spect_train {spect} | R Documentation |
Generates a trained caret model using the given primary binary classification. Optionally generates a stacked ensemble model if a list of base learners is supplied.
Description
Generates a trained caret model using the given primary binary classification. Optionally generates a stacked ensemble model if a list of base learners is supplied.
Usage
spect_train(
test_prop = 0.2,
censor_type = "half",
bin_slices = 10,
method = "repeatedcv",
resampling_number = 10,
kfold_repeats = 3,
model_algorithm,
base_learner_list = list(),
metric = "Kappa",
rng_seed = 42,
use_parallel = TRUE,
cores = 0,
modeling_data,
event_indicator_var,
survival_time_var,
obs_window
)
Arguments
test_prop |
optional proportion of the data set to reserve for testing |
censor_type |
optional method used to determine censorship in a given bin - may be "half", "prev" or "same". see createDiscreteDat for usage. |
bin_slices |
optional number of intervals to use for predictions. |
method |
optional caret parameter |
resampling_number |
optional for repeated cv |
kfold_repeats |
optional number of folds |
model_algorithm |
primary classification algorithm. Trains a stack-ensemble model if 'base_learner_list' is supplied, otherwise trains a simple classifier model. |
base_learner_list |
optional list of base learner algorithms |
metric |
optional metric for model calibration |
rng_seed |
optional random number generation seed for reproducibility |
use_parallel |
optioanlly make use of the caret multicore training cluster |
cores |
optioanl number of cores for multicore training. If zero, spect will attempt to make a good choice. Note: only relevant if 'use_parallel' is set to TRUE, otherwise this parameter is ignored. |
modeling_data |
This data set must have one column for time and one column for the event indicator. The remaining columns are treated as covariates for modeling. |
event_indicator_var |
The name of the column containing the event indicator (values in this column must be zero or one). |
survival_time_var |
The name of the column containing the time variable |
obs_window |
The last time to use for generating person-period data. Any event occurring after this time will be administratively censored. In general, choosing a time at or near the end of the max observed time will include most events. |
Value
A list containing all intermediate data sets created by 'spect_train', a trained caret model object, the following parameters passed to 'spect_train': 'obs_window', 'survival_time_var', 'event_indicator_var', 'base_learner_list', 'bin_slices', and the bounds of each interval generated by the training data set.
Author(s)
Stephen Abrams, stephen.abrams@louisville.edu