pamr.predict {pamr} | R Documentation

## A function producing predicted information, from a nearest shrunken centroid fit.

### Description

A function producing predicted information, from a nearest shrunken centroid fit

### Usage

    pamr.predict(fit, newx, threshold, type= c("class", "posterior", "centroid", "nonzero"), prior = object$prior, threshold.scale = object$
            threshold.scale)

### Arguments

`fit` | The result of a call to pamr.train
`newx` | Input (feature) matrix for which predictions are desired
`threshold` | The desired threshold value
`type` | Type of prediction desired: class predictions, posterior probabilities, (unshrunken) class centroids, vector of genes surviving the threshold
`prior` | Prior probabilities for each class. Default is that specified in "fit"
`threshold.scale` | Additional scaling factors to be applied to the thresholds. Vector of length equal to the number of classes. Default is that specified in "fit".

### Details

`pamr.predict` Give a cross-tabulation of true versus predicted classes for the fit returned by pamr.train or pamr.cv, at the specified threshold

### Author(s)

Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan, and Gilbert Chu

### References

### Examples

    set.seed(120)
    x <- matrix(rnorm(1000*20),ncol=20)
    y <- sample(c(1:4),size=20,replace=TRUE)
    mydata <- list(x=x,y=y)
    mytrain <-   pamr.train(mydata)
    mycv <- pamr.cv(mytrain,mydata)
    pamr.predict(mytrain, mydata$x , threshold=1)

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