cv.glmtlp {glmtlp}

Cross-validation for glmtlp

Description

Performs k-fold cross-validation for l0, l1, or TLP-penalized regression models over a grid of values for the regularization parameter lambda (if penalty="l0") or kappa (if penalty="l0").

Usage

cv.glmtlp(X, y, ..., seed = NULL, nfolds = 10, obs.fold = NULL, ncores = 1)

Arguments

X

input matrix, of dimension nobs x nvars, as in glmtlp.

y

response, of length nobs, as in glmtlp.

...

Other arguments that can be passed to glmtlp.

seed

the seed for reproduction purposes

nfolds

number of folds; default is 10. The smallest value allowable is nfolds=3

obs.fold

an optional vector of values between 1 and nfolds identifying what fold each observation is in. If supplied, nfolds can be missing.

ncores

number of cores utilized; default is 1. If greater than 1, then doParallel::foreach will be used to fit each fold; if equal to 1, then for loop will be used to fit each fold. Users don't have to register parallel clusters outside.

Details

The function calls glmtlp nfolds+1 times; the first call to get the lambda or kappa sequence, and then the rest to compute the fit with each of the folds omitted. The cross-validation error is based on deviance (check here for more details). The error is accumulated over the folds, and the average error and standard deviation is computed.

When family = "binomial", the fold assignment (if not provided by the user) is generated in a stratified manner, where the ratio of 0/1 outcomes are the same for each fold.

Value

an object of class "cv.glmtlp" is returned, which is a list with the ingredients of the cross-validation fit.

call

the function call

cv.mean

The mean cross-validated error - a vector of length length(kappa) if penalty = "l0" and length{lambda} otherwise.

cv.se

estimate of standard error of cv.mean.

fit

a fitted glmtlp object for the full data.

idx.min

the index of the lambda or kappa sequence that corresponding to the smallest cv mean error.

kappa

the values of kappa used in the fits, available when penalty = 'l0'.

kappa.min

the value of kappa that gives the minimum cv.mean, available when penalty = 'l0'.

lambda

the values of lambda used in the fits.

lambda.min

value of lambda that gives minimum cv.mean, available when penalty is 'l1' or 'tlp'.

null.dev

null deviance of the model.

obs.fold

the fold id for each observation used in the CV.

Author(s)

Chunlin Li, Yu Yang, Chong Wu
Maintainer: Yu Yang [e-mail]

References

Shen, X., Pan, W., & Zhu, Y. (2012). Likelihood-based selection and sharp parameter estimation. Journal of the American Statistical Association, 107(497), 223-232.
Shen, X., Pan, W., Zhu, Y., & Zhou, H. (2013). On constrained and regularized high-dimensional regression. Annals of the Institute of Statistical Mathematics, 65(5), 807-832.
Li, C., Shen, X., & Pan, W. (2021). Inference for a Large Directed Graphical Model with Interventions. arXiv preprint arXiv:2110.03805.
Yang, Y., & Zou, H. (2014). A coordinate majorization descent algorithm for l1 penalized learning. Journal of Statistical Computation and Simulation, 84(1), 84-95.
Two R package Github: ncvreg and glmnet.

See Also

glmtlp and plot, predict, and coef methods for "cv.glmtlp" objects.

Examples

# Gaussian
X <- matrix(rnorm(100 * 20), 100, 20)
y <- rnorm(100)
cv.fit <- cv.glmtlp(X, y, family = "gaussian", penalty = "l1", seed=2021)

# Binomial
X <- matrix(rnorm(100 * 20), 100, 20)
y <- sample(c(0,1), 100, replace = TRUE)
cv.fit <- cv.glmtlp(X, y, family = "binomial", penalty = "l1", seed=2021)