Package: survex 1.2.0.9001

Mikołaj Spytek

survex: Explainable Machine Learning in Survival Analysis

Survival analysis models are commonly used in medicine and other areas. Many of them are too complex to be interpreted by human. Exploration and explanation is needed, but standard methods do not give a broad enough picture. 'survex' provides easy-to-apply methods for explaining survival models, both complex black-boxes and simpler statistical models. They include methods specific to survival analysis such as SurvSHAP(t) introduced in Krzyzinski et al., (2023) <doi:10.1016/j.knosys.2022.110234>, SurvLIME described in Kovalev et al., (2020) <doi:10.1016/j.knosys.2020.106164> as well as extensions of existing ones described in Biecek et al., (2021) <doi:10.1201/9780429027192>.

Authors:Mikołaj Spytek [aut, cre], Mateusz Krzyziński [aut], Sophie Langbein [aut], Hubert Baniecki [aut], Lorenz A. Kapsner [ctb], Przemyslaw Biecek [aut]

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survex.pdf |survex.html
survex/json (API)
NEWS

# Install 'survex' in R:
install.packages('survex', repos = c('https://modeloriented.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/modeloriented/survex/issues

On CRAN:

biostatisticsbrier-scorescensored-datacox-modelcox-regressionexplainable-aiexplainable-machine-learningexplainable-mlexplanatory-model-analysisinterpretable-machine-learninginterpretable-mlmachine-learningprobabilistic-machine-learningshapsurvival-analysistime-to-eventvariable-importancexai

8.91 score 103 stars 113 scripts 543 downloads 31 exports 109 dependencies

Last updated 5 months agofrom:cb0852a385. Checks:OK: 5 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 08 2024
R-4.5-winOKNov 08 2024
R-4.5-linuxOKNov 08 2024
R-4.4-winOKNov 08 2024
R-4.4-macOKNov 08 2024
R-4.3-winERRORNov 08 2024
R-4.3-macERRORNov 08 2024

Exports:brier_scorec_indexcd_auccumulative_hazard_to_survivalexplainexplain_survivalextract_predict_survshapintegrated_brier_scoreintegrated_cd_aucloss_adapt_mlr3probaloss_brier_scoreloss_integrateloss_integrated_brier_scoreloss_one_minus_c_indexloss_one_minus_cd_aucloss_one_minus_integrated_cd_aucmodel_diagnosticsmodel_partsmodel_performancemodel_profilemodel_profile_2dmodel_survshappredict_partspredict_profilerisk_from_chfset_theme_survexsurv_model_infosurvival_to_cumulative_hazardtheme_default_survextheme_vertical_default_survextransform_to_stepfunction

Dependencies:backportsbase64encbslibcachemcheckmatecliclustercmprskcodetoolscolorspaceDALEXdata.tablediagramdigestdoParallelevaluatefansifarverfastmapfontawesomeforeachforeignFormulafsfuturefuture.applyggplot2globalsgluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsiBreakDowningredientsisobanditeratorsjquerylibjsonlitekernelshapKernSmoothknitrlabelinglatticelavalifecyclelistenvmagrittrMASSMatrixMatrixModelsmemoisemetsmgcvmimemultcompmunsellmvtnormnlmennetnumDerivparallellypatchworkpecpillarpkgconfigplotrixpolsplineprodlimprogressrPublishquantregR6rangerrappdirsRColorBrewerRcppRcppArmadilloRcppEigenriskRegressionrlangrmarkdownrmsrpartrstudioapisandwichsassscalesshapeSparseMSQUAREMstringistringrsurvivalTH.datatibbletimeregtinytexutf8vctrsviridisviridisLitewithrxfunyamlzoo

Creating custom explainers

Rendered fromcustom-explainers.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2022-09-27
Started: 2022-08-31

Global explanations with SurvSHAP(t)

Rendered fromglobal-survshap.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2023-08-30
Started: 2023-08-30

Package usage

Rendered fromsurvex-usage.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2023-08-30
Started: 2022-08-31

Partial Dependence Explanations

Rendered frompdp.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2023-08-30
Started: 2023-08-30

Readme and manuals

Help Manual

Help pageTopics
Calculate Brier scorebrier_score loss_brier_score
Compute the Harrell's Concordance indexc_index
Calculate Cumulative/Dynamic AUCcd_auc
Transform Cumulative Hazard to Survivalcumulative_hazard_to_survival
A model-agnostic explainer for survival modelsexplain explain.default explain_survival
Extract Local SurvSHAP(t) from Global SurvSHAP(t)extract_predict_survshap
Calculate integrated Brier scoreintegrated_brier_score loss_integrated_brier_score
Calculate integrated C/D AUCintegrated_cd_auc
Adapt mlr3proba measures for use with survexloss_adapt_mlr3proba
Calculate integrated metrics based on time-dependent metrics.loss_integrate
Calculate the Concordance index lossloss_one_minus_c_index
Calculate Cumulative/Dynamic AUC lossloss_one_minus_cd_auc
Calculate integrated C/D AUC lossloss_one_minus_integrated_cd_auc
Dataset Level Model Diagnosticsmodel_diagnostics model_diagnostics.surv_explainer
Dataset Level Variable Importance for Survival Modelsmodel_parts model_parts.surv_explainer
Dataset Level Performance Measuresmodel_performance model_performance.surv_explainer
Dataset Level Variable Profile as Partial Dependence Explanations for Survival Modelsmodel_profile model_profile.surv_explainer
Dataset Level 2-Dimensional Variable Profile for Survival Modelsmodel_profile_2d model_profile_2d.surv_explainer
Global SHAP Valuesmodel_survshap model_survshap.surv_explainer
Plot Aggregated SurvSHAP(t) Explanations for Survival Modelsplot.aggregated_surv_shap
Plot Model Diagnostics for Survival Modelsplot.model_diagnostics_survival
Plot Model Parts for Survival Modelsplot.model_parts_survival
Plot Model Performance for Survival Modelsplot.model_performance_survival
Plot 2-Dimensional Model Profile for Survival Modelsplot.model_profile_2d_survival
Plot Model Profile for Survival Modelsplot.model_profile_survival
Plot Predict Parts for Survival Modelsplot.predict_parts_survival
Plot Predict Profile for Survival Modelsplot.predict_profile_survival
Plot Permutational Feature Importance for Survival Modelsplot.surv_feature_importance
Plot SurvLIME Explanations for Survival Modelsplot.surv_lime
Plot Model Performance Metrics for Survival Modelsplot.surv_model_performance
Plot ROC Curves for Survival Modelsplot.surv_model_performance_rocs
Plot SurvSHAP(t) Explanations for Survival Modelsplot.surv_shap
Instance Level Parts of Survival Model Predictionspredict_parts predict_parts.surv_explainer
Instance Level Profile as Ceteris Paribus for Survival Modelspredict_profile predict_profile.surv_explainer
Model Predictions for Survival Modelspredict.surv_explainer
Generate Risk Prediction based on the Survival Functionrisk_from_chf
Default Theme for survex plotsset_theme_survex theme_default_survex theme_vertical_default_survex
Extract additional information from the modelsurv_model_info surv_model_info.coxph surv_model_info.cph surv_model_info.default surv_model_info.flexsurvreg surv_model_info.LearnerSurv surv_model_info.model_fit surv_model_info.ranger surv_model_info.rfsrc surv_model_info.sksurv
Transform Survival to Cumulative Hazardsurvival_to_cumulative_hazard
Transform Fixed Point Prediction into a Stepfunctiontransform_to_stepfunction