Sophie, sorry for any possibly duplicate email, my email client currently does not work correctly. I understand this snapshot as being a subset of your data only. But I do miss the factor "Sitename", which appears in your lmer model as a random factor. Also, by looking at the subset, "Presencebsence" appears be a binary response variable. Does your response imply that you tried to call
(m1<-lmer(Presencebsence~Habitatype*Width+(1|Sitename),family=binomial)) and got the same error? (Note: I previously mispelled "family") I also observe that many factors in your data appear to be closely correlated, e.g. "Habitatype" and "Width", at least in the subset you passed along. I suspect this correlation to be the reason for the lmer error. Hence either use "Width" or "Habitatype". Finally I'd propose you to put all your data into a dataframe, e.g. mydata<-NULL mydata$PresenceAbsence <- as.factor(Presencebsence) mydata$Habitattype <- as.factor(Habitatype) mydata$Substratetype <- as.factor(Substratetype) mydata$Width <- Width mydata$Banktype <- as.factor(Banktype) mydata$BankIncline <- BankIncline mydata$Bankheight <- as.factor(Bankheight) mydata$Waterdepth <- as.factor(Waterdepth) mydata$Sitename <- as.factor(Sitename) and then pass the dataframe to lmer by using data=mydata; mainly because passing a bunch of variables directly from the environment hightens the risk of inadvertently using stale copies, but also because str(mydata) would then produce a well arranged summary of all your variables. Kind regards Hugo On Sunday 26 June 2011 11:26:45 Sophie Higgins wrote: > > Hello Hugo, > Thank you for your reply. > This is a snap shot of what my data looks like: > > > > > > > > Presencebsence > Habitatype > Substratetype > Width > Banktype > BankIncline > Bankheight > Waterdepth > > > 0 > Lake > Rocksgravel > 600 > Earth > 0.45 > less1 > greater2 > > > 0 > Lake > Rocksgravel > 600 > Earth > 0.45 > less1 > greater2 > > > 1 > Lake > Rocksgravel > 600 > Earth > 0.45 > less1 > greater2 > > > 0 > Lake > Rocksgravel > 600 > Earth > 0.45 > less1 > greater2 > > > 0 > Lake > Rocksgravel > 600 > Earth > 0.45 > less1 > greater2 > > > 0 > Stream > Rocksgravel > 1 > Rocks > 0.45 > less1 > 025to05 > > > 0 > Stream > Rocksgravel > 1 > Rocks > 0.45 > less1 > 025to05 > > > 0 > Stream > Rocksgravel > 1 > Rocks > 0.45 > less1 > 025to05 > > > 0 > > > > Stream > Rocksgravel > 1 > Rocks > 0.45 > less1 > 025to05 > > > > > > > > > > > > > > > > > > > > > I am trying to find out if any off the above factors so substrate type, > width, bank type etc have an effect on the presence/absence of the species in question. But as stated below I keep getting an error message up and I have no idea how to fix it in order for me to fun the lmer. > Sophie > > From: hugo.mildenber...@web.de > > To: r-help@r-project.org > > CC: england...@hotmail.com > > Subject: Re: [R] Help with lmer > > Date: Fri, 24 Jun 2011 17:19:00 +0200 > > > > Sophie, > > > > I'm myself quite new to linear mixed effect models, but "PresenceAbsence" > > sounds like > > a binary response variable. So wouldn't be > > > > m1<-lmer(Presencebsence~Habitatype*Width+(1|Sitename),familiy=binomial) > > > > the first thing to try? There is also a special mailing list for linear - > > mixed -effect > > models: > > > > r-sig-mixed-mod...@r-project.org > > > > But with numeric problems like this one you really should provide a self > > contained > > example (i.e. with data), at least the output of str(yourdata), if ever > > possible. > > > > Kind regards > > > > Hugo > > > > On Friday 24 June 2011 13:11:23 Sophie Higgins wrote: > > > > > > Hey, > > > I am having trouble with lmer. I am looking at the presence/absence of > > > water shrews against habitat and other factors e.g > > > so I used this: > > > m1<-lmer(Presencebsence~Habitatype*Width+(1|Sitename))summary(m1) > > > But i keep getting this error up > > > Error in mer_finalize(ans) : Downdated X'X is not positive definite, 16.> > > > summary(m1)Error in asMethod(object) : matrix is not symmetric [1,2] > > > What does this mean and now can I fix it? > > > Sophie > > > [[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.