search for: lmeoptim

...ealier on the list by Doug Bates). So I did: fm2 <- lmer(resistance ~ ET + position + (1|Grp), Semiconductor,method='ML') simdata<-simulate(fm2,nsim=1) ynew <- simdata[,1] mer <- fm2 .Call("mer_update_y", mer, ynew, PACKAGE = "Matrix") mer1u <- LMEoptimize(mer, lmerControl(mer)) What puzzles me is that this call alters my original model fm2 as some kind of side effect. In fact, after the call fm2 is the same as mer1u. Is this side effect intentional and is it possible to avoid? A detail is that "LMEoptmize" and "LMEoptimize<-&q...

...#39;fn' In addition: Warning message: Leading minor of size 1 of downdated X'X is indefinite Error in .local(object, ...) : Leading 2 minor of Omega[[1]] not positive definite In addition: Warning messages: 1: optim or nlminb returned message ERROR: ABNORMAL_TERMINATION_IN_LNSRCH in: "LMEoptimize<-"(`*tmp*`, value = list(maxIter = 200, msMaxIter = 200, 2: optim or nlminb returned message ERROR: ABNORMAL_TERMINATION_IN_LNSRCH in: "LMEoptimize<-"(`*tmp*`, value = list(maxIter = 200, msMaxIter = 200, thanks for any help. -eduardo

...pe and intercept model where the rate can change differently with temperature for different individuals: model<-lmer(int.length~mean.sst+(mean.sst|female)) However, I get the following warning message: Warning message: Estimated variance-covariance for factor 'female' is singular in: `LMEoptimize<-`(`*tmp*`, value = list(maxIter = 200L, tolerance = 1.49011611938477e-08, summary(model) Linear mixed-effects model fit by REML Formula: int.length ~ mean.sst + (mean.sst | female) AIC BIC logLik MLdeviance REMLdeviance 155.4 164.5 -72.7 142.8 145.4 Random effects: Group...

Hi: I'm using function lmer from package lme4, and I get this message: " There were 12 warnings (use warnings() to see them)" So I checked them: Warnings 1 to 11 said: 1: optim returned message ERROR: ABNORMAL_TERMINATION_IN_LNSRCH in: "LMEoptimize<-"(`*tmp*`, value = structure(list(maxIter = 50, ... and Warning 12 said: 12: IRLS iterations for glmm did not converge in: lmer(Enfermo ~ Bloque + Trat * Var * dia + (1 | IDfruto), data = desinf, ... There was no error message in the call of lmer function, so: What do these...

Dear all, I am analyzing some data that requires a mixed model. I have been reading Pinheiro and Bates' book, but cannot find the notation to fit the following model: Suppose I have the dataset below. Here I am fitting variable p as a fixed effect, variable h as a random effect and variable t as nested within h. I would like to include the variable j as well as an independent (non-nested)

...rror in fun(...): couldn't find function "assignInNamespace" Error: .onLoad failed in 'loadNamespace' for 'Matrix' The only object in my .RData is last.warning, thus: > last.warning $"optim or nlminb returned message false convergence (8)" "LMEoptimize<-"(`*tmp*`, value = list(maxIter = 200, tolerance = 1.49011611938477e-08, msMaxIter = 200, msVerbose = