diff --git a/articles/global-survshap_files/figure-html/unnamed-chunk-5-1.png b/articles/global-survshap_files/figure-html/unnamed-chunk-5-1.png index 471c679..afc9fe9 100644 Binary files a/articles/global-survshap_files/figure-html/unnamed-chunk-5-1.png and b/articles/global-survshap_files/figure-html/unnamed-chunk-5-1.png differ diff --git a/articles/mlr3proba-usage.html b/articles/mlr3proba-usage.html index 0599656..ebbeed0 100644 --- a/articles/mlr3proba-usage.html +++ b/articles/mlr3proba-usage.html @@ -121,43 +121,25 @@

mlr3proba and additional packages
 
 if (!require("ooplah")) install.packages("ooplah")
-#> Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-#> logical.return = TRUE, : there is no package called 'ooplah'
 
 if (!require("dictionar6")) install.packages("dictionar6")
-#> Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-#> logical.return = TRUE, : there is no package called 'dictionar6'
 
 if (!require("set6")) install.packages("set6",
                                          repos = "https://mlr-org.r-universe.dev")
-#> Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-#> logical.return = TRUE, : there is no package called 'set6'
 
 if (!require("param6")) install.packages("param6",
                                          repos = "https://mlr-org.r-universe.dev")
-#> Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-#> logical.return = TRUE, : there is no package called 'param6'
 
 if (!require("distr6")) install.packages("distr6",
                                          repos = "https://mlr-org.r-universe.dev")
-#> Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-#> logical.return = TRUE, : there is no package called 'distr6'
 
 if (!require("mlr3")) install.packages("mlr3")
-#> Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-#> logical.return = TRUE, : there is no package called 'mlr3'
 
 if (!require("mlr3proba")) install.packages("mlr3proba",
                                             repos = "https://mlr-org.r-universe.dev")
-#> Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-#> logical.return = TRUE, : there is no package called 'mlr3proba'
 if (!require("mlr3extralearners")) install.packages("mlr3extralearners",
                                                     repos = "https://mlr-org.r-universe.dev")
-#> Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-#> logical.return = TRUE, : there is no package called 'mlr3extralearners'
 if (!require("mlr3pipelines")) install.packages("mlr3pipelines")
-#> Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-#> logical.return = TRUE, : there is no package called 'mlr3pipelines'
 
 library(mlr3proba)
 library(mlr3extralearners)
diff --git a/articles/mlr3proba-usage_files/figure-html/unnamed-chunk-3-1.png b/articles/mlr3proba-usage_files/figure-html/unnamed-chunk-3-1.png
index ddf58df..5211018 100644
Binary files a/articles/mlr3proba-usage_files/figure-html/unnamed-chunk-3-1.png and b/articles/mlr3proba-usage_files/figure-html/unnamed-chunk-3-1.png differ
diff --git a/articles/mlr3proba-usage_files/figure-html/unnamed-chunk-4-1.png b/articles/mlr3proba-usage_files/figure-html/unnamed-chunk-4-1.png
index d286720..6a7d253 100644
Binary files a/articles/mlr3proba-usage_files/figure-html/unnamed-chunk-4-1.png and b/articles/mlr3proba-usage_files/figure-html/unnamed-chunk-4-1.png differ
diff --git a/articles/mlr3proba-usage_files/figure-html/unnamed-chunk-5-1.png b/articles/mlr3proba-usage_files/figure-html/unnamed-chunk-5-1.png
index 5307165..3b56665 100644
Binary files a/articles/mlr3proba-usage_files/figure-html/unnamed-chunk-5-1.png and b/articles/mlr3proba-usage_files/figure-html/unnamed-chunk-5-1.png differ
diff --git a/articles/mlr3proba-usage_files/figure-html/unnamed-chunk-6-1.png b/articles/mlr3proba-usage_files/figure-html/unnamed-chunk-6-1.png
index 9cf2ddb..031c58c 100644
Binary files a/articles/mlr3proba-usage_files/figure-html/unnamed-chunk-6-1.png and b/articles/mlr3proba-usage_files/figure-html/unnamed-chunk-6-1.png differ
diff --git a/articles/pdp.html b/articles/pdp.html
index bf5e7f1..f2c2400 100644
--- a/articles/pdp.html
+++ b/articles/pdp.html
@@ -233,7 +233,9 @@ 
Partial Dependence Explanations

 "accumulated".

