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tests/testthat/_snaps/summary.md
In predictNMB: Evaluate Clinical Prediction Models by Net Monetary Benefit
predictNMBsim - summary (default) works
# A tibble: 8 x 3
method median `95% CI`
<chr> <dbl> <chr>
1 all -1.19 -1.2 to -1.2
2 cost minimising -0.39 -0.5 to -0.4
3 index of union -0.61 -0.7 to -0.6
4 none -0.39 -0.4 to -0.4
5 prod sens spec -0.6 -0.7 to -0.6
6 roc01 -0.6 -0.7 to -0.6
7 value optimising -0.39 -0.4 to -0.4
8 youden -0.59 -0.7 to -0.5
predictNMBsim - summary (rename_vector) works
# A tibble: 8 x 3
method median `95% CI`
<chr> <dbl> <chr>
1 Treat All -1.19 -1.2 to -1.2
2 Treat None -0.39 -0.4 to -0.4
3 cost minimising -0.39 -0.5 to -0.4
4 index of union -0.61 -0.7 to -0.6
5 prod sens spec -0.6 -0.7 to -0.6
6 roc01 -0.6 -0.7 to -0.6
7 value optimising -0.39 -0.4 to -0.4
8 youden -0.59 -0.7 to -0.5
predictNMBsim - summary (what) works
# A tibble: 8 x 3
method median `95% CI`
<chr> <dbl> <chr>
1 all 0 0 to 0
2 cost minimising 0.5 0.5 to 0.5
3 index of union 0.12 0.1 to 0.2
4 none 1 1 to 1
5 prod sens spec 0.12 0.1 to 0.2
6 roc01 0.12 0.1 to 0.2
7 value optimising 0.54 0.4 to 1
8 youden 0.13 0.1 to 0.2
# A tibble: 7 x 3
method median `95% CI`
<chr> <dbl> <chr>
1 cost minimising 0.8 0.8 to 0.8
2 index of union 0.6 0.5 to 0.6
3 none 0.81 0.8 to 0.8
4 prod sens spec 0.59 0.5 to 0.6
5 roc01 0.6 0.5 to 0.6
6 value optimising 0.8 0.8 to 0.8
7 youden 0.6 0.5 to 0.7
predictNMBsim - summary (agg_functions) works
# A tibble: 8 x 4
method mean min max
<chr> <dbl> <dbl> <dbl>
1 all -1.20 -1.22 -1.18
2 cost minimising -0.395 -0.464 -0.356
3 index of union -0.616 -0.694 -0.55
4 none -0.391 -0.436 -0.356
5 prod sens spec -0.624 -0.71 -0.55
6 roc01 -0.619 -0.699 -0.55
7 value optimising -0.394 -0.445 -0.356
8 youden -0.593 -0.71 -0.475
predictNMBscreen - summary works
sim_auc fx_nmb_training all_median all_95% CI none_median none_95% CI
1 0.7 f1 -1.2 -1.2 to -1.2 -0.4 -0.5 to -0.3
2 0.7 f2 -1.2 -1.2 to -1.2 -0.4 -0.5 to -0.3
3 0.8 f1 -1.2 -1.2 to -1.2 -0.4 -0.5 to -0.3
4 0.8 f2 -1.2 -1.2 to -1.2 -0.4 -0.5 to -0.3
5 0.9 f1 -1.2 -1.2 to -1.2 -0.4 -0.5 to -0.3
6 0.9 f2 -1.2 -1.2 to -1.2 -0.4 -0.5 to -0.3
value optimising_median value optimising_95% CI youden_median youden_95% CI
1 -0.40 -0.5 to -0.3 -0.64 -0.9 to -0.4
2 -0.40 -0.5 to -0.3 -0.64 -0.9 to -0.4
3 -0.40 -0.5 to -0.3 -0.56 -0.8 to -0.4
4 -0.40 -0.5 to -0.3 -0.56 -0.8 to -0.4
5 -0.38 -0.5 to -0.3 -0.47 -0.7 to -0.4
6 -0.38 -0.4 to -0.3 -0.47 -0.6 to -0.4
cost minimising_median cost minimising_95% CI prod sens spec_median
1 -0.40 -0.5 to -0.3 -0.64
2 -0.40 -0.5 to -0.3 -0.63
3 -0.40 -0.5 to -0.3 -0.55
