Out-of-fold predictions from a caret_list — oof_predictions.caret

Retrieve the out-of-fold predictions corresponding to the best hyperparameter setting of the trained caret models. These predictions come from the resampling process (not the final refit) and can optionally be aggregated across resamples to produce a single prediction per training instance.

Usage

# S3 method for class 'caret_list'
oof_predictions(
  object,
  drop_redundant_class = TRUE,
  aggregate_resamples = TRUE,
  intersection_only = TRUE,
  ...
)

Arguments

object: A caret_list object
drop_redundant_class: Logical, whether to exclude the first class level from prediction output. Default is TRUE.
aggregate_resamples: Logical, whether to aggregate resamples across folds. Default is TRUE.
intersection_only: Logical, whether to trim down the out-of-fold predictions to only the intersection of samples that are present across all models in the list (i.e., the intersection of training indices used during resampling). Default is TRUE.
...: Not used. Included for S3 compatibility.

Value

A data.table::data.table of out-of-fold predictions, with samples as rows and predictions as columns.

Examples

# Load pre-trained example caret_stack object
data(heart_failure_stack)

# Extract the caret_list object from the caret_stack
base_models <- heart_failure_stack$caret_list

oof_predictions(base_models)
#>          cells     holter       mrna     proteins
#>          <num>      <num>      <num>        <num>
#>  1: 0.39487649 0.36909270 0.48528211 9.997811e-01
#>  2: 0.30042999 0.19092831 0.25769494 9.373699e-02
#>  3: 0.30951676 0.19776753 0.22497670 9.997515e-01
#>  4: 0.16856438 0.25586004 0.38829387 6.776068e-01
#>  5: 0.41325201 0.26108068 0.69638737 2.019989e-03
#>  6: 0.27731047 0.32077126 0.11945148 2.088767e-01
#>  7: 0.22868693 0.72770916 0.16006647 5.968584e-02
#>  8: 0.19812130 0.22315924 0.29885868 7.371038e-01
#>  9: 0.28245069 0.20305767 0.43981899 9.565369e-01
#> 10: 0.32602141 0.26537554 0.37696868 1.859125e-01
#> 11: 0.37483007 0.33358529 0.33333452 1.326082e-01
#> 12: 0.08630381 0.23597303 0.05027060 7.750342e-01
#> 13: 0.23705848 0.51748407 0.16169914 3.635292e-01
#> 14: 0.24890462 0.24752704 0.31577410 2.528748e-01
#> 15: 0.16485817 0.19310453 0.03896005 2.168373e-05
#> 16: 0.29836034 0.12731196 0.42092830 2.089819e-04
#> 17: 0.25248249 0.13824433 0.37510932 1.357990e-04
#> 18: 0.22111569 0.15846676 0.15097042 2.080887e-03
#> 19: 0.11506052 0.20298222 0.03965684 3.071741e-05
#> 20: 0.16720343 0.03408682 0.10517658 6.491938e-07
#> 21: 0.34169763 0.17087990 0.37915054 1.102010e-04
#> 22: 0.28499000 0.09697545 0.15869489 1.040837e-02
#> 23: 0.28998987 0.10841931 0.14548990 3.764977e-02
#> 24: 0.17026367 0.21782593 0.15414731 2.325022e-02
#> 25: 0.26097078 0.16607275 0.21527392 7.759198e-03
#> 26: 0.11557337 0.25547405 0.06512819 1.321670e-03
#> 27: 0.16806976 0.18684416 0.14001222 2.881488e-02
#> 28: 0.16140874 0.18343853 0.07281529 2.992745e-05
#> 29: 0.50363587 0.23432261 0.37152920 4.614976e-02
#> 30: 0.19335680 0.12323529 0.16026750 9.997972e-01
#> 31: 0.17046073 0.34741307 0.02591532 6.183194e-04
#> 32: 0.20395259 0.37475152 0.12137290 8.519739e-07
#> 33: 0.13475327 0.10556385 0.19182175 6.580083e-02
#> 34: 0.15205573 0.20320057 0.19483368 1.028951e-05
#> 35: 0.14307066 0.27616614 0.08411645 3.921382e-02
#> 36: 0.15406917 0.19031075 0.08721875 5.018993e-04
#> 37: 0.21878420 0.25251581 0.13351247 1.677715e-01
#> 38: 0.28762801 0.18878866 0.48419982 3.165184e-02
#> 39: 0.15848359 0.14055961 0.23861337 1.354355e-01
#> 40: 0.24134243 0.41930328 0.07057693 2.875275e-01
#> 41: 0.15603955 0.26941514 0.30355477 4.717852e-05
#> 42: 0.20344174 0.08548813 0.08988793 3.211487e-04
#> 43: 0.17211102 0.22394581 0.02238737 2.896243e-03
#> 44: 0.33876761 0.28533890 0.24602523 2.438060e-01
#> 45: 0.12614383 0.28878973 0.10738733 9.614251e-01
#> 46: 0.19607071 0.28419276 0.25867224 2.755540e-02
#> 47: 0.21257159 0.10444129 0.05393685 6.689628e-03
#> 48: 0.07923487 0.13012582 0.04952718 4.846500e-05
#> 49: 0.14327767 0.25349360 0.17677482 1.888111e-02
#> 50: 0.16109377 0.23186888 0.07240264 8.267249e-02
#> 51: 0.26002939 0.14337773 0.51303076 3.782414e-09
#> 52: 0.14196009 0.14765268 0.14732178 9.418949e-05
#> 53: 0.31849286 0.11478657 0.35674453 1.960297e-05
#> 54: 0.21928963 0.24589906 0.20535335 1.495299e-03
#> 55: 0.15713077 0.23479474 0.16622478 1.901394e-01
#> 56: 0.16761851 0.23202842 0.13296251 2.630405e-03
#> 57: 0.23673749 0.08269332 0.15435143 4.290682e-04
#> 58: 0.14136814 0.08577594 0.06301069 5.692005e-06
#>          cells     holter       mrna     proteins
#>          <num>      <num>      <num>        <num>