 
 pdp_2d  <- model_profile_2d(exp, variables = list(c("karno", "age")))
-#> Aggregating predictions.. Progress: 67%. Estimated remaining time: 15 seconds.
+#> Aggregating predictions.. Progress: 31%. Estimated remaining time: 1 minute, 8 seconds.
+#> Aggregating predictions.. Progress: 62%. Estimated remaining time: 38 seconds.
+#> Aggregating predictions.. Progress: 93%. Estimated remaining time: 7 seconds.
 pdp_2d_num_cat <- model_profile_2d(exp, variables = list(c("karno", "celltype")))

 
These explanations can be plotted using the plot function.

 
diff --git a/pkgdown.yml b/pkgdown.yml
index ac544aa..612be6a 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -7,7 +7,7 @@ articles:
   global-survshap: global-survshap.html
   pdp: pdp.html
   survex-usage: survex-usage.html
-last_built: 2023-10-24T19:08Z
+last_built: 2023-10-24T19:21Z
 urls:
   reference: https://modeloriented.github.io/survex/reference
   article: https://modeloriented.github.io/survex/articles
diff --git a/reference/Rplot002.png b/reference/Rplot002.png
index 73a7f3d..5f97bf9 100644
Binary files a/reference/Rplot002.png and b/reference/Rplot002.png differ
diff --git a/reference/Rplot003.png b/reference/Rplot003.png
index 6a6cb56..10fc405 100644
Binary files a/reference/Rplot003.png and b/reference/Rplot003.png differ
diff --git a/reference/Rplot004.png b/reference/Rplot004.png
index ba46130..b8cf100 100644
Binary files a/reference/Rplot004.png and b/reference/Rplot004.png differ
diff --git a/reference/Rplot005.png b/reference/Rplot005.png
index d8a7e28..871e5ba 100644
Binary files a/reference/Rplot005.png and b/reference/Rplot005.png differ
diff --git a/reference/Rplot006.png b/reference/Rplot006.png
index e988d5c..346ab7a 100644
Binary files a/reference/Rplot006.png and b/reference/Rplot006.png differ
diff --git a/reference/extract_predict_survshap-1.png b/reference/extract_predict_survshap-1.png
index 6d0e7c0..fd95ce4 100644
Binary files a/reference/extract_predict_survshap-1.png and b/reference/extract_predict_survshap-1.png differ
diff --git a/reference/model_diagnostics.surv_explainer-1.png b/reference/model_diagnostics.surv_explainer-1.png
index 8442ba8..32d19a4 100644
Binary files a/reference/model_diagnostics.surv_explainer-1.png and b/reference/model_diagnostics.surv_explainer-1.png differ
diff --git a/reference/model_diagnostics.surv_explainer-2.png b/reference/model_diagnostics.surv_explainer-2.png
index 3f394b0..26fb0dc 100644
Binary files a/reference/model_diagnostics.surv_explainer-2.png and b/reference/model_diagnostics.surv_explainer-2.png differ
diff --git a/reference/model_parts.surv_explainer-1.png b/reference/model_parts.surv_explainer-1.png
index b2a9498..e7c2e34 100644
Binary files a/reference/model_parts.surv_explainer-1.png and b/reference/model_parts.surv_explainer-1.png differ
diff --git a/reference/model_parts.surv_explainer-2.png b/reference/model_parts.surv_explainer-2.png
index a3f3e54..866d0ff 100644
Binary files a/reference/model_parts.surv_explainer-2.png and b/reference/model_parts.surv_explainer-2.png differ
diff --git a/reference/model_parts.surv_explainer.html b/reference/model_parts.surv_explainer.html
index 0fcc6fb..c305dc7 100644
--- a/reference/model_parts.surv_explainer.html
+++ b/reference/model_parts.surv_explainer.html
@@ -192,20 +192,20 @@ 
Examples

 
 cph_model_parts_brier <- model_parts(cph_exp)
 print(head(cph_model_parts_brier$result))
-#>    _times_ _full_model_           trt      celltype        karno     diagtime
-#> 1      1.5            0  5.256927e-05 -0.0004332791 0.0002107716 9.425258e-08
-#> 12     4.0            0 -7.430163e-05 -0.0002120110 0.0018899828 1.491936e-06
-#> 23     7.0            0  2.436943e-04  0.0009262378 0.0055721212 2.720173e-06
-#> 35     8.0            0  6.340322e-05  0.0030181084 0.0110558455 5.798739e-06
-#> 48    10.0            0 -6.445876e-04  0.0011089194 0.0144497411 7.101680e-06
-#> 57    12.0            0 -1.618452e-03  0.0010867304 0.0182603948 7.471981e-06
-#>             age         prior    _baseline_ _permutation_ label
-#> 1  1.865661e-05  1.246491e-05 -1.297031e-05             0 coxph
-#> 12 5.460953e-04  1.124311e-05  2.361437e-03             0 coxph
-#> 23 7.186469e-04 -7.165984e-05  6.461760e-03             0 coxph
-#> 35 8.083450e-04  9.299490e-05  1.206747e-02             0 coxph
-#> 48 1.076200e-03  2.029838e-04  1.578048e-02             0 coxph
-#> 57 1.107444e-03  4.655921e-04  1.838133e-02             0 coxph
+#>    _times_ _full_model_           trt      celltype        karno      diagtime
+#> 1      1.5            0  5.384453e-05 -0.0006463206 0.0001495106  1.675973e-07
+#> 12     4.0            0 -4.042871e-05 -0.0005889617 0.0018788167 -1.648536e-07
+#> 23     7.0            0  3.305696e-04  0.0005491735 0.0051575035 -8.028706e-07
+#> 35     8.0            0  1.201396e-04  0.0026284416 0.0099418733  3.802442e-06
+#> 48    10.0            0 -5.279865e-04  0.0015202360 0.0133966257  5.520314e-06
+#> 57    12.0            0 -1.633204e-03  0.0015996782 0.0160609741  5.534143e-06
+#>             age         prior   _baseline_ _permutation_ label
+#> 1  3.852603e-05  1.342322e-05 0.0001331684             0 coxph
+#> 12 6.224512e-04  5.164115e-05 0.0026680886             0 coxph
+#> 23 8.361780e-04 -6.511282e-05 0.0080994631             0 coxph
+#> 35 1.146135e-03  4.772656e-05 0.0148464072             0 coxph
+#> 48 1.397579e-03  1.407626e-04 0.0185161336             0 coxph
+#> 57 1.533032e-03  4.182685e-04 0.0210313057             0 coxph
 plot(cph_model_parts_brier)
 
 
@@ -213,19 +213,19 @@ 
Examples

 rsf_ranger_model_parts <- model_parts(rsf_ranger_exp)
 print(head(rsf_ranger_model_parts$result))
 #>    _times_ _full_model_          trt    celltype       karno    diagtime
-#> 1      1.5            0 0.0002258422 0.001653738 0.002154695 0.001362203
-#> 12     4.0            0 0.0011207249 0.002459063 0.009308037 0.003410368
-#> 23     7.0            0 0.0014091835 0.003266176 0.016353161 0.004723243
-#> 35     8.0            0 0.0016703949 0.005425894 0.025991293 0.010953146
-#> 48    10.0            0 0.0020650091 0.005600829 0.036227678 0.013873516
-#> 57    12.0            0 0.0026297856 0.007873114 0.042640749 0.015943279
-#>           age        prior  _baseline_ _permutation_  label
-#> 1  0.00231664 0.0002449811 0.005470502             0 ranger
-#> 12 0.01019244 0.0006931186 0.019393118             0 ranger
-#> 23 0.01330631 0.0011607115 0.027884967             0 ranger
-#> 35 0.01388119 0.0019286487 0.042736373             0 ranger
-#> 48 0.01540402 0.0032001327 0.057502499             0 ranger
-#> 57 0.01629742 0.0046273271 0.063597659             0 ranger
+#> 1      1.5            0 0.0003115301 0.001556636 0.002646500 0.001245264
+#> 12     4.0            0 0.0010205195 0.002063602 0.009721017 0.003006407
+#> 23     7.0            0 0.0021020184 0.002524944 0.016230909 0.005217535
+#> 35     8.0            0 0.0020020205 0.005217134 0.026749237 0.010858156
+#> 48    10.0            0 0.0020480513 0.005525208 0.036590431 0.012341841
+#> 57    12.0            0 0.0023285155 0.007464444 0.043412324 0.012280778
+#>            age        prior  _baseline_ _permutation_  label
+#> 1  0.002890486 0.0003491360 0.006128302             0 ranger
+#> 12 0.010110876 0.0005853273 0.018235571             0 ranger
+#> 23 0.012040734 0.0004456972 0.025525952             0 ranger
+#> 35 0.012641973 0.0012363720 0.039549505             0 ranger
+#> 48 0.013881765 0.0017909214 0.050174769             0 ranger
+#> 57 0.014074994 0.0028008218 0.055612244             0 ranger
 plot(cph_model_parts_brier, rsf_ranger_model_parts)
 
 # }
diff --git a/reference/model_performance.surv_explainer-1.png b/reference/model_performance.surv_explainer-1.png
index 5c98e35..e32055d 100644
Binary files a/reference/model_performance.surv_explainer-1.png and b/reference/model_performance.surv_explainer-1.png differ
diff --git a/reference/model_performance.surv_explainer-2.png b/reference/model_performance.surv_explainer-2.png
index 2b8a047..253e30b 100644
Binary files a/reference/model_performance.surv_explainer-2.png and b/reference/model_performance.surv_explainer-2.png differ
diff --git a/reference/model_profile.surv_explainer-1.png b/reference/model_profile.surv_explainer-1.png
index 4b53fe9..e696ca8 100644
Binary files a/reference/model_profile.surv_explainer-1.png and b/reference/model_profile.surv_explainer-1.png differ
diff --git a/reference/model_profile.surv_explainer-2.png b/reference/model_profile.surv_explainer-2.png
index e6b369e..1457e94 100644
Binary files a/reference/model_profile.surv_explainer-2.png and b/reference/model_profile.surv_explainer-2.png differ
diff --git a/reference/model_profile.surv_explainer.html b/reference/model_profile.surv_explainer.html
index 79470ab..016d1b1 100644
--- a/reference/model_profile.surv_explainer.html
+++ b/reference/model_profile.surv_explainer.html
@@ -212,12 +212,12 @@ 
Examples

 
 head(cph_model_profile$result)
 #>   _vname_   _vtype_ _label_   _x_ _times_    _yhat_ _ids_
-#> 1     age numerical   coxph 34.00     1.5 0.9811826     0
-#> 2     age numerical   coxph 34.94     1.5 0.9813333     0
-#> 3     age numerical   coxph 35.00     1.5 0.9813428     0
-#> 4     age numerical   coxph 35.88     1.5 0.9814827     0
-#> 5     age numerical   coxph 36.00     1.5 0.9815017     0
-#> 6     age numerical   coxph 36.82     1.5 0.9816310     0
+#> 1     age numerical   coxph 34.00     1.5 0.9806619     0
+#> 2     age numerical   coxph 34.94     1.5 0.9808166     0
+#> 3     age numerical   coxph 35.00     1.5 0.9808264     0
+#> 4     age numerical   coxph 35.88     1.5 0.9809701     0
+#> 5     age numerical   coxph 36.82     1.5 0.9811223     0
+#> 6     age numerical   coxph 37.00     1.5 0.9811513     0
 
 plot(cph_model_profile)
 
@@ -230,12 +230,12 @@ 
Examples

 
 head(rsf_model_profile$result)
 #>   _vname_   _vtype_ _label_ _x_ _times_    _yhat_ _ids_
-#> 1     age numerical   rfsrc  34     1.5 0.8168101     0
-#> 2     age numerical   rfsrc  34     4.0 0.7394619     0
-#> 3     age numerical   rfsrc  34     7.0 0.7221792     0
-#> 4     age numerical   rfsrc  34     8.0 0.6995498     0
-#> 5     age numerical   rfsrc  34    10.0 0.6866869     0
-#> 6     age numerical   rfsrc  34    12.0 0.6744986     0
+#> 1     age numerical   rfsrc  34     1.5 0.9773011     0
+#> 2     age numerical   rfsrc  34     4.0 0.9505166     0
+#> 3     age numerical   rfsrc  34     7.0 0.9314135     0
+#> 4     age numerical   rfsrc  34     8.0 0.9066210     0
+#> 5     age numerical   rfsrc  34    10.0 0.8920943     0
+#> 6     age numerical   rfsrc  34    12.0 0.8713509     0
 
 plot(rsf_model_profile, variables = c("age", "celltype"), numerical_plot_type = "contours")
 
diff --git a/reference/model_profile_2d.surv_explainer-1.png b/reference/model_profile_2d.surv_explainer-1.png
index a1b58fa..251eb85 100644
Binary files a/reference/model_profile_2d.surv_explainer-1.png and b/reference/model_profile_2d.surv_explainer-1.png differ
diff --git a/reference/model_profile_2d.surv_explainer-2.png b/reference/model_profile_2d.surv_explainer-2.png
index 3415cdb..bc919ec 100644
Binary files a/reference/model_profile_2d.surv_explainer-2.png and b/reference/model_profile_2d.surv_explainer-2.png differ
diff --git a/reference/model_profile_2d.surv_explainer.html b/reference/model_profile_2d.surv_explainer.html
index 7bd1976..177c2ef 100644
--- a/reference/model_profile_2d.surv_explainer.html
+++ b/reference/model_profile_2d.surv_explainer.html
@@ -188,12 +188,12 @@ 
Examples

