Re: [R] Different output from lm() and lmPerm lmp() if categorical variables are included in the analysis

RTFM!!! :-) The help explicitly says The default contrasts are set internally to (contr.sum, contr.poly) . Set options(contrasts=c(contr.sum,contr.poly)) before your call to lm() and atest will agree with aptest all down the line. cheers, Rolf Turner On 11/08/13 21:35,

[R] Different output from lm() and lmPerm lmp() if categorical variables are included in the analysis

I've found a problem when using categorical variables in lmp() from package lmPerm According to help(lmp): This function will behave identically to lm() if the following parameters are set: perm=, seq=TRUE, center=FALSE.) But not in the case of including categorical variables: require(lmPerm)