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Help with lmer
5 messages · Sophie Higgins, Hugo Mildenberger, Iker Vaquero Alba
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-models at 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 at 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.
1 day later
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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.Mildenberger at web.de
To: r-help at r-project.org
CC: england116 at 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-models at 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 at 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.