 #> 5      age celltype numerical categorical 41.8333333333333     adeno     1.5
 #> 6      age celltype numerical categorical 43.7916666666667     adeno     1.5
 #>   _label_    _yhat_
-#> 1   coxph 0.9728298
-#> 2   coxph 0.9732800
-#> 3   coxph 0.9737229
-#> 4   coxph 0.9741587
-#> 5   coxph 0.9745873
-#> 6   coxph 0.9750089
+#> 1   coxph 0.9706123
+#> 2   coxph 0.9710977
+#> 3   coxph 0.9715752
+#> 4   coxph 0.9720450
+#> 5   coxph 0.9725072
+#> 6   coxph 0.9729619
 plot(cph_model_profile_2d)
 #> Warning: Plot will be prepared for the median survial time. For another time point, set the value of `times`.
 
@@ -204,19 +204,19 @@ 
Examples

 )
 head(cph_model_profile_2d_ale$result)
 #>   _v1name_ _v2name_  _v1type_  _v2type_ _v1value_ _v2value_ _times_    _yhat_
-#> 1      age    karno numerical numerical        34        10     1.5 0.9826099
-#> 2      age    karno numerical numerical        34        10     4.0 0.9575688
-#> 3      age    karno numerical numerical        34        10     7.0 0.9333803
-#> 4      age    karno numerical numerical        34        10     8.0 0.9025179
-#> 5      age    karno numerical numerical        34        10    10.0 0.8877701
-#> 6      age    karno numerical numerical        34        10    12.0 0.8666934
+#> 1      age    karno numerical numerical        34        20     1.5 0.9821463
+#> 2      age    karno numerical numerical        34        20     4.0 0.9561551
+#> 3      age    karno numerical numerical        34        20     7.0 0.9307331
+#> 4      age    karno numerical numerical        34        20     8.0 0.8978583
+#> 5      age    karno numerical numerical        34        20    10.0 0.8819841
+#> 6      age    karno numerical numerical        34        20    12.0 0.8591286
 #>   _right_ _left_ _top_ _bottom_ _count_ _label_
-#> 1      36     34    10       20       0   coxph
-#> 2      36     34    10       20       0   coxph
-#> 3      36     34    10       20       0   coxph
-#> 4      36     34    10       20       0   coxph
-#> 5      36     34    10       20       0   coxph
-#> 6      36     34    10       20       0   coxph
+#> 1      38     34    20       25       0   coxph
+#> 2      38     34    20       25       0   coxph
+#> 3      38     34    20       25       0   coxph
+#> 4      38     34    20       25       0   coxph
+#> 5      38     34    20       25       0   coxph
+#> 6      38     34    20       25       0   coxph
 plot(cph_model_profile_2d_ale)
 #> Warning: Plot will be prepared for the median survial time. For another time point, set the value of `times`.
 
diff --git a/reference/model_survshap.surv_explainer-1.png b/reference/model_survshap.surv_explainer-1.png
index 719bdbc..ab11616 100644
Binary files a/reference/model_survshap.surv_explainer-1.png and b/reference/model_survshap.surv_explainer-1.png differ
diff --git a/reference/model_survshap.surv_explainer-2.png b/reference/model_survshap.surv_explainer-2.png
index 3a0fe5c..7463cc2 100644
Binary files a/reference/model_survshap.surv_explainer-2.png and b/reference/model_survshap.surv_explainer-2.png differ
diff --git a/reference/model_survshap.surv_explainer-3.png b/reference/model_survshap.surv_explainer-3.png
index cd82e2f..d4220b7 100644
Binary files a/reference/model_survshap.surv_explainer-3.png and b/reference/model_survshap.surv_explainer-3.png differ
diff --git a/reference/plot.aggregated_surv_shap-1.png b/reference/plot.aggregated_surv_shap-1.png
index ffd5ed2..1287192 100644
Binary files a/reference/plot.aggregated_surv_shap-1.png and b/reference/plot.aggregated_surv_shap-1.png differ
diff --git a/reference/plot.aggregated_surv_shap-2.png b/reference/plot.aggregated_surv_shap-2.png
index 145bfd3..41e6ac5 100644
Binary files a/reference/plot.aggregated_surv_shap-2.png and b/reference/plot.aggregated_surv_shap-2.png differ
diff --git a/reference/plot.aggregated_surv_shap-3.png b/reference/plot.aggregated_surv_shap-3.png
index b45f95e..ee5b2f8 100644
Binary files a/reference/plot.aggregated_surv_shap-3.png and b/reference/plot.aggregated_surv_shap-3.png differ
diff --git a/reference/plot.aggregated_surv_shap-4.png b/reference/plot.aggregated_surv_shap-4.png
index 73f9fb5..98fc07f 100644
Binary files a/reference/plot.aggregated_surv_shap-4.png and b/reference/plot.aggregated_surv_shap-4.png differ
diff --git a/reference/plot.aggregated_surv_shap-5.png b/reference/plot.aggregated_surv_shap-5.png
index 5922998..a4ec83b 100644
Binary files a/reference/plot.aggregated_surv_shap-5.png and b/reference/plot.aggregated_surv_shap-5.png differ
diff --git a/reference/plot.aggregated_surv_shap.html b/reference/plot.aggregated_surv_shap.html
index 53c60c7..ec55c54 100644
--- a/reference/plot.aggregated_surv_shap.html
+++ b/reference/plot.aggregated_surv_shap.html
@@ -215,11 +215,8 @@ 
Examples

