chore: merged upstream changes into kapsner-fork

Author: kapsner

.github/workflows/test-coverage.yaml

@@ -27,5 +27,5 @@ jobs:
           needs: coverage
 
       - name: Test coverage
-        run: covr::codecov(quiet = FALSE, function_exclusions=c("surv_model_info\\.", "explain.LearnerSurv", "loss_adapt_mlr3proba"))
+        run: covr::codecov(quiet = FALSE, function_exclusions=c("surv_model_info\\.", "explain.LearnerSurv", "loss_adapt_mlr3proba", "explain.sksurv"))
         shell: Rscript {0}

DESCRIPTION

@@ -1,10 +1,11 @@
 Package: survex
 Title: Explainable Machine Learning in Survival Analysis
-Version: 1.0.0.9001
+Version: 1.1.1
 Authors@R: 
     c(
         person("Mikołaj", "Spytek", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7111-2286")),
         person("Mateusz", "Krzyziński", role = c("aut"), comment = c(ORCID = "0000-0001-6143-488X")),
+        person("Sophie", "Langbein", role = c("aut")), 
         person("Hubert", "Baniecki", role = c("aut"), comment = c(ORCID = "0000-0001-6661-5364")),
         person("Przemyslaw", "Biecek", role = c("aut"), comment = c(ORCID = "0000-0001-8423-1823"))
     )
@@ -22,27 +23,29 @@ RoxygenNote: 7.2.3
 Depends: R (>= 3.5.0)
 Imports:
     DALEX (>= 2.2.1),
-    ggplot2,
+    ggplot2 (>= 3.4.0),
     kernelshap,
     treeshap,
     pec,
     survival,
-    patchwork,
-    data.table
+    patchwork
 Suggests:
-    censored,
+    censored (>= 0.2.0),
     covr,
+    flexsurv,
     gbm,
     generics,
     glmnet,
     ingredients,
-    knitr,
+    knitr (>= 1.42),
     mboost,
     parsnip,
     progressr,
     randomForestSRC,
     ranger,
+    reticulate,
     rmarkdown,
+    rms,
     testthat (>= 3.0.0),
     withr,
     xgboost

NAMESPACE

@@ -3,22 +3,28 @@
 S3method(explain,LearnerSurv)
 S3method(explain,coxph)
 S3method(explain,default)
+S3method(explain,flexsurvreg)
 S3method(explain,model_fit)
 S3method(explain,ranger)
 S3method(explain,rfsrc)
+S3method(explain,sksurv)
+S3method(model_diagnostics,surv_explainer)
 S3method(model_parts,default)
 S3method(model_parts,surv_explainer)
 S3method(model_performance,default)
 S3method(model_performance,surv_explainer)
 S3method(model_profile,default)
 S3method(model_profile,surv_explainer)
-S3method(plot,feature_importance_explainer)
+S3method(model_profile_2d,surv_explainer)
+S3method(model_survshap,surv_explainer)
+S3method(plot,aggregated_surv_shap)
+S3method(plot,model_diagnostics_survival)
 S3method(plot,model_parts_survival)
 S3method(plot,model_performance_survival)
+S3method(plot,model_profile_2d_survival)
 S3method(plot,model_profile_survival)
 S3method(plot,predict_parts_survival)
 S3method(plot,predict_profile_survival)
-S3method(plot,surv_ceteris_paribus)
 S3method(plot,surv_feature_importance)
 S3method(plot,surv_lime)
 S3method(plot,surv_model_performance)
@@ -29,6 +35,8 @@ S3method(predict_parts,default)
 S3method(predict_parts,surv_explainer)
 S3method(predict_profile,default)
 S3method(predict_profile,surv_explainer)
+S3method(print,model_diagnostics_survival)
+S3method(print,model_profile_2d_survival)
 S3method(print,model_profile_survival)
 S3method(print,surv_ceteris_paribus)
 S3method(print,surv_feature_importance)
@@ -38,15 +46,18 @@ S3method(surv_model_info,LearnerSurv)
 S3method(surv_model_info,coxph)
 S3method(surv_model_info,cph)
 S3method(surv_model_info,default)
+S3method(surv_model_info,flexsurvreg)
 S3method(surv_model_info,model_fit)
 S3method(surv_model_info,ranger)
 S3method(surv_model_info,rfsrc)
+S3method(surv_model_info,sksurv)
 export(brier_score)
 export(c_index)
 export(cd_auc)
 export(cumulative_hazard_to_survival)
 export(explain)
 export(explain_survival)
+export(extract_predict_survshap)
 export(integrated_brier_score)
 export(integrated_cd_auc)
 export(loss_adapt_mlr3proba)
@@ -56,9 +67,12 @@ export(loss_integrated_brier_score)
 export(loss_one_minus_c_index)
 export(loss_one_minus_cd_auc)
 export(loss_one_minus_integrated_cd_auc)
+export(model_diagnostics)
 export(model_parts)
 export(model_performance)
 export(model_profile)
+export(model_profile_2d)
+export(model_survshap)
 export(predict_parts)
 export(predict_profile)
 export(risk_from_chf)
@@ -68,7 +82,6 @@ export(survival_to_cumulative_hazard)
 export(theme_default_survex)
 export(theme_vertical_default_survex)
 export(transform_to_stepfunction)
-import(data.table)
 import(ggplot2)
 import(patchwork)
 import(survival)
@@ -77,18 +90,25 @@ importFrom(DALEX,theme_drwhy)
 importFrom(DALEX,theme_drwhy_vertical)
 importFrom(DALEX,theme_ema)
 importFrom(DALEX,theme_ema_vertical)
+importFrom(graphics,par)
 importFrom(stats,aggregate)
 importFrom(stats,as.formula)
+importFrom(stats,ave)
+importFrom(stats,cmdscale)
+importFrom(stats,ecdf)
 importFrom(stats,median)
 importFrom(stats,model.frame)
 importFrom(stats,model.matrix)
 importFrom(stats,na.omit)
 importFrom(stats,optim)
 importFrom(stats,predict)
+importFrom(stats,qnorm)
 importFrom(stats,quantile)
 importFrom(stats,reorder)
+importFrom(stats,reshape)
 importFrom(stats,rnorm)
 importFrom(stats,stepfun)
+importFrom(stats,xtabs)
 importFrom(utils,head)
 importFrom(utils,stack)
 importFrom(utils,tail)

NEWS.md

@@ -1,6 +1,18 @@
-# survex (development)
+# survex 1.1.0
 
-* Fix not being able to plot or print SurvLIME results for the cph model sometimes. ([#72](https://github.com/ModelOriented/survex/issues/72))
+* fixed not being able to plot or print SurvLIME results for the cph model sometimes. ([#72](https://github.com/ModelOriented/survex/issues/72))
+* added global explanations via the SurvSHAP(t) method (see `model_survshap()` function)
+* added plots for global SurvSHAP(t) explanations (see `plot.aggregated_surv_shap()`)
+* added Accumulated Local Effects (ALE) explanations (see `model_profile(..., type = "accumulated")`)
+* added 2-dimensional PDP and ALE plots (see `model_profile_2d()` function)
+* added `plot(..., geom="variable")` function for plotting PDP and ALE explanations without the time dimension
+* new explainers: for `flexsurv` models and for Python scikit-survival models (can be used with `reticulate`)
+* new plot type for `model_survshap()` - curves (with functional box plot)
+* added diagnostic explanations - residual analysis (see `model_diagnostics()` function)
+* added new times generation method `"survival_quantiles"` and setting it as default (see `explain()`) 
+* made improvements on the vignettes for the package (see `vignette("pdp")` and `vignette("global-survshap")`)
+* increased the test coverage of the package
+* reduced the number of expensive `requireNamespace()` calls ([#83](https://github.com/ModelOriented/survex/issues/83))
 
 # survex 1.0.0