Your contrasts are not linearly independent and therefore there are an infinite number of possible correct answers, this tends to confuse computers (take 1/3 times the 3rd col, plus 2/3 times the 4th col, plus 3/3 times the 5th col and compare that to the 1st col). You need to replace one of the contrasts with something else that makes them all linearly independent/full rank.
Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -----Original Message----- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.org] On Behalf Of doris gomez > Sent: Friday, July 10, 2009 7:23 AM > To: r-help@r-project.org > Subject: [R] problems with contrast matrix > > Dear lme and lmer -ers, > I have some problems using "home-made" contrast matrix in lme and lmer. > > I > did an experiment to investigate the relationship between the response > of an animal and some factors, namely the light wavelength (WA), the > light intensity to which this animal was exposed and the sex of the > animal > tested. > > - The response can be a variable LA (normal > distribution) or another variable PE (normal distribution). Each > analysed separately. > - WA has 6 different levels: 400, 430, 470, 540, 570, 620 nm. > - the light intensity has 4 different levels: 1, 2, 7, 50. > - the same animal was used in several tests. > I > suspect the response varies quadratically with WA (intermediate > wavelengths more efficient to evoke a response than extreme > wavelengths) but I would like to know if 470 is different from 540 nm, > if 430 is different from 570 nm... > > I analyse the response with WA as an ordered factor, either with lmer > (for PE) or with lme (for LA). > All models tested converge but the by-default contrast matrix is really > hard > to interpret because all the contrasts always involve all the > wavelengths. > > Here is an example of the syntax for lmer and lme, for the complete > model: > model1<- > lmer(PE~Sex+LightIntensity+ordered(WA)+(1|Animal),data=datamic,na.actio > n=na.omit,family="poisson",REML=FALSE) > model2<- > lme(LA~Sex+LightIntensity+ordered(WA),random=~1|Animal,data=datamic,na. > action=na.omit,method="ML") > > > So I built a specific contrast matrix: > > cmat.r<-matrix(c(-3/6,-2/6,-1/6,+1/6,+2/6,+3/6, # linear effect > -3/6,+1/6,+2/6,+2/6,+1/6,-3/6, # main quadratic > effect > 0,0,-1/2,+1/2,0,0, # mid wavelengths > 0,-1/2,0,0,+1/2,0, #intermediate wavelengths > -1/2,0,0,0,0,+1/2),6,5) # extreme wavelengths > colnames(cmat.r) <- c(".L",".Q",".mid",".inter",".extr") > contrasts(ordered(datamic$WA)<- cmat.r > > When I run the lme models, for all models involving WA, I get an error > message (approximate English translation): > Error in MEEM(object, conLin, control$niterEM) : > Singularity encountered in inverse resolution in level 0, block 1 > > When I run the lmer models, for all models involving WA, I get an error > message (approximate English translation): > Warning message: > In mer_finalize(ans) : gr cannot be computed at initial par (65) > > > What is/are the problems and the solutions? > - Is the contrast matrix of a rank inferior to what it should be? > - Are there some other code lines I should have put to facilitate > convergence? > > Thank you for your help. > Doris Gomez > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