4 -0.40 -0.5 to -0.3 -0.56
5 -0.38 -0.5 to -0.3 -0.47
6 -0.38 -0.4 to -0.3 -0.47
prod sens spec_95% CI roc01_median roc01_95% CI index of union_median
1 -0.8 to -0.5 -0.64 -0.8 to -0.5 -0.64
2 -0.8 to -0.5 -0.63 -0.8 to -0.5 -0.64
3 -0.7 to -0.4 -0.55 -0.7 to -0.4 -0.55
4 -0.7 to -0.4 -0.56 -0.7 to -0.4 -0.56
5 -0.6 to -0.4 -0.47 -0.6 to -0.4 -0.47
6 -0.6 to -0.4 -0.46 -0.6 to -0.4 -0.46
index of union_95% CI
1 -0.8 to -0.5
2 -0.8 to -0.5
3 -0.7 to -0.4
4 -0.7 to -0.5
5 -0.6 to -0.4
6 -0.6 to -0.4
sim_auc fx_nmb_training Treat All_mean Treat All_min Treat All_max
1 0.7 f1 -1.199592 -1.268 -1.130
2 0.7 f2 -1.198992 -1.256 -1.144
3 0.8 f1 -1.200352 -1.264 -1.150
4 0.8 f2 -1.199896 -1.256 -1.142
5 0.9 f1 -1.199988 -1.260 -1.156
6 0.9 f2 -1.200256 -1.254 -1.142
Treat None_mean Treat None_min Treat None_max value optimising_mean
1 -0.399184 -0.536 -0.260 -0.408276
2 -0.397984 -0.512 -0.288 -0.408688
3 -0.400704 -0.528 -0.300 -0.400800
4 -0.399792 -0.512 -0.284 -0.400154
5 -0.399976 -0.520 -0.312 -0.382228
6 -0.400512 -0.508 -0.284 -0.382186
value optimising_min value optimising_max youden_mean youden_min youden_max
1 -1.245 -0.264 -0.650752 -0.975 -0.371
2 -1.225 -0.296 -0.645796 -1.003 -0.373
3 -0.518 -0.298 -0.567532 -0.887 -0.347
4 -0.507 -0.301 -0.572142 -0.933 -0.351
5 -0.502 -0.298 -0.480682 -0.807 -0.328
6 -0.475 -0.278 -0.474018 -0.811 -0.308
cost minimising threshold_mean cost minimising threshold_min
1 -0.400036 -0.539
2 -0.398764 -0.512
3 -0.398862 -0.518
4 -0.398204 -0.500
5 -0.380126 -0.492
6 -0.379994 -0.482
cost minimising threshold_max prod sens spec_mean prod sens spec_min
1 -0.264 -0.641890 -0.904
2 -0.289 -0.630782 -0.874
3 -0.299 -0.558626 -0.807
4 -0.300 -0.566424 -0.815
5 -0.294 -0.474916 -0.763
6 -0.281 -0.470020 -0.701
prod sens spec_max roc01_mean roc01_min roc01_max index of union_mean
1 -0.390 -0.638180 -0.903 -0.439 -0.640204
2 -0.373 -0.632544 -0.874 -0.433 -0.638788
3 -0.347 -0.554978 -0.776 -0.385 -0.558036
4 -0.351 -0.562972 -0.808 -0.351 -0.565276
5 -0.333 -0.470748 -0.697 -0.330 -0.470538
6 -0.308 -0.463606 -0.655 -0.327 -0.465722
index of union_min index of union_max
1 -0.836 -0.479
2 -0.838 -0.462
3 -0.727 -0.386
4 -0.805 -0.406
5 -0.663 -0.330
6 -0.691 -0.312
n_sims n_valid fx_nmb_training fx_nmb_evaluation sample_size sim_auc
1 500 1000 f1 unnamed-nmb-function-1 189 0.7
2 500 1000 f2 unnamed-nmb-function-1 189 0.7
3 500 1000 f1 unnamed-nmb-function-1 139 0.8
4 500 1000 f2 unnamed-nmb-function-1 139 0.8
5 500 1000 f1 unnamed-nmb-function-1 139 0.9
6 500 1000 f2 unnamed-nmb-function-1 139 0.9
event_rate min_events meet_min_events .sim_id all_median all_95% CI
