Package index • mlr3proba

Package

mlr3proba mlr3proba-package: mlr3proba: Probabilistic Supervised Learning for 'mlr3'

Building Blocks

TaskSurv: Survival Task

LearnerSurv: Survival Learner

PredictionSurv: Prediction Object for Survival

MeasureSurv: Survival Measure

TaskCompRisks: Competing Risks Task

LearnerCompRisks: Competing Risks Learner

PredictionCompRisks: Prediction Object for Competing Risks

MeasureCompRisks: Competing Risks Measure

TaskDens: Density Task

LearnerDens: Density Learner

PredictionDens: Prediction Object for Density

MeasureDens: Density Measure

Survival Learners

mlr_learners_surv.coxph LearnerSurvCoxPH: Cox Proportional Hazards Survival Learner

mlr_learners_surv.kaplan LearnerSurvKaplan: Kaplan-Meier Estimator Survival Learner

mlr_learners_surv.rpart LearnerSurvRpart: Rpart Survival Trees Survival Learner

Survival Measures

mlr_measures_surv.calib_alpha MeasureSurvCalibrationAlpha: Van Houwelingen's Calibration Alpha Survival Measure

mlr_measures_surv.calib_beta MeasureSurvCalibrationBeta: Van Houwelingen's Calibration Beta Survival Measure

mlr_measures_surv.calib_index MeasureSurvICI: Integrated Calibration Index Survival Measure

mlr_measures_surv.chambless_auc MeasureSurvChamblessAUC: Chambless and Diao's AUC Survival Measure

mlr_measures_surv.cindex MeasureSurvCindex: Concordance Statistics Survival Measure

mlr_measures_surv.dcalib MeasureSurvDCalibration experimental: D-Calibration Survival Measure

mlr_measures_surv.graf MeasureSurvGraf MeasureSurvBrier mlr_measures_surv.brier: Integrated Brier Score Survival Measure

mlr_measures_surv.hung_auc MeasureSurvHungAUC: Hung and Chiang's AUC Survival Measure

mlr_measures_surv.intlogloss MeasureSurvIntLogloss: Integrated Log-Likelihood Survival Measure

mlr_measures_surv.logloss MeasureSurvLogloss: Negative Log-Likelihood Survival Measure

mlr_measures_surv.mae MeasureSurvMAE: Mean Absolute Error Survival Measure

mlr_measures_surv.mse MeasureSurvMSE: Mean Squared Error Survival Measure

mlr_measures_surv.nagelk_r2 MeasureSurvNagelkR2: Nagelkerke's R2 Survival Measure

mlr_measures_surv.oquigley_r2 MeasureSurvOQuigleyR2: O'Quigley, Xu, and Stare's R2 Survival Measure

mlr_measures_surv.rcll MeasureSurvRCLL: Right-Censored Log Loss Survival Measure

mlr_measures_surv.rmse MeasureSurvRMSE: Root Mean Squared Error Survival Measure

mlr_measures_surv.schmid MeasureSurvSchmid: Integrated Schmid Score Survival Measure

mlr_measures_surv.song_auc MeasureSurvSongAUC: Song and Zhou's AUC Survival Measure

mlr_measures_surv.song_tnr MeasureSurvSongTNR: Song and Zhou's TNR Survival Measure

mlr_measures_surv.song_tpr MeasureSurvSongTPR: Song and Zhou's TPR Survival Measure

mlr_measures_surv.uno_auc MeasureSurvUnoAUC: Uno's AUC Survival Measure

mlr_measures_surv.uno_tnr MeasureSurvUnoTNR: Uno's TNR Survival Measure

mlr_measures_surv.uno_tpr MeasureSurvUnoTPR: Uno's TPR Survival Measure

mlr_measures_surv.xu_r2 MeasureSurvXuR2: Xu and O'Quigley's R2 Survival Measure

Survival Tasks

mlr_task_generators_simsurv TaskGeneratorSimsurv: Survival Task Generator for Package 'simsurv'

mlr_task_generators_coxed TaskGeneratorCoxed: Survival Task Generator for Package 'coxed'

mlr_tasks_actg: ACTG 320 Survival Task

mlr_tasks_gbsg: German Breast Cancer Study Survival Task

mlr_tasks_mgus: Monoclonal Gammopathy Survival Task

mlr_tasks_veteran: Veteran Survival Task

mlr_tasks_gbcs: German Breast Cancer Study Survival Task

mlr_tasks_grace: GRACE 1000 Survival Task

mlr_tasks_lung: Lung Cancer Survival Task

mlr_tasks_rats: Rats Survival Task

mlr_tasks_whas: Worcester Heart Attack Study (WHAS) Survival Task

Survival PipeOps

mlr_pipeops_compose_breslow_distr PipeOpBreslow: Wrap a learner into a PipeOp with survival predictions estimated by the Breslow estimator

