similar to: bug in lme4?

Dear list, I am fitting a logistic multi-level regression model and need to test the difference between the ordinary logistic regression from a glm() fit and the mixed effects fit from glmer(), basically I want to do a likelihood ratio test between the two fits. The data are like this: My outcome is a (1,0) for health status, I have several (1,0) dummy variables RURAL, SMOKE, DRINK, EMPLOYED,

Hello, I have compared the potentials of R and Stata about GLMM, analysing the dataset 'ohio' in the package 'faraway' (the same dataset is analysed with GEE in the book 'Extending the linear model with R' by Julian Faraway). Basically, I've tried the 2 commands 'glmmPQL' and 'glmer' of R and the command 'xtmelogit' of Stata. If I'm not

Dear all, I'm trying to estimate the parameters of a special case of a poisson model, where the specified equation has an integral and several fixed parameters. I think that the MLE command in STATS4 package could be a good choice, but it's a little complicated. I've got some problems with the offset and I don't understand some of the functions. Do you know where can I find some

Dear all, I have a very basic question: how does the logLik function work for poisson models? Example: I simulate 20 observations from a Poisson distribution with mean 800. y <- rpois(20,800) model <- glm(y ~ 1, family=poisson()) logLik(model) I would like to know what's the exact formula the function logLik uses. I looked at ?extractAIC but I cannot sort it out. Can you please

Dear list, I have another (again possibly boneheaded) puzzle about importing, again encapsulated in a nearly trivial package. (The package is posted at <http://www.math.mcmaster.ca/bolker/misc/coefsumtest_0.001.tar.gz>.) The package consists (only) of the following S3 method definitions: coeftab <- function(object, ...) UseMethod("coeftab",object) coeftab.default <-

Hello, I need to perform a mixed-model (with nesting) MANCOVA, using Type III sums of squares. I know how to perform each of these types of tests individually, but I am not sure if performing a mixed-model MANCOVA is possible. Please let me know. Erika <>< <>< <>< <>< <>< <>< <>< Erika Crispo, PhD candidate

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

Hello, I'm trying to save a graph as a .ps file to include it in a LaTex presentation, but R replies: Error: Invalid font type In addition: Warning messages: 1: font family not found in PostScript font database 2: font family not found in PostScript font database If I load the package grDevices and type "postscript()" then I can save it, but it creates also a text file saying:

Dear list, I am trying to use MuMIn to compare all possible mixed models using the dredge function on binomial data but I am getting an error message that I cannot decode. This error only occurs when I use glmer. When I use an lmer analysis on a different response variable every works great. Example using a simplified glmer model global model: mod<- glmer(cbind(st$X2.REP.LIVE,

Dear Wolfgang Viechtbauer and R users, I have few questions regarding the development of the package 'metafor. As you suggested , I post to the R-help mailing list. I read you're planning an extension of this method to the multivariate case. I think it would be a useful tool. I'm currently performing some analyses with R on multiple outcomes, using the Stata command mvmeta to get

Dear R users, I'm trying to specify a generalized linear mixed model in R, basically a Poisson model to describe monthly series of counts in different regions. My aim is to fit subject-specific curves, modelling a non-linear trend for each region through random effects for linear splines components (see Durban et al, Stat Med 2005, or " Semiparametric regression" by Ruppert et al,

Dear all, I've tried to solve the Es. 12, cap 4 of "Introduction to GLM" by Annette Dobson. It's about the relationship between survival time of leukemia patients and blood cell count. I tried to fit a model with exponential distribution, first by glm (family gamma and then dispersion parameter fixed to 1) and then with survreg. They gave me the same point estimates but the

Hi all, I am trying to run a glm with mixed effects. My response variable is number of seedlings emerging; my fixed effects are the tree species and distance from the tree (in two classes - near and far).; my random effect is the individual tree itself (here called Plot). The command I've used is: mod <- glmer(number ~ Species + distance + offset(area) + (1|Plot), family = poisson)

Dear R-users, I've just installed the last version of R (2.10.0) in Windows and found a completely new version of the help pages. Basically, they now appear as a simple (even if slightly embellished) text file. I tried to install it with a customized startup and realized that the old CHM files (the default for Windows up to 2.9.2) are not included anymore as a possible choice. I don't

Dear R users, I found a small problem with the package creation procedure in R 2.9.0 under Windows. Basically, I input in the command prompt; Rcmd BUILD --binary --use-zip namepackage The procedure works, but the titles in the help pages of the created package lose the usual colours and font. Conversely, the result is perfect using R 2.8.1 (changing the path) and the same version of Rtools

Dear all, I need to fit a gee model with an auto-regressive correlation structure and I faced some problems. I attach a simple example: ####################################################### library(gee) library(geepack) # I SIMULATE DATA FROM POISSON DISTRIBUTION, 10 OBS FOR EACH OF 50 GROUPS set.seed(1) y <- rpois(500,50) x <- rnorm(500) id <- rep(1:50,each=10) # EXAMPLES FOR

Dear R users, I created some functions I want to convert in a package under Windows (Vista or XP). I carefully read both "Writing R extensions" by the R Development Core Team and "Creating R packages: a tutorial" by Friedrich Leisch. I've also installed Rtools as suggested. These tutorials are very useful, but I'm struggling with the last step of the installation

Dear R users, I included 2 internal functions in the package 'dlnm', called 'mkbasis' and 'mklagbasis'. Despite they are not meant to be called by the users, I included them in the namespace in order to make them available, keeping the process more transparent and giving the opportunity to change or improve them. I included an help page 'dlnm-internal.Rd' to

Dear R users, I included 2 internal functions in the package 'dlnm', called 'mkbasis' and 'mklagbasis'. Despite they are not meant to be called by the users, I included them in the namespace in order to make them available, keeping the process more transparent and giving the opportunity to change or improve them. I included an help page 'dlnm-internal.Rd' to

Dear all, I am running glmer() in R. How can I retrieve the estimates of fixed effects and the variance of the random effects from the result? Thank you so much. Joe ___________________________________________________ ±zªº¥Í¬¡§Y®É³q ¡Ð ·¾³q¡B®T¼Ö¡B¥Í¬¡¡B¤u§@¤@¦¸·d©w¡I [[alternative HTML version deleted]]