1 0.1 19 TRUE 1 -1.2 -1.2 to -1.2
2 0.1 19 TRUE 2 -1.2 -1.2 to -1.2
3 0.1 14 TRUE 3 -1.2 -1.2 to -1.2
4 0.1 14 TRUE 4 -1.2 -1.2 to -1.2
5 0.1 14 TRUE 5 -1.2 -1.2 to -1.2
6 0.1 14 TRUE 6 -1.2 -1.2 to -1.2
none_median none_95% CI value optimising_median value optimising_95% CI
1 -0.4 -0.5 to -0.3 -0.40 -0.5 to -0.3
2 -0.4 -0.5 to -0.3 -0.40 -0.5 to -0.3
3 -0.4 -0.5 to -0.3 -0.40 -0.5 to -0.3
4 -0.4 -0.5 to -0.3 -0.40 -0.5 to -0.3
5 -0.4 -0.5 to -0.3 -0.38 -0.5 to -0.3
6 -0.4 -0.5 to -0.3 -0.38 -0.4 to -0.3
youden_median youden_95% CI cost minimising_median cost minimising_95% CI
1 -0.64 -0.9 to -0.4 -0.40 -0.5 to -0.3
2 -0.64 -0.9 to -0.4 -0.40 -0.5 to -0.3
3 -0.56 -0.8 to -0.4 -0.40 -0.5 to -0.3
4 -0.56 -0.8 to -0.4 -0.40 -0.5 to -0.3
5 -0.47 -0.7 to -0.4 -0.38 -0.5 to -0.3
6 -0.47 -0.6 to -0.4 -0.38 -0.4 to -0.3
prod sens spec_median prod sens spec_95% CI roc01_median roc01_95% CI
1 -0.64 -0.8 to -0.5 -0.64 -0.8 to -0.5
2 -0.63 -0.8 to -0.5 -0.63 -0.8 to -0.5
3 -0.55 -0.7 to -0.4 -0.55 -0.7 to -0.4
4 -0.56 -0.7 to -0.4 -0.56 -0.7 to -0.4
5 -0.47 -0.6 to -0.4 -0.47 -0.6 to -0.4
6 -0.47 -0.6 to -0.4 -0.46 -0.6 to -0.4
index of union_median index of union_95% CI
1 -0.64 -0.8 to -0.5
2 -0.64 -0.8 to -0.5
3 -0.55 -0.7 to -0.4
4 -0.56 -0.7 to -0.5
5 -0.47 -0.6 to -0.4
6 -0.46 -0.6 to -0.4
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predictNMB documentation built on June 7, 2023, 6:31 p.m.
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predictNMBsim - summary (default) works
# A tibble: 8 x 3
method median `95% CI`
<chr> <dbl> <chr>
1 all -1.19 -1.2 to -1.2
2 cost minimising -0.39 -0.5 to -0.4
3 index of union -0.61 -0.7 to -0.6
4 none -0.39 -0.4 to -0.4
5 prod sens spec -0.6 -0.7 to -0.6
6 roc01 -0.6 -0.7 to -0.6
7 value optimising -0.39 -0.4 to -0.4
8 youden -0.59 -0.7 to -0.5
predictNMBsim - summary (rename_vector) works
# A tibble: 8 x 3
method median `95% CI`
<chr> <dbl> <chr>
1 Treat All -1.19 -1.2 to -1.2
2 Treat None -0.39 -0.4 to -0.4
3 cost minimising -0.39 -0.5 to -0.4
4 index of union -0.61 -0.7 to -0.6
5 prod sens spec -0.6 -0.7 to -0.6
6 roc01 -0.6 -0.7 to -0.6
7 value optimising -0.39 -0.4 to -0.4
8 youden -0.59 -0.7 to -0.5
predictNMBsim - summary (what) works
# A tibble: 8 x 3
method median `95% CI`
<chr> <dbl> <chr>
1 all 0 0 to 0
2 cost minimising 0.5 0.5 to 0.5
3 index of union 0.12 0.1 to 0.2
4 none 1 1 to 1
5 prod sens spec 0.12 0.1 to 0.2
6 roc01 0.12 0.1 to 0.2
7 value optimising 0.54 0.4 to 1
8 youden 0.13 0.1 to 0.2
# A tibble: 7 x 3
method median `95% CI`
<chr> <dbl> <chr>
1 cost minimising 0.8 0.8 to 0.8
2 index of union 0.6 0.5 to 0.6
3 none 0.81 0.8 to 0.8
