similar to: different results across versions for glmer/lmer with the quasi-poisson or quasi-binomial families: the lattest version might not be accurate...

Dear all, I found a problem with 'lme4'. Basically, once you load the package 'aod' (Analysis of Overdispersed Data), the functions 'lmer' and 'glmer' don't work anymore: library(lme4) (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)) (gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd), family = binomial, data

I am currently attempting to hack the recently featured profileModels package so that it can handle models generated by the lme4 (mixed models) package. I'm getting really confused by different behavior of summary() before and after loading the lme4 package, and inside and outside the profileMethod() function. The basic behavior is that with lme4 loaded, and "obj" a fitted object

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 <-

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)

Hi all, how do you update R on Debian lenny? I have tried to re-install r-base after adding deb http://<favorite-cran-mirror>/bin/linux/debian lenny-cran/ to my backport lists but it keeps installing R 2.7.1. What should I be doing to get the lattest R release? I need it to install a package (plyr) Thanks, David. [[alternative HTML version deleted]]

If you need a newer version of R for installing the latest version of plyr, perhaps another solution (as very new versions of R -2-11.0- will come out soonly ) , which needs 2 lines of bash!, might be to download an old version of plyr : wget \ http://cran.at.r-project.org/src/contrib/Archive/plyr/plyr_0.1.1.tar.gz and install it R CMD INSTALL plyr_0.1.1.tar.gz (and then reshape

An lme4 user pointed out <https://github.com/lme4/lme4/issues/491> that passing contrasts as a string or symbol to [g]lmer (which would work if we were using `contrasts<-` to set contrasts on a factor variable) is *silently ignored*. This goes back to model.matrix(), and seems bad (this is a very easy mistake to make, because of the multitude of ways to specify contrasts for factors in R

On Thu, Feb 21, 2019 at 7:49 AM Fox, John <jfox at mcmaster.ca> wrote: > > Dear Ben, > > Perhaps I'm missing the point, but contrasts.arg is documented to be a list. From ?model.matrix: "contrasts.arg: A list, whose entries are values (numeric matrices or character strings naming functions) to be used as replacement values for the contrasts replacement function and whose

Dear Ben, Perhaps I'm missing the point, but contrasts.arg is documented to be a list. From ?model.matrix: "contrasts.arg: A list, whose entries are values (numeric matrices or character strings naming functions) to be used as replacement values for the contrasts replacement function and whose names are the names of columns of data containing factors." This isn't entirely

Dear Martin and Ben, I agree that a warning is a good idea (and perhaps that wasn't clear in my response to Ben's post). Also, it would be nice to correct the omission in the help file, which as far as I could see doesn't mention that a contrast-generating function (as opposed to its quoted name) can be an element of the contrasts.arg list. Best, John > -----Original

>>>>> Fox, John >>>>> on Fri, 22 Feb 2019 17:40:15 +0000 writes: > Dear Martin and Ben, I agree that a warning is a good idea > (and perhaps that wasn't clear in my response to Ben's > post). > Also, it would be nice to correct the omission in the help > file, which as far as I could see doesn't mention that a

>>>>> Ben Bolker >>>>> on Thu, 21 Feb 2019 08:18:51 -0500 writes: > On Thu, Feb 21, 2019 at 7:49 AM Fox, John <jfox at mcmaster.ca> wrote: >> >> Dear Ben, >> >> Perhaps I'm missing the point, but contrasts.arg is documented to be a list. From ?model.matrix: "contrasts.arg: A list, whose entries are

Hi everybody, I am currently trying to forecast some double seasonal time series by using the function dshw. I want to access the standard errors to build the confident interval for my forecast. I am using to following code : fit<-dshw(eem,period1=7,period2=48,h=48) then by using summary(fit), I see that my se are contained in the vector : $s20 but when I call fit$s20, I get NULL. I

Hello all, My question is how do I write a multilevel regression model of individual responses to environmental predictors that accounts for social interactions between individuals. i.e.; 1) Individual response is nested within a group response. 2) The same environmental predictors apply to both hierarchical levels but, 3) Lower level slope/intercept are also affected by high-level response.

Dear list, When running the script below, the optim function returns the message 'Error in function (par) : could not find function "fn"'. I've re-read the code a few times and just can't figure out why it's happening. Any help/suggestion is appreciated. Regards, Rubem ## R script library(tweedie) period<-factor(1:4) herd<-factor(1:10)

Hello, I''m completely new to Rspec testing and I''m finding it very difficult to mock specific objects. In this test, I have a before block setup as such: [code] before do setup_controller_for_warden controller.session[:operation_id] = 1 @operator = Factory :operator sign_in :operator, @operator @persist_herd = Herd.new

Hi, I tried two different approaches. 1.) Convert an existing Image with qemu-img ================================================ qemu-img convert -t directsync lubuntu-14.04.3-desktop-i386.iso sheepdog:lubuntu1404.iso ================================================= results in ==================================================== root@orion2:/var/lib/libvirt/xml# virsh vol-dumpxml --pool

Dear all, I've been having problems running update() to re-fit a cpglm model inside a function (as in the code below). The solution is probably simple, but I'm stuck. If anyone could help, I'd greatly appreciate it. Regards, Rubem ## R code library(cplm) ## Data simulation period<-factor(1:4)                        herd<-factor(1:50)  

On Thu, Jan 14, 2016 at 12:12:53PM -0800, Leonid Yegoshin wrote: > On 01/14/2016 04:04 AM, Will Deacon wrote: > >Consequently, it's important that the architecture back-ends > >implement these portable primitives (e.g. smp_mb()) in a way that > >satisfies the kernel memory model so that core code doesn't need > >to worry about the underlying architecture for

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,