hdnom (version 5.0)

hdcox.enet: Elastic-Net Model Selection for High-Dimensional Cox Models

Description

Automatic elastic-net model selection for high-dimensional Cox models, evaluated by penalized partial-likelihood.

Usage

hdcox.enet(x, y, nfolds = 5L, alphas = seq(0.05, 0.95, 0.05),
  rule = c("lambda.min", "lambda.1se"), seed = 1001, parallel = FALSE)

Arguments

x

Data matrix.

y

Response matrix made by Surv.

nfolds

Fold numbers of cross-validation.

alphas

Alphas to tune in cv.glmnet.

rule

Model selection criterion, "lambda.min" or "lambda.1se". See cv.glmnet for details.

seed

A random seed for cross-validation fold division.

parallel

Logical. Enable parallel parameter tuning or not, default is FALSE. To enable parallel tuning, load the doParallel package and run registerDoParallel() with the number of CPU cores before calling this function.

Examples

# NOT RUN {
library("survival")
library("rms")

# Load imputed SMART data
data("smart")
x = as.matrix(smart[, -c(1, 2)])
time = smart$TEVENT
event = smart$EVENT
y = Surv(time, event)

# To enable parallel parameter tuning, first run:
# library("doParallel")
# registerDoParallel(detectCores())
# then set hdcox.enet(..., parallel = TRUE).

# Fit Cox model with elastic-net penalty
fit = hdcox.enet(x, y, nfolds = 3, alphas = c(0.3, 0.7),
                 rule = "lambda.1se", seed = 11)

# Prepare data for hdnom.nomogram
x.df = as.data.frame(x)
dd = datadist(x.df)
options(datadist = "dd")

# Generate hdnom.nomogram objects and plot nomogram
nom = hdnom.nomogram(
  fit$enet_model, model.type = "enet",
  x, time, event, x.df, pred.at = 365 * 2,
  funlabel = "2-Year Overall Survival Probability")

plot(nom)
# }