4 prod sens spec 0.59 0.5 to 0.6
5 roc01 0.6 0.5 to 0.6
6 value optimising 0.8 0.8 to 0.8
7 youden 0.6 0.5 to 0.7
predictNMBsim - summary (agg_functions) works
# A tibble: 8 x 4
method mean min max
<chr> <dbl> <dbl> <dbl>
1 all -1.20 -1.22 -1.18
2 cost minimising -0.395 -0.464 -0.356
3 index of union -0.616 -0.694 -0.55
4 none -0.391 -0.436 -0.356
5 prod sens spec -0.624 -0.71 -0.55
6 roc01 -0.619 -0.699 -0.55
7 value optimising -0.394 -0.445 -0.356
8 youden -0.593 -0.71 -0.475
predictNMBscreen - summary works
sim_auc fx_nmb_training all_median all_95% CI none_median none_95% CI
1 0.7 f1 -1.2 -1.2 to -1.2 -0.4 -0.5 to -0.3
2 0.7 f2 -1.2 -1.2 to -1.2 -0.4 -0.5 to -0.3
3 0.8 f1 -1.2 -1.2 to -1.2 -0.4 -0.5 to -0.3
4 0.8 f2 -1.2 -1.2 to -1.2 -0.4 -0.5 to -0.3
5 0.9 f1 -1.2 -1.2 to -1.2 -0.4 -0.5 to -0.3
6 0.9 f2 -1.2 -1.2 to -1.2 -0.4 -0.5 to -0.3
value optimising_median value optimising_95% CI youden_median youden_95% CI
1 -0.40 -0.5 to -0.3 -0.64 -0.9 to -0.4
2 -0.40 -0.5 to -0.3 -0.64 -0.9 to -0.4
3 -0.40 -0.5 to -0.3 -0.56 -0.8 to -0.4
4 -0.40 -0.5 to -0.3 -0.56 -0.8 to -0.4
5 -0.38 -0.5 to -0.3 -0.47 -0.7 to -0.4
6 -0.38 -0.4 to -0.3 -0.47 -0.6 to -0.4
cost minimising_median cost minimising_95% CI prod sens spec_median
1 -0.40 -0.5 to -0.3 -0.64
2 -0.40 -0.5 to -0.3 -0.63
3 -0.40 -0.5 to -0.3 -0.55
4 -0.40 -0.5 to -0.3 -0.56
5 -0.38 -0.5 to -0.3 -0.47
6 -0.38 -0.4 to -0.3 -0.47
prod sens spec_95% CI roc01_median roc01_95% CI index of union_median
1 -0.8 to -0.5 -0.64 -0.8 to -0.5 -0.64
2 -0.8 to -0.5 -0.63 -0.8 to -0.5 -0.64
3 -0.7 to -0.4 -0.55 -0.7 to -0.4 -0.55
4 -0.7 to -0.4 -0.56 -0.7 to -0.4 -0.56
5 -0.6 to -0.4 -0.47 -0.6 to -0.4 -0.47
6 -0.6 to -0.4 -0.46 -0.6 to -0.4 -0.46
index of union_95% CI
1 -0.8 to -0.5
2 -0.8 to -0.5
3 -0.7 to -0.4
4 -0.7 to -0.5
5 -0.6 to -0.4
6 -0.6 to -0.4
sim_auc fx_nmb_training Treat All_mean Treat All_min Treat All_max
1 0.7 f1 -1.199592 -1.268 -1.130
2 0.7 f2 -1.198992 -1.256 -1.144
3 0.8 f1 -1.200352 -1.264 -1.150
4 0.8 f2 -1.199896 -1.256 -1.142
5 0.9 f1 -1.199988 -1.260 -1.156
6 0.9 f2 -1.200256 -1.254 -1.142
Treat None_mean Treat None_min Treat None_max value optimising_mean
1 -0.399184 -0.536 -0.260 -0.408276
2 -0.397984 -0.512 -0.288 -0.408688
3 -0.400704 -0.528 -0.300 -0.400800
4 -0.399792 -0.512 -0.284 -0.400154
5 -0.399976 -0.520 -0.312 -0.382228
6 -0.400512 -0.508 -0.284 -0.382186
value optimising_min value optimising_max youden_mean youden_min youden_max
1 -1.245 -0.264 -0.650752 -0.975 -0.371
2 -1.225 -0.296 -0.645796 -1.003 -0.373
3 -0.518 -0.298 -0.567532 -0.887 -0.347
4 -0.507 -0.301 -0.572142 -0.933 -0.351
5 -0.502 -0.298 -0.480682 -0.807 -0.328
