PermTest: Permutation test for lm, lme and glm (binomial and Poisson)...

In pgirmess: Spatial Analysis and Data Mining for Field Ecologists

Permutation test for lm, lme and glm (binomial and Poisson) objects

Description

Permutation test for lm, lme and glm (binomial and Poisson) objects

Usage

    PermTest(obj, B=1000,...)

    ## S3 method for class 'lm'
PermTest(obj, B=1000,...)
    ## S3 method for class 'lme'
PermTest(obj, B=1000,...)
    ## S3 method for class 'glm'
PermTest(obj, B=1000,...)

Arguments

obj	an object of class lm, lme, or glm
B	number of permutations, default = 1000
...	used to pass other arguments

Details

For glm, when the response is a two-column matrix with the columns giving the numbers of successes and failures, PermTest.glm uses permcont(); PermTest.lme requires the library nlme.

Value

A list object of class PermTest including:

p.value	the p value obtained
B	the number of permutations
call	the call

Warning

This generic function is implemented in R language, thus can be quite slow.

Note

The implementation of PermTest.lme has been helped by Renaud Lancelot

Examples

if(require(MASS)){
mylm<-lm(Postwt~Prewt,data=anorexia)
PermTest(mylm,B=250)


## Dobson (1990) Page 93: Randomized Controlled Trial :
    counts <- c(18,17,15,20,10,20,25,13,12)
    outcome <- gl(3,1,9)
    treatment <- gl(3,3)
    glm.D93 <- glm(counts ~ outcome + treatment, family=poisson)
    PermTest(glm.D93,B=100)
    }

if(require(nlme)){
fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)
PermTest(fm2,B=100)
}

  

pgirmess documentation built on April 8, 2023, 1:12 a.m.