similar to: zero random effect sizes with binomial lmer

I am fitting models to the responses to a questionnaire that has seven yes/no questions (Item). For each combination of Subject and Item, the variable Response is coded as 0 or 1. I want to include random effects for both Subject and Item. While I understand that the datasets are fairly small, and there are a lot of invariant subjects, I do not understand something that is happening here, and in

> > If one compares the random effect estimates, in fact, one sees that > > they are in the correct proportion, with the expected signs. They are > > just approximately eight orders of magnitude too small. Is this a bug? > > BLUPs are essentially shrinkage estimates, where shrinkage is > determined with magnitude of variance. Lower variance more > shrinkage towards

I'm estimating two models for data with n = 179 with four clusters (21, 70, 36, and 52) named siteid. I'm estimating a logistic regression model with random intercept and another version with random intercept and random slope for one of the independent variables. fit.1 <- lmer(glaucoma~(1|siteid)+x1 +x2,family=binomial,data=set1,method="ML",

Dear R-users, Half a year ago we put out the R package "glmmADMB" for fitting overdispersed count data. http://otter-rsch.com/admbre/examples/glmmadmb/glmmADMB.html Several people who used this package have requested additional features. We now have a new version ready. The major new feature is that glmmADMB allows Bernoulli responses with logistic and probit links. In addition there

hello, i'd appreciate help with my glmer. i have a dependent which is an index (MH.index) ranging from 0-1. this index can also be considered as a propability. as i have a fixed factor (stage) and a nested random factor (site) i tried to model with glmer. i read that it's possible to use a quasibinomial distribution, for this kind of data, which i than actually did - but firstly (1)

I am using mice package for multiple imputation. For one data (attached), mice doesn't impute all missing values. Specifically, some variables were not imputed at all. the reproducible code library(mice) test.df<-read.table(c:\\test.txt',header=T,sep=',') mi<-mice(test.df,maxit=10,m=5) sum(is.na(complete(mi,1))) >129 and x41, x50... were not imputed at all. Any

I was working with the rmetrics portfolioBacktesting function and dug into the code to try to find why my formula with 113 items, i.e. A1 thru A113, was being truncated and I only get 85 items, not 113. Is it due to a string length limitation in R or is it a bug in the strsplit or gsub functions, or in my string? I'd very much appreciate any suggestions ============Input script:

hello, i can't figure out how to set position of panels of my stripplot - i`d like the panels of one level of the factor stage (nr. of panels within each stage, A: 12, B: 12, C: 12, D: 4, each panel representing a site) to be in one column, with A to D from left to right and with descending site.nr at each row. like: A1 B1 C1 D1 A2 B2 .. .. A3 .. .. .. how is this achieved? any help

The coxme package has a ranef() method, as does lme4. I'm having trouble getting them to play together, as shown below. (The particular model in the example isn't defensible, but uses a standard data set.) The problem is that most of the time only one of lme4 or coxme will be loaded, so each needs to define the basic ranef function as well as a method for it. But when loaded together

Using ranef() (package nlme, version 3.1-75) with an 'lme' object I can obtain random effects for intercept and slope of a certain level (say: 1) - this corresponds to (say level 1) "residuals" in MLWin. Maybe I'm mistaken here, but the results are identical. However, if I try to get the standardized random effects adding the paramter "standard=T" to the

I'm testing out a new version of coxme and R CMD check fails with "could not find function ranef" (or random.effects or fixef, or anything from nlme). The NAMESPACE file has the line below importFrom(nlme, ranef, random.effects, fixef, fixed.effects, VarCorr) and nlme is declared in the DESCRIPTION file as an import. I feel that I must be staring at some obvious (but

Hi All I am having 2 very long character strings (550chars) and I want to put them as expressions together with c(). The problem is that I also get these double-quotes, as seen below in 'fct'. How can I remove these double-quotes? I tried as.name() but it did not work (because of size?). These are creating trouble with subsequent programs, which I tested with strings that for some

I'm trying to use the lmeSplines package together with lme4. Below is (1) an example of lmeSplines together with nlme (2) an attempt to use lmeSplines with lme4 (3) then a comparison of the random effects from the two different methods. (1) require(lmeSplines) data(smSplineEx1) dat <- smSplineEx1 dat.lo <- loess(y~time, data=dat) plot(dat.lo) dat$all <- rep(1,nrow(dat)) times20

User of the coxme library (mixed effects Cox models) are instructed to use ranef(), fixed(), VarCorr(), etc to retrieve bits out of a fitted model; it purposely uses the same methods as nlme and/or lmer. The current behavior is to "depend" on nlme. If I defined the methods myself in coxme, then someone who had both nlme and coxme loaded will suffer from "last loaded wins",

library(nlme) data(Phenobarb) na.include <- function(x)x phe1 <- nlme(conc~phenoModel(Subject, time, dose, lCl, lV), data = Phenobarb, fixed = lCl+lV~1, random= pdDiag(lCl+lV~1), start = c(-5,0), na.action = na.include, naPattern = ~!is.na(conc)) phe.ranef <- ranef(phe1,augFrame=TRUE) plot(phe.ranef, form=lCl~Wt+ApgarInd) [Error in max(length(x0),

Dear users, is anybody of you aware of a R command to perform laplace transform or even its inversion? Thank you very much. Luca

> On Mar 24, 2015, at 12:08 PM, Xinliang David Li <davidxl at google.com> wrote: > > On Tue, Mar 24, 2015 at 10:54 AM, Bob Wilson <bob.wilson at apple.com> wrote: >> >>> On Mar 24, 2015, at 10:53 AM, Diego Novillo <dnovillo at google.com> wrote: >>> >>> On Tue, Mar 24, 2015 at 1:48 PM, Bob Wilson <bob.wilson at apple.com> wrote:

I have been struggling all day to import a particular function/method combination (ranef(), which extracts the random effects from a mixed model fit) from the nlme package into another package ... so far without success. The NAMESPACE for nlme contains the following lines: export(..., ranef, ...) S3method(ranef, lme) ranef is defined as a standard S3 generic, function (object, ...)

> On Mar 24, 2015, at 3:22 PM, Xinliang David Li <davidxl at google.com> wrote: > > On Tue, Mar 24, 2015 at 2:47 PM, Bob Wilson <bob.wilson at apple.com <mailto:bob.wilson at apple.com>> wrote: >> >>> On Mar 24, 2015, at 12:08 PM, Xinliang David Li <davidxl at google.com> wrote: >>> >>> On Tue, Mar 24, 2015 at 10:54 AM, Bob

Shantanu, let's continue here. You first noticed this on a Dell OptiPlex 755. I think it covers all Dell OptiPlex/Latitude/Precision models that are PCIe based with Intel LoM (LAN on motherboard) utilizing the BIOS PXE OROM, based on the similarity of these systems. The symptoms are that PXELINUX requests pxelinux.cfg/<UUID> by TFTP (but it might not strictly be a TFTP issue) when not