6 -0.475 -0.278 -0.474018 -0.811 -0.308
cost minimising threshold_mean cost minimising threshold_min
1 -0.400036 -0.539
2 -0.398764 -0.512
3 -0.398862 -0.518
4 -0.398204 -0.500
5 -0.380126 -0.492
6 -0.379994 -0.482
cost minimising threshold_max prod sens spec_mean prod sens spec_min
1 -0.264 -0.641890 -0.904
2 -0.289 -0.630782 -0.874
3 -0.299 -0.558626 -0.807
4 -0.300 -0.566424 -0.815
5 -0.294 -0.474916 -0.763
6 -0.281 -0.470020 -0.701
prod sens spec_max roc01_mean roc01_min roc01_max index of union_mean
1 -0.390 -0.638180 -0.903 -0.439 -0.640204
2 -0.373 -0.632544 -0.874 -0.433 -0.638788
3 -0.347 -0.554978 -0.776 -0.385 -0.558036
4 -0.351 -0.562972 -0.808 -0.351 -0.565276
5 -0.333 -0.470748 -0.697 -0.330 -0.470538
6 -0.308 -0.463606 -0.655 -0.327 -0.465722
index of union_min index of union_max
1 -0.836 -0.479
2 -0.838 -0.462
3 -0.727 -0.386
4 -0.805 -0.406
5 -0.663 -0.330
6 -0.691 -0.312
n_sims n_valid fx_nmb_training fx_nmb_evaluation sample_size sim_auc
1 500 1000 f1 unnamed-nmb-function-1 189 0.7
2 500 1000 f2 unnamed-nmb-function-1 189 0.7
3 500 1000 f1 unnamed-nmb-function-1 139 0.8
4 500 1000 f2 unnamed-nmb-function-1 139 0.8
5 500 1000 f1 unnamed-nmb-function-1 139 0.9
6 500 1000 f2 unnamed-nmb-function-1 139 0.9
event_rate min_events meet_min_events .sim_id all_median all_95% CI
1 0.1 19 TRUE 1 -1.2 -1.2 to -1.2
2 0.1 19 TRUE 2 -1.2 -1.2 to -1.2
3 0.1 14 TRUE 3 -1.2 -1.2 to -1.2
4 0.1 14 TRUE 4 -1.2 -1.2 to -1.2
5 0.1 14 TRUE 5 -1.2 -1.2 to -1.2
6 0.1 14 TRUE 6 -1.2 -1.2 to -1.2
none_median none_95% CI value optimising_median value optimising_95% CI
1 -0.4 -0.5 to -0.3 -0.40 -0.5 to -0.3
2 -0.4 -0.5 to -0.3 -0.40 -0.5 to -0.3
3 -0.4 -0.5 to -0.3 -0.40 -0.5 to -0.3
4 -0.4 -0.5 to -0.3 -0.40 -0.5 to -0.3
5 -0.4 -0.5 to -0.3 -0.38 -0.5 to -0.3
6 -0.4 -0.5 to -0.3 -0.38 -0.4 to -0.3
youden_median youden_95% CI cost minimising_median cost minimising_95% CI
1 -0.64 -0.9 to -0.4 -0.40 -0.5 to -0.3
2 -0.64 -0.9 to -0.4 -0.40 -0.5 to -0.3
3 -0.56 -0.8 to -0.4 -0.40 -0.5 to -0.3
4 -0.56 -0.8 to -0.4 -0.40 -0.5 to -0.3
5 -0.47 -0.7 to -0.4 -0.38 -0.5 to -0.3
6 -0.47 -0.6 to -0.4 -0.38 -0.4 to -0.3
prod sens spec_median prod sens spec_95% CI roc01_median roc01_95% CI
1 -0.64 -0.8 to -0.5 -0.64 -0.8 to -0.5
2 -0.63 -0.8 to -0.5 -0.63 -0.8 to -0.5
3 -0.55 -0.7 to -0.4 -0.55 -0.7 to -0.4
4 -0.56 -0.7 to -0.4 -0.56 -0.7 to -0.4
5 -0.47 -0.6 to -0.4 -0.47 -0.6 to -0.4
6 -0.47 -0.6 to -0.4 -0.46 -0.6 to -0.4
index of union_median index of union_95% CI
1 -0.64 -0.8 to -0.5
2 -0.64 -0.8 to -0.5
3 -0.55 -0.7 to -0.4
4 -0.56 -0.7 to -0.5
5 -0.47 -0.6 to -0.4
6 -0.46 -0.6 to -0.4
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