penalizedS3: S3-wrapper for S4 function penalized

In riskRegression: Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks

S3-wrapper for S4 function penalized

Description

S3-wrapper for S4 function penalized

Usage

penalizedS3(formula, data, type = "elastic.net", lambda1, lambda2, fold, ...)

Arguments

formula	Communicated outcome and explanatory variables. See examples.
data	Data set in which formula is to be interpreted
type	String specifying the type of penalization. Should match one of the following values: "ridge", "lasso", "elastic.net".
lambda1	Lasso penalty
lambda2	ridge penalty
fold	passed to penalized::profL1
...	Arguments passed to penalized

Examples

library(prodlim)
## Not run: 
## too slow
if (require("penalized",quietly=TRUE)){
library(penalized)
set.seed(8)
d <- sampleData(200,outcome="binary")
newd <- sampleData(80,outcome="binary")
fitridge <- penalizedS3(Y~X1+X2+pen(7:8), data=d, type="ridge",
                standardize=TRUE, model="logistic",trace=FALSE)
fitlasso <- penalizedS3(Y~X1+X2+pen(7:8), data=d, type="lasso",
                standardize=TRUE, model="logistic",trace=FALSE)
# fitnet <- penalizedS3(Y~X1+X2+pen(7:8), data=d, type="elastic.net",
# standardize=TRUE, model="logistic",trace=FALSE)
predictRisk(fitridge,newdata=newd)
predictRisk(fitlasso,newdata=newd)
# predictRisk(fitnet,newdata=newd)
Score(list(fitridge),data=newd,formula=Y~1)
Score(list(fitridge),data=newd,formula=Y~1,split.method="bootcv",B=2)
data(nki70) ## S4 fit
fitS4 <- penalized(Surv(time, event), penalized = nki70[,8:77],
                 unpenalized = ~ER+Age+Diam+N+Grade, data = nki70,
                 lambda1 = 1)
fitS3 <- penalizedS3(Surv(time,event)~ER+Age+Diam+pen(8:77)+N+Grade,
                     data=nki70, lambda1=1)
## or
penS3 <- penalizedS3(Surv(time,event)~ER+pen(TSPYL5,Contig63649_RC)+pen(10:77)+N+Grade,
                     data=nki70, lambda1=1)
## also this works
penS3 <- penalizedS3(Surv(time,event)~ER+Age+pen(8:33)+Diam+pen(34:77)+N+Grade,
                    data=nki70, lambda1=1)
}
## End(Not run)

riskRegression documentation built on June 8, 2025, 11:33 a.m.