R: Compute values of likelihood ratio test from supervised...

superpc.lrtest.curv {superpc} | R Documentation

## Compute values of likelihood ratio test from supervised principal components fit

### Description

Compute values of likelihood ratio test from supervised principal components fit

### Usage

    superpc.lrtest.curv(object, data, newdata, n.components = 1, threshold = NULL, n.threshold = 20)

### Arguments

`object` | Object returned by superpc.train
`data` | List of training data, of form described in superpc.train documentation
`newdata` | List of test data; same form as training data
`n.components` | Number of principal components to compute. Should be 1,2 or 3.
`threshold` | Set of thresholds for scoresL default is n.threshold values equally spaced over the range of the feature scores
`n.threshold` | Number of thresholds to use; default 20. Should be 1,2 or 3.

### Value

If it is a LIST, use

`lrtest` | Values of likelihood ratio test statistic
`comp2` | Description of 'comp2'
`threshold` | Thresholds used
`num.features` | Number of features exceeding threshold
`type` | Type of outcome variable
`call` | calling sequence

### Author(s)

Eric Bair and Robert Tibshirani

### References

~put references to the literature/web site here ~

### Examples

    set.seed(332)
    #generate some data

    x<-matrix(rnorm(1000*20),ncol=20)
    y<-10+svd(x[1:30,])$v[,1]+ .1*rnorm(20)
    ytest<-10+svd(x[1:30,])$v[,1]+ .1*rnorm(20)
    censoring.status<- sample(c(rep(1,17),rep(0,3)))
    censoring.status.test<- sample(c(rep(1,17),rep(0,3)))

    featurenames <- paste("feature",as.character(1:1000),sep="")
    data<-list(x=x,y=y, censoring.status=censoring.status, featurenames=featurenames)
    data.test<-list(x=x,y=ytest, censoring.status=censoring.status.test, featurenames= featurenames)

    a<- superpc.train(data, type="survival")

    fit<- superpc.predict(a, data, data.test, threshold=1.0, n.components=1, prediction.type="continuous")

    aa<- superpc.lrtest.curv(a, data, data.test)
    superpc.plot.lrtest(aa)

[Package superpc version 1.09 Index]