Survival Measure	MeasureSurvIntLogloss mlr_measures_surv.intlogloss
Negative Log-Likelihood Survival Measure	MeasureSurvLogloss mlr_measures_surv.logloss
Mean Absolute Error Survival Measure	MeasureSurvMAE mlr_measures_surv.mae
Mean Squared Error Survival Measure	MeasureSurvMSE mlr_measures_surv.mse
Nagelkerke's R2 Survival Measure	MeasureSurvNagelkR2 mlr_measures_surv.nagelk_r2
O'Quigley, Xu, and Stare's R2 Survival Measure	MeasureSurvOQuigleyR2 mlr_measures_surv.oquigley_r2
Right-Censored Log Loss Survival Measure	MeasureSurvRCLL mlr_measures_surv.rcll
Root Mean Squared Error Survival Measure	MeasureSurvRMSE mlr_measures_surv.rmse
Integrated Schmid Score Survival Measure	MeasureSurvSchmid mlr_measures_surv.schmid
Song and Zhou's AUC Survival Measure	MeasureSurvSongAUC mlr_measures_surv.song_auc
Song and Zhou's TNR Survival Measure	MeasureSurvSongTNR mlr_measures_surv.song_tnr
Song and Zhou's TPR Survival Measure	MeasureSurvSongTPR mlr_measures_surv.song_tpr
Uno's AUC Survival Measure	MeasureSurvUnoAUC mlr_measures_surv.uno_auc
Uno's TNR Survival Measure	MeasureSurvUnoTNR mlr_measures_surv.uno_tnr
Uno's TPR Survival Measure	MeasureSurvUnoTPR mlr_measures_surv.uno_tpr
Xu and O'Quigley's R2 Survival Measure	MeasureSurvXuR2 mlr_measures_surv.xu_r2
Wrap a learner into a PipeOp with survival predictions estimated by the Breslow estimator	mlr_pipeops_compose_breslow_distr PipeOpBreslow
PipeOpProbregr	mlr_pipeops_compose_probregr PipeOpProbregr
PipeOpCrankCompositor	mlr_pipeops_crankcompose PipeOpCrankCompositor
PipeOpDistrCompositor	mlr_pipeops_distrcompose PipeOpDistrCompositor
PipeOpResponseCompositor	mlr_pipeops_responsecompose PipeOpResponseCompositor
PipeOpSurvAvg	mlr_pipeops_survavg PipeOpSurvAvg
PipeOpPredClassifSurvDiscTime	mlr_pipeops_trafopred_classifsurv_disctime PipeOpPredClassifSurvDiscTime
PipeOpPredClassifSurvIPCW	mlr_pipeops_trafopred_classifsurv_IPCW PipeOpPredClassifSurvIPCW
PipeOpPredRegrSurv	mlr_pipeops_trafopred_regrsurv PipeOpPredRegrSurv
PipeOpPredSurvRegr	mlr_pipeops_trafopred_survregr PipeOpPredSurvRegr
PipeOpTaskRegrSurv	mlr_pipeops_trafotask_regrsurv PipeOpTaskRegrSurv
PipeOpTaskSurvClassifDiscTime	mlr_pipeops_trafotask_survclassif_disctime PipeOpTaskSurvClassifDiscTime
PipeOpTaskSurvClassifIPCW	mlr_pipeops_trafotask_survclassif_IPCW PipeOpTaskSurvClassifIPCW
PipeOpTaskSurvRegr	mlr_pipeops_trafotask_survregr PipeOpTaskSurvRegr
Survival Task Generator for Package 'coxed'	mlr_task_generators_coxed TaskGeneratorCoxed
Density Task Generator for Package 'distr6'	mlr_task_generators_simdens TaskGeneratorSimdens
Survival Task Generator for Package 'simsurv'	mlr_task_generators_simsurv TaskGeneratorSimsurv
ACTG 320 Survival Task	mlr_tasks_actg
Old Faithful Eruptions Density Task	mlr_tasks_faithful
German Breast Cancer Study Survival Task	mlr_tasks_gbcs
German Breast Cancer Study Survival Task	mlr_tasks_gbsg
GRACE 1000 Survival Task	mlr_tasks_grace
Lung Cancer Survival Task	mlr_tasks_lung
Monoclonal Gammopathy Survival Task	mlr_tasks_mgus
Primary Biliary Cholangitis Survival Task	mlr_tasks_pbc
Annual Precipitation Density Task	mlr_tasks_precip
Rats Survival Task	mlr_tasks_rats
Unemployment Duration Survival Task	mlr_tasks_unemployment
Veteran Survival Task	mlr_tasks_veteran
Worcester Heart Attack Study (WHAS) Survival Task	mlr_tasks_whas
Prediction Error Curves for PredictionSurv and LearnerSurv	pecs pecs.list pecs.PredictionSurv
PipeOpPredTransformer	PipeOpPredTransformer
PipeOpTaskTransformer	PipeOpTaskTransformer
PipeOpTransformer	PipeOpTransformer
Visualise probabilistic regression distribution predictions	plot_probregr
Visualization of fitted 'LearnerSurv' objects	plot.LearnerSurv
Prediction Object for Density	PredictionDens
Prediction Object for Survival	PredictionSurv
Density Task	TaskDens
Survival Task	TaskSurv
Worcester Heart Attack Study (WHAS) Dataset	whas