similar to: Help_Unable to run glmer

I've searched the help archives of both lists and apologize if I missed the answer to my question: Is there an update on developing mcmcsamp for glmer? I'm using R v. 2.7.2 (on our Unix server - will hopefully be updated soon) and 2.8.1 on my PC and get the message for both: gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),family = binomial, data = cbpp)

I am running a multi-level model. I use the following commands with validatedRS6 as the outcome, random as the predictor and clustno as the random effects variable. new<-as.data.frame(read.delim("BABEX.dat", header=TRUE)) install.packages("lme4") library(lme4) model1<- glmer(validatedRS6 ~ random + (1|clustno), data=new, family=binomial("logit"), nAGQ)

Dear R and lme4 users- I am trying to fit a mixed-effects model, with the glmer function in lme4, to right-skewed, zero-inflated, non-normal data representing understory grass and forb biomass (continuous) as a function of tree density (indicated by leaf-area). Thus, I have tried to specify a Gamma distribution with a log-link function but consistently receive an error as follows: >

After upgrading to R 2.6.0, I'm having trouble running lmer: model <- lmer(primed ~ log(dist.time)*role + 1|target.utt, data=data.utts) Error in UseMethod("as.logical") : no applicable method for "as.logical" So I thought I'd upgrade lme4 to the latest version, but unfortunately the compilation fails - perhaps there's a missing #include: R CMD INSTALL

Dear R-Help, I need to convert a set of '.pdf' files into an equivalent set of '.txt' files. This is so that i can do some text mining on the content. In the latest R-News letter (http://cran.r-project.org/doc/Rnews/ Rnews_2008-2.pdf), the package 'tm' for text mining is mentioned. In that lovely package, there is a function called 'readPDF()'. In order to use

Hello, I'm having some trouble figuring out the correct model specification for my data. The system consists of multiple populations of an organism, which have been genetically sampled for several years. The problem is this: A minority of individuals are found in more than one sample, either they have survived into the next sampling at the same location, or have migrated to another another

I've got a problem with "mcmcsamp" used with glmer objects produced with "lmer" from the lme4 package. When calling mcmcsamp, I get the error Error in if (var(y) == 0) { : missing value where TRUE/FALSE needed This does not occur with all models, but I can't find anything wrong with the dataset. If the error is in my data, can someone tell me what I am looking

All, I'm trying to put an xyplot and a plot produced via curve() on the same page. It seems that mfrow and layout don't work, and now I'm trying print but that does not work either. Any suggestions much appreciated. Cheers, David p.11 = xyplot(1:10 ~ 1:10) curve(sin, 0,3, ylim=c(-3,3), ylab="sin and cos", lty = 1) curve(cos, 0,3, ylim=c(-3,3), lty = 5, add=TRUE)

Hello, I originally posted this on the stats stack exchange site, but given its focus on R software, it was removed -- so I figured I'd post here. I'm having trouble interpreting a change in effect direction and significance when I add an interaction term to my glmer() model. *Part 1* I ran an experiment in which participants made categorical decisions (out of two categories) in one of

Is it possible to use the step() function with a glmer() as an object? I obtain the following error message when I try to do it: "Error in x$terms : $ operator not defined for this S4 class". I perform the glmer correctly but I can't do the step. Thank you so much. -- View this message in context: http://n4.nabble.com/step-and-glmer-tp1474390p1474390.html Sent from the R help

Full_Name: susscorfa Version: 2.7.1 OS: ubuntu Submission from: (NULL) (129.125.177.31) Incorrect implementation of the grouping variable in the function glmer crashes R a small example: require(lme4); a<-data.frame(b=rpois(1000,10), c=gl(20,50), d=rnorm(1000,3), e=rnorm(1000,5), f=rnorm(1000,2)+5); glmer(b~d+f|c+(e), family=poisson, data=a) It crashes R on debian linux (2 independant

Dear R Help, I would like to use the glmer.nb function for mixed modelling using negative binomial distribution please. On the CRAN website apparently this function is called from the lme4 package (version 0.99999911-1). I have downloaded the latest version of the lme4 package (version 0.999999-2) and have recently reinstalled the latest version of 64-bit R (version 3.0.1) but after

I've built a poisson regression model for multiple subjects by using the GLMER function. I've also developed some curves for defining its limits but I did not succeed in developing confidence interval for the model's curve (confint or predict does not work - only for glm). Does anyone know how can I produce confidence interva for a glmer model? I'll appriciate any help... Liat --

dear R-users, I have to model counts where all counts above some threshold have been censored. In the same dataset I have too many zeroes for a Poisson or even a negative binomial distribution to make sense, so I would need a zero-inflated-censored negative binomial family for use in glmer (or glmmADMB?). That seems not to exist. my question is : how could I add a custom-built family of

Dear all, I am using function glmer from package lme4 to fit a generalized linear mixed effect model. My model is as follows: model1 <- glmer(fruitset ~ Dist*wire + (1|Site), data, binomial) summary(model1) Generalized linear mixed model fit by the Laplace approximation Formula: fruitset ~ Dist * wire + (1 | Site) Data: data AIC BIC logLik deviance 68.23 70.65 -29.11 58.23 Random

Hello, I am using glmer() from lmer(lme4) to run generalized linear mixed models. I can't figure out how to extract the z values for the fixed effects that are reported using the summary function . Any help would be appreciated. Thanks, Spencer [[alternative HTML version deleted]]

Hello, I am using glmer() from lmer(lme4) to run generalized linear mixed models. However, I am having a problem extracting the standard errors for the fixed effects. I have used: summary(model)$coef fixed.effects(model) coef(model) to get out the parameter estimates, but do not seem able to extract the se's. Anybody have a solution? Thanks, John

Dear all, A am trying to fit a generalized linear mixed effects model with a binomial link function, my response data is binary, using the lme4 R package, for the glmer model but with the cauchit link function (CDF of Cauchy distribution), under the package this has not yet been coded and was wondering if anyone knew a way in which I could incorporate this link function into the code. Thankyou

Having briefly fallen for the notion that the negative.binomial family in MASS could be used in glmer, I want to use these lists for a sanity check on my final (?) plans. I want to use glmer for logistic regression and for poisson regression on a data set of 10,000 items. There will be two crossed random effects. For the logistic regression, I want odds ratios with confidence intervals.For the

Sub: using glmer to fit a mixed-effects model with gamma-distributed response variable Hello, I'm currently trying to fit a mixed effects model , i.e.: > burnedmodel1.2<-glmer(gpost.f.crwn.length~lg.shigo.av+dbh+leaf.area+ bark.thick.bh+ht.any+ht.alive+(1|site/transect/plot), family=gaussian, na.action=na.omit, data=rws30.BL) If I run this code, I get the error below: Error: