diff --git a/man/orsf.Rd b/man/orsf.Rd
index da540775..60d1de57 100644
--- a/man/orsf.Rd
+++ b/man/orsf.Rd
@@ -520,12 +520,12 @@ The AUC values, from highest to lowest:
}\if{html}{\out{}}
\if{html}{\out{
}}\preformatted{## model times AUC se lower upper
-## 1: net 1788 0.9134593 0.02079935 0.8726933 0.9542253
-## 2: cph 1788 0.9109155 0.02111657 0.8695278 0.9523032
-## 3: accel 1788 0.9099638 0.02122647 0.8683607 0.9515669
-## 4: rlt 1788 0.9069752 0.02132529 0.8651783 0.9487720
-## 5: rando 1788 0.9023489 0.02218936 0.8588586 0.9458393
-## 6: pca 1788 0.8994220 0.02201713 0.8562692 0.9425748
+## 1: net 1788 0.9179396 0.02012887 0.8784877 0.9573915
+## 2: accel 1788 0.9106396 0.02076004 0.8699507 0.9513286
+## 3: cph 1788 0.9061167 0.02277540 0.8614777 0.9507556
+## 4: rlt 1788 0.9012605 0.02178982 0.8585533 0.9439678
+## 5: rando 1788 0.8997729 0.02201363 0.8566270 0.9429188
+## 6: pca 1788 0.8996927 0.02245483 0.8556821 0.9437034
}\if{html}{\out{
}}
And the indices of prediction accuracy:
@@ -534,12 +534,12 @@ And the indices of prediction accuracy:
}\if{html}{\out{}}
\if{html}{\out{}}\preformatted{## model times IPA
-## 1: net 1788 0.4916815
-## 2: cph 1788 0.4833913
-## 3: accel 1788 0.4749974
-## 4: rlt 1788 0.4630984
-## 5: pca 1788 0.4371223
-## 6: rando 1788 0.4258456
+## 1: net 1788 0.5020652
+## 2: cph 1788 0.4759061
+## 3: accel 1788 0.4743392
+## 4: pca 1788 0.4398468
+## 5: rlt 1788 0.4373910
+## 6: rando 1788 0.4219209
## 7: Null model 1788 0.0000000
}\if{html}{\out{
}}
@@ -651,29 +651,29 @@ glimpse(results)
\if{html}{\out{}}\preformatted{## Rows: 276
## Columns: 23
-## $ id 3, 39, 43, 48, 50, 54, 64, 66, 78, 80, 83, 114, 131, 141, ~
-## $ trt d_penicill_main, d_penicill_main, d_penicill_main, placebo~
-## $ age 70.07255, 55.39220, 48.87064, 49.13621, 53.50856, 39.19781~
-## $ sex m, f, f, m, f, f, f, m, f, m, f, m, f, f, f, f, m, f, f, f~
-## $ ascites 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0~
-## $ hepato 0, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 0, 1, 1~
-## $ spiders 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0~
-## $ edema 0.5, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, ~
-## $ bili 1.4, 0.7, 1.1, 1.9, 1.1, 1.3, 2.1, 1.4, 6.3, 7.2, 1.3, 3.2~
-## $ chol 176, 282, 361, 259, 257, 288, 373, 427, 436, 247, 250, 259~
-## $ albumin 3.48, 3.00, 3.64, 3.70, 3.36, 3.40, 3.50, 3.70, 3.02, 3.72~
-## $ copper 210, 52, 36, 281, 43, 262, 52, 105, 75, 269, 48, 208, 74, ~
-## $ alk.phos 516.0, 9066.8, 5430.2, 10396.8, 1080.0, 5487.2, 1009.0, 19~
-## $ ast 96.10, 72.24, 67.08, 188.34, 106.95, 73.53, 150.35, 182.90~
-## $ trig 55, 111, 89, 178, 73, 125, 188, 171, 104, 91, 100, 78, 104~
-## $ platelet 151, 563, 203, 214, 128, 254, 178, 123, 236, 360, 81, 268,~
-## $ protime 12.0, 10.6, 10.6, 11.0, 10.6, 11.0, 11.0, 11.0, 10.6, 11.2~
-## $ stage 4, 4, 2, 3, 4, 4, 3, 3, 4, 4, 4, 3, 4, 2, 3, 4, 2, 3, 4, 3~