mlr_pipeops_compose_probregr PipeOpProbregr experimental: PipeOpProbregr

mlr_pipeops_crankcompose PipeOpCrankCompositor: PipeOpCrankCompositor

mlr_pipeops_distrcompose PipeOpDistrCompositor experimental: PipeOpDistrCompositor

mlr_pipeops_responsecompose PipeOpResponseCompositor: PipeOpResponseCompositor

mlr_pipeops_survavg PipeOpSurvAvg: PipeOpSurvAvg

mlr_pipeops_trafopred_classifsurv_IPCW PipeOpPredClassifSurvIPCW: PipeOpPredClassifSurvIPCW

mlr_pipeops_trafopred_classifsurv_disctime PipeOpPredClassifSurvDiscTime: PipeOpPredClassifSurvDiscTime

mlr_pipeops_trafopred_regrsurv_pem PipeOpPredRegrSurvPEM: PipeOpPredRegrSurvPEM

mlr_pipeops_trafotask_survclassif_IPCW PipeOpTaskSurvClassifIPCW: PipeOpTaskSurvClassifIPCW

mlr_pipeops_trafotask_survclassif_disctime PipeOpTaskSurvClassifDiscTime: PipeOpTaskSurvClassifDiscTime

mlr_pipeops_trafotask_survregr_pem PipeOpTaskSurvRegrPEM: PipeOpTaskSurvRegrPEM

Survival Pipelines

pipeline_crankcompositor(): Estimate Survival crank Predict Type Pipeline

pipeline_distrcompositor() experimental: Estimate Survival distr Predict Type Pipeline

pipeline_probregr() experimental: Estimate Regression distr Predict Type Pipeline

pipeline_responsecompositor(): Estimate Survival Time/Response Predict Type Pipeline

pipeline_survaverager(): Survival Prediction Averaging Pipeline

pipeline_survbagging(): Survival Prediction Averaging Pipeline

pipeline_survtoclassif_IPCW(): Survival to Classification Reduction using IPCW Pipeline

pipeline_survtoclassif_disctime(): Survival to Classification Reduction using Discrete Time Pipeline

pipeline_survtoregr_pem(): Survival to Poisson Regression Reduction Pipeline

Competing Risk Learners

mlr_learners_cmprsk.aalen LearnerCompRisksAalenJohansen: Aalen Johansen Competing Risks Learner

Competing Risk Measures

mlr_measures_cmprsk.auc MeasureCompRisksAUC: Blanche's AUC Competing Risks Measure

Competing Risk Tasks

mlr_tasks_pbc: Primary Biliary Cholangitis Competing Risks Task

Density Learners

mlr_learners_dens.hist LearnerDensHistogram: Histogram Density Estimator

mlr_learners_dens.kde LearnerDensKDE: Kernel Density Estimator

Density Measures

mlr_measures_dens.logloss MeasureDensLogloss: Log Loss Density Measure

Density Tasks

mlr_tasks_faithful: Old Faithful Eruptions Density Task

mlr_tasks_precip: Annual Precipitation Density Task

mlr_task_generators_simdens TaskGeneratorSimdens: Density Task Generator for Package 'distr6'

Probabilistic Regression Measures

mlr_measures_regr.logloss MeasureRegrLogloss: Log Loss Regression Measure

S3 Methods

as_prediction_cmprsk(): Convert to a Competing Risk Prediction

as_prediction_dens(): Convert to a Density Prediction

as_prediction_surv(): Convert to a Survival Prediction

as_task_cmprsk(): Convert to a Competing Risks Task

as_task_dens(): Convert to a Density Task

as_task_surv(): Convert to a Survival Task

Visualisation

pecs(): Prediction Error Curves for PredictionSurv and LearnerSurv

plot_probregr(): Visualise probabilistic regression distribution predictions

autoplot(<PredictionSurv>): Plot for PredictionSurv

autoplot(<TaskDens>): Plot for Density Tasks

autoplot(<TaskSurv>): Plot for Survival Tasks

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

Internal

.surv_return(): Get Survival Predict Types

breslow(): Survival probabilities using Breslow's estimator

assert_surv(): Assert survival object

assert_surv_matrix(): Assert survival matrix

assert_cif_list(): Assert CIF list

get_mortality(): Calculate the expected mortality risks from a survival matrix

MeasureSurvAUC: Abstract Class for survAUC Measures