MEmixgbm: Mixture of Mixed Effect GBM

In nguforche/MEml: Mixed Effect Machine Learning

Description

Trains a Mixed Effect gradient boosted machine where the random effects are assumed to follow a mixture of gaussian distribution.

Usage

MEmixgbm(form, dat, groups = NULL, rand.vars = "1", para = NULL,
  tol = 1e-05, max.iter = 100, include.RE = FALSE, verbose = FALSE,
  maxdepth = 5, glmer.Control = glmerControl(optimizer = "bobyqa"),
  nAGQ = 0, likelihoodCheck = TRUE, K = 3, krange = 2:5,
  decay = 0.05, ...)

Arguments

groups	character name of the column containing the group identifier
rand.vars	random effect variables
para	named list of gbm training parameters
tol	convergence tolerance
max.iter	maximum number of iterations
include.RE	(logical) to include random effect Zb as predictor in gbm?
verbose	verbose for lme4
likelihoodCheck	(logical) to use log likelihood of glmer to check for convergence?
...	Further arguments passed to or from other methods.
X	data.frame with predictors
Y	binary response vector
gbm.dist	gbm loss function
lme.family	glmer control
type	of predictions of gbm to pass to lme4 as population estimates (these will be used as offset)

Value

An object of class MEgbm; a list with items

gbmfit	fitted gbm model
glmer.fit	fitted mixed effect logistic regression model
logLik	log likelihood of mixed effect logistic regression
random.effects	random effect parameter estimates
boost.form	gbm formula for fitted model
glmer.form	lmer4 formula
glmer.CI	estimates of mixed effect logistic regression with approximate confidence intervals on the logit scale. More accurate values can be obtained by bootstrap
fitted.probs	fitted probabilites for final model
fitted.class	fitted class labels for final model
train.perf	various performance measures for final model on training set
threshold	classification cut-off

Author(s)

Che Ngufor <[e-mail]>

References

Che Ngufor, Holly Van Houten, Brian S. Caffo , Nilay D. Shah, Rozalina G. McCoy Mixed Effect Machine Learning: a framework for predicting longitudinal change in hemoglobin A1c, in Journal of Biomedical Informatics, 2018

nguforche/MEml documentation built on April 20, 2020, 7:26 a.m.