-## $ time 1012, 2297, 4556, 4427, 2598, 1434, 1487, 4191, 1690, 890,~
-## $ status 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 0, 1, 0, 0, 0, 1, 0~
-## $ pred_aorsf 0.76027848, 0.25291419, 0.06284001, 0.59437152, 0.15286015~
-## $ pred_rfsrc 0.47891074, 0.16833427, 0.05141013, 0.46526027, 0.06438684~
-## $ pred_ranger 0.61304990, 0.13930022, 0.03715869, 0.48395613, 0.04959462~
+## $ id 16, 29, 43, 62, 79, 82, 103, 105, 111, 114, 115, 139, 141,~
+## $ trt placebo, placebo, d_penicill_main, placebo, d_penicill_mai~
+## $ age 40.44353, 63.87680, 48.87064, 60.70637, 46.51608, 67.31006~
+## $ sex f, f, f, f, f, f, f, f, f, m, f, f, f, f, f, f, f, f, f, f~
+## $ ascites 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0~
+## $ hepato 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 1, 1~
+## $ spiders 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 1~
+## $ edema 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0~
+## $ bili 0.7, 0.7, 1.1, 1.3, 0.8, 4.5, 2.5, 1.1, 5.5, 3.2, 0.7, 1.1~
+## $ chol 204, 370, 361, 302, 315, 472, 188, 464, 528, 259, 303, 328~
+## $ albumin 3.66, 3.78, 3.64, 2.75, 4.24, 4.09, 3.67, 4.20, 4.18, 4.30~
+## $ copper 28, 24, 36, 58, 13, 154, 57, 38, 77, 208, 81, 159, 59, 76,~
+## $ alk.phos 685.0, 5833.0, 5430.2, 1523.0, 1637.0, 1580.0, 1273.0, 164~
+## $ ast 72.85, 73.53, 67.08, 43.40, 170.50, 117.80, 119.35, 151.90~
+## $ trig 58, 86, 89, 112, 70, 272, 102, 102, 78, 78, 156, 134, 56, ~
+## $ platelet 198, 390, 203, 329, 426, 412, 110, 348, 467, 268, 307, 142~
+## $ protime 10.8, 10.6, 10.6, 13.2, 10.9, 11.1, 11.1, 10.3, 10.7, 11.7~
+## $ stage 3, 2, 2, 4, 3, 3, 4, 3, 3, 3, 3, 4, 2, 2, 3, 4, 2, 3, 4, 4~
+## $ time 3672, 4509, 4556, 3090, 3707, 3574, 110, 3092, 2350, 3395,~
+## $ status 0, 0, 0, 1, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0~
+## $ pred_aorsf 0.02210163, 0.12510110, 0.07571520, 0.59580668, 0.12839078~
+## $ pred_rfsrc 0.01861595, 0.15632904, 0.07635485, 0.62281617, 0.19145913~
+## $ pred_ranger 0.02143363, 0.13367920, 0.05892584, 0.54481330, 0.21380654~
}\if{html}{\out{
}}
And finish by aggregating the predictions and computing performance in
@@ -699,16 +699,16 @@ counts.
## Results by model:
##
## model times AUC lower upper
-## 1: aorsf 1826 90.9 86.7 95.1
-## 2: rfsrc 1826 90.0 85.8 94.3
-## 3: ranger 1826 90.1 86.0 94.3
+## 1: aorsf 1826 91.0 86.8 95.2
+## 2: rfsrc 1826 89.2 84.8 93.7
+## 3: ranger 1826 89.6 85.3 94.0
##
## Results of model comparisons:
##
-## times model reference delta.AUC lower upper p
-## 1: 1826 rfsrc aorsf -0.9 -2.2 0.5 0.2
-## 2: 1826 ranger aorsf -0.8 -2.1 0.6 0.3
-## 3: 1826 ranger rfsrc 0.1 -0.8 1.0 0.8
+## times model reference delta.AUC lower upper p
+## 1: 1826 rfsrc aorsf -1.7 -3.4 -0.1 0.04
+## 2: 1826 ranger aorsf -1.3 -2.9 0.2 0.08
+## 3: 1826 ranger rfsrc 0.4 -0.8 1.6 0.52
##
## NOTE: Values are multiplied by 100 and given in \%.
@@ -722,19 +722,19 @@ counts.
##
## model times Brier lower upper IPA
## 1: Null model 1826.25 20.5 18.1 22.9 0.0
-## 2: aorsf 1826.25 10.8 8.5 13.0 47.4
-## 3: rfsrc 1826.25 11.8 9.6 13.9 42.6
-## 4: ranger 1826.25 11.7 9.6 13.8 42.7
+## 2: aorsf 1826.25 10.9 8.7 13.1 46.9
+## 3: rfsrc 1826.25 12.0 9.9 14.2 41.3
+## 4: ranger 1826.25 12.0 9.9 14.1 41.5
##
## Results of model comparisons:
##
## times model reference delta.Brier lower upper p
-## 1: 1826.25 aorsf Null model -9.7 -12.4 -7.0 2.820785e-12
-## 2: 1826.25 rfsrc Null model -8.7 -11.0 -6.4 5.857526e-14
-## 3: 1826.25 ranger Null model -8.7 -11.1 -6.4 1.380943e-13
-## 4: 1826.25 rfsrc aorsf 1.0 0.2 1.8 1.507974e-02
-## 5: 1826.25 ranger aorsf 1.0 0.3 1.7 8.236836e-03
-## 6: 1826.25 ranger rfsrc -0.0 -0.5 0.4 9.336601e-01
+## 1: 1826.25 aorsf Null model -9.6 -12.2 -7.0 9.364941e-13
+## 2: 1826.25 rfsrc Null model -8.5 -10.7 -6.2 2.074175e-13
+## 3: 1826.25 ranger Null model -8.5 -10.8 -6.2 3.712823e-13
+## 4: 1826.25 rfsrc aorsf 1.1 0.3 2.0 1.075856e-02
+## 5: 1826.25 ranger aorsf 1.1 0.3 1.9 4.825778e-03
+## 6: 1826.25 ranger rfsrc -0.1 -0.6 0.5 8.429772e-01
##
## NOTE: Values are multiplied by 100 and given in \%.
diff --git a/man/orsf_control_custom.Rd b/man/orsf_control_custom.Rd
index fe1e66dd..d2b4b1d7 100644
--- a/man/orsf_control_custom.Rd
+++ b/man/orsf_control_custom.Rd
@@ -70,7 +70,7 @@ fit_rando
## Average leaves per tree: 20
## Min observations in leaf: 5
## Min events in leaf: 1
-## OOB stat value: 0.83
+## OOB stat value: 0.84
## OOB stat type: Harrell's C-statistic
## Variable importance: anova
##
@@ -110,7 +110,7 @@ prediction accuracy based on out-of-bag predictions:
\if{html}{\out{}}\preformatted{library(riskRegression)
}\if{html}{\out{
}}
-\if{html}{\out{}}\preformatted{## riskRegression version 2023.09.08
+\if{html}{\out{
}}\preformatted{## riskRegression version 2023.03.22
}\if{html}{\out{
}}
\if{html}{\out{
}}\preformatted{library(survival)
@@ -135,15 +135,15 @@ The PCA ORSF does quite well! (higher IPA is better)
##
## model times Brier lower upper IPA
## 1: Null model 1788 20.479 18.090 22.868 0.000
-## 2: rando 1788 11.809 9.727 13.890 42.338
-## 3: pca 1788 12.967 10.983 14.950 36.683
+## 2: rando 1788 11.604 9.535 13.673 43.339
+## 3: pca 1788 12.870 10.872 14.869 37.154
##
## Results of model comparisons:
##
## times model reference delta.Brier lower upper p
-## 1: 1788 rando Null model -8.670 -10.843 -6.498 5.218847e-15
-## 2: 1788 pca Null model -7.512 -9.183 -5.842 1.226512e-18
-## 3: 1788 pca rando 1.158 0.305 2.011 7.810716e-03
+## 1: 1788 rando Null model -8.875 -11.063 -6.688 1.852437e-15
+## 2: 1788 pca Null model -7.609 -9.351 -5.866 1.143284e-17
+## 3: 1788 pca rando 1.267 0.449 2.084 2.381056e-03
##
## NOTE: Values are multiplied by 100 and given in \%.