 #> Observations with outlying SurvSHAP(t) values:
 #>     trt  celltype karno diagtime age prior
 #> 1     1  squamous    60        7  69     0
-#> 2     1  squamous    70        5  64    10
 #> 3     1  squamous    60        3  38     0
-#> 4     1  squamous    60        9  63    10
 #> 18    1 smallcell    40        2  35     0
-#> 19    1 smallcell    80        4  63    10
 #> 127   2     large    70       15  68    10
 #> 128   2     large    30        4  39    10
 
diff --git a/reference/plot.model_parts_survival-1.png b/reference/plot.model_parts_survival-1.png
index 39ae935..517bcc3 100644
Binary files a/reference/plot.model_parts_survival-1.png and b/reference/plot.model_parts_survival-1.png differ
diff --git a/reference/plot.model_performance_survival-1.png b/reference/plot.model_performance_survival-1.png
index 68d779c..1ebf113 100644
Binary files a/reference/plot.model_performance_survival-1.png and b/reference/plot.model_performance_survival-1.png differ
diff --git a/reference/plot.model_performance_survival-2.png b/reference/plot.model_performance_survival-2.png
index 24573fb..2fd5c79 100644
Binary files a/reference/plot.model_performance_survival-2.png and b/reference/plot.model_performance_survival-2.png differ
diff --git a/reference/plot.model_profile_2d_survival-1.png b/reference/plot.model_profile_2d_survival-1.png
index 948c89f..6072ad7 100644
Binary files a/reference/plot.model_profile_2d_survival-1.png and b/reference/plot.model_profile_2d_survival-1.png differ
diff --git a/reference/plot.model_profile_2d_survival-2.png b/reference/plot.model_profile_2d_survival-2.png
index c8da471..1e59008 100644
Binary files a/reference/plot.model_profile_2d_survival-2.png and b/reference/plot.model_profile_2d_survival-2.png differ
diff --git a/reference/plot.model_profile_2d_survival.html b/reference/plot.model_profile_2d_survival.html
index 0d29c4e..faeec03 100644
--- a/reference/plot.model_profile_2d_survival.html
+++ b/reference/plot.model_profile_2d_survival.html
@@ -172,19 +172,19 @@ 
Examples

 )
 head(cph_model_profile_2d$result)
 #>   _v1name_ _v2name_  _v1type_    _v2type_        _v1value_ _v2value_ _times_
-#> 1      age celltype numerical categorical               35     adeno     1.5
-#> 2      age celltype numerical categorical 36.5416666666667     adeno     1.5
-#> 3      age celltype numerical categorical 38.0833333333333     adeno     1.5
-#> 4      age celltype numerical categorical           39.625     adeno     1.5
-#> 5      age celltype numerical categorical 41.1666666666667     adeno     1.5
-#> 6      age celltype numerical categorical 42.7083333333333     adeno     1.5
+#> 1      age celltype numerical categorical               34     adeno     1.5
+#> 2      age celltype numerical categorical 35.9583333333333     adeno     1.5
+#> 3      age celltype numerical categorical 37.9166666666667     adeno     1.5
+#> 4      age celltype numerical categorical           39.875     adeno     1.5
+#> 5      age celltype numerical categorical 41.8333333333333     adeno     1.5
+#> 6      age celltype numerical categorical 43.7916666666667     adeno     1.5
 #>   _label_    _yhat_
-#> 1   coxph 0.9698524
-#> 2   coxph 0.9702453
-#> 3   coxph 0.9706333
-#> 4   coxph 0.9710162
-#> 5   coxph 0.9713943
-#> 6   coxph 0.9717676
+#> 1   coxph 0.9726739
+#> 2   coxph 0.9731259
+#> 3   coxph 0.9735706
+#> 4   coxph 0.9740081
+#> 5   coxph 0.9744384
+#> 6   coxph 0.9748619
 plot(cph_model_profile_2d, variables = list(c("age", "celltype")), times = cph_exp$times[20])
 
 
@@ -194,19 +194,19 @@ 
Examples

 )
 head(cph_model_profile_2d_ale$result)
 #>   _v1name_ _v2name_  _v1type_  _v2type_ _v1value_ _v2value_ _times_    _yhat_
-#> 1      age    karno numerical numerical        34        10     1.5 0.9808187
-#> 2      age    karno numerical numerical        34        10     4.0 0.9529722
-#> 3      age    karno numerical numerical        34        10     7.0 0.9258121
-#> 4      age    karno numerical numerical        34        10     8.0 0.8907776
-#> 5      age    karno numerical numerical        34        10    10.0 0.8738869
-#> 6      age    karno numerical numerical        34        10    12.0 0.8495871
+#> 1      age    karno numerical numerical        36        20     1.5 0.9828368
+#> 2      age    karno numerical numerical        36        20     4.0 0.9576114
+#> 3      age    karno numerical numerical        36        20     7.0 0.9326503
+#> 4      age    karno numerical numerical        36        20     8.0 0.8999269
+#> 5      age    karno numerical numerical        36        20    10.0 0.8839397
+#> 6      age    karno numerical numerical        36        20    12.0 0.8607034
 #>   _right_ _left_ _top_ _bottom_ _count_ _label_
-#> 1      36     34    10       15       0   coxph
-#> 2      36     34    10       15       0   coxph
-#> 3      36     34    10       15       0   coxph
-#> 4      36     34    10       15       0   coxph
-#> 5      36     34    10       15       0   coxph
-#> 6      36     34    10       15       0   coxph
+#> 1      37     36    20       25       0   coxph
+#> 2      37     36    20       25       0   coxph
+#> 3      37     36    20       25       0   coxph
+#> 4      37     36    20       25       0   coxph
+#> 5      37     36    20       25       0   coxph
+#> 6      37     36    20       25       0   coxph
 plot(cph_model_profile_2d_ale, times = cph_exp$times[c(10, 20)], marginalize_over_time = TRUE)
 
 # }
diff --git a/reference/plot.model_profile_survival-1.png b/reference/plot.model_profile_survival-1.png
index 471d495..d1ef651 100644
Binary files a/reference/plot.model_profile_survival-1.png and b/reference/plot.model_profile_survival-1.png differ
diff --git a/reference/plot.model_profile_survival-2.png b/reference/plot.model_profile_survival-2.png
index 119513e..bae8e4c 100644
Binary files a/reference/plot.model_profile_survival-2.png and b/reference/plot.model_profile_survival-2.png differ
diff --git a/reference/plot.model_profile_survival-3.png b/reference/plot.model_profile_survival-3.png
index 121d367..7876e0d 100644
Binary files a/reference/plot.model_profile_survival-3.png and b/reference/plot.model_profile_survival-3.png differ
diff --git a/reference/plot.model_profile_survival-4.png b/reference/plot.model_profile_survival-4.png
index c8f8e90..5ffc552 100644
Binary files a/reference/plot.model_profile_survival-4.png and b/reference/plot.model_profile_survival-4.png differ
diff --git a/reference/plot.model_profile_survival-5.png b/reference/plot.model_profile_survival-5.png
index b33d28e..bc8ce8e 100644
Binary files a/reference/plot.model_profile_survival-5.png and b/reference/plot.model_profile_survival-5.png differ
diff --git a/reference/plot.model_profile_survival-6.png b/reference/plot.model_profile_survival-6.png
index 1f8b241..f7cb8b1 100644
Binary files a/reference/plot.model_profile_survival-6.png and b/reference/plot.model_profile_survival-6.png differ
diff --git a/reference/plot.predict_parts_survival-1.png b/reference/plot.predict_parts_survival-1.png
index cabd5d5..4783621 100644
Binary files a/reference/plot.predict_parts_survival-1.png and b/reference/plot.predict_parts_survival-1.png differ
diff --git a/reference/plot.predict_parts_survival-2.png b/reference/plot.predict_parts_survival-2.png
index fbd2f83..50b8e5b 100644
Binary files a/reference/plot.predict_parts_survival-2.png and b/reference/plot.predict_parts_survival-2.png differ
diff --git a/reference/plot.predict_profile_survival-1.png b/reference/plot.predict_profile_survival-1.png
index ce2d96c..e33e6e3 100644
Binary files a/reference/plot.predict_profile_survival-1.png and b/reference/plot.predict_profile_survival-1.png differ
diff --git a/reference/plot.predict_profile_survival-2.png b/reference/plot.predict_profile_survival-2.png
index 4f23c34..4e29587 100644
Binary files a/reference/plot.predict_profile_survival-2.png and b/reference/plot.predict_profile_survival-2.png differ
diff --git a/reference/plot.surv_feature_importance-1.png b/reference/plot.surv_feature_importance-1.png
index 9a6761f..6a3f6fe 100644
Binary files a/reference/plot.surv_feature_importance-1.png and b/reference/plot.surv_feature_importance-1.png differ
diff --git a/reference/plot.surv_lime-1.png b/reference/plot.surv_lime-1.png
index f400df1..391b5ae 100644
Binary files a/reference/plot.surv_lime-1.png and b/reference/plot.surv_lime-1.png differ
diff --git a/reference/plot.surv_model_performance-1.png b/reference/plot.surv_model_performance-1.png
index fe4c5b4..1d68ab1 100644
Binary files a/reference/plot.surv_model_performance-1.png and b/reference/plot.surv_model_performance-1.png differ
diff --git a/reference/plot.surv_model_performance_rocs-1.png b/reference/plot.surv_model_performance_rocs-1.png
index 2f1b66d..dcbc5ba 100644
Binary files a/reference/plot.surv_model_performance_rocs-1.png and b/reference/plot.surv_model_performance_rocs-1.png differ
diff --git a/reference/plot.surv_shap-1.png b/reference/plot.surv_shap-1.png
index 19e7f50..c2abfe5 100644
Binary files a/reference/plot.surv_shap-1.png and b/reference/plot.surv_shap-1.png differ
diff --git a/reference/predict.surv_explainer.html b/reference/predict.surv_explainer.html
index 4225468..31a7e5e 100644
--- a/reference/predict.surv_explainer.html
+++ b/reference/predict.surv_explainer.html
@@ -170,8 +170,8 @@ 
Examples

 #> 0.7354128 
 
 predict(rsf_ranger_exp, veteran[1, ], output_type = "chf")[, 1:10]
-#>  [1] 0.009623403 0.009623403 0.027945423 0.033625319 0.035069764 0.061802719
-#>  [7] 0.067580103 0.073109355 0.073219245 0.075695435
+#>  [1] 0.003423611 0.003423611 0.013874369 0.020623477 0.021181070 0.037540270
+#>  [7] 0.038987288 0.043607269 0.059390098 0.059622656
 
 

     
diff --git a/reference/predict_parts.surv_explainer-2.png b/reference/predict_parts.surv_explainer-2.png
index 9cc602f..4279fd4 100644
Binary files a/reference/predict_parts.surv_explainer-2.png and b/reference/predict_parts.surv_explainer-2.png differ
diff --git a/reference/predict_parts.surv_explainer.html b/reference/predict_parts.surv_explainer.html
index b598aa4..ab85706 100644
--- a/reference/predict_parts.surv_explainer.html
+++ b/reference/predict_parts.surv_explainer.html
@@ -205,10 +205,10 @@ 
Examples

     type = "survlime"
 )
 head(cph_predict_parts_survlime$result)
-#>            trt         karno      diagtime          age       prior
-#> 1 -0.002017738 -0.0009651749 -0.0001565814 0.0007578033 0.001391971
-#>   celltypelarge celltypesmallcell celltypesquamous
-#> 1   -0.03618306      -0.002838358      -0.01624022
+#>          trt        karno     diagtime         age       prior celltypelarge
+#> 1 0.03141601 -0.002646798 0.0004528845 0.002646209 0.002380806   -0.08812856
+#>   celltypesmallcell celltypesquamous
+#> 1       -0.03838122      -0.09017215
 plot(cph_predict_parts_survlime, type = "local_importance")
 
 # }
diff --git a/reference/theme_survex-1.png b/reference/theme_survex-1.png
index 09f28e5..e983c1f 100644
Binary files a/reference/theme_survex-1.png and b/reference/theme_survex-1.png differ
diff --git a/reference/theme_survex-2.png b/reference/theme_survex-2.png
index 3d29778..51118f4 100644
Binary files a/reference/theme_survex-2.png and b/reference/theme_survex-2.png differ