pamr.indeterminate: A function that takes estimate class probabilities and...

In pamr: Pam: Prediction Analysis for Microarrays

Description

A function that takes estimate class probabilities and produces a class prediction or indeterminate prediction

Usage

pamr.indeterminate(prob, mingap=0) 

Arguments

prob	Estimated class probabilities, from pamr.predict with type="posterior")
mingap	Minimum difference between highest and second highest probability. If difference is < mingap, prediction is set to indeterminate (NA)

Author(s)

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

Examples

suppressWarnings(RNGversion("3.5.0"))
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)
prob<- pamr.predict(mytrain, mydata$x , threshold=1, type="posterior")
pamr.indeterminate(prob,mingap=.75)

Example output

Loading required package: cluster
Loading required package: survival
123456789101112131415161718192021222324252627282930 [1] 4    3    4    2    1    <NA> 3    <NA> 3    3    4    <NA> <NA> 4    <NA>
[16] <NA> 4    1    <NA> 1   
Levels: 1 2 3 4

pamr documentation built on May 2, 2019, 12:35 p.m.