riskRegression (version 1.3.7)

penalizedS3: S3-wrapper for S4 function penalized

Description

S3-wrapper for S4 function penalized

Usage

penalizedS3(formula, data, type = "ridge", ...)

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".

...

Arguments passed to penalized

Examples

## too slow
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,splitMethod="bootcv",B=2)

 data(nki70) ## S4 fit pen <- penalized(Surv(time, event),
penalized = nki70[,8:77], unpenalized = ~ER+Age+Diam+N+Grade, data
= nki70, lambda1 = 1) penS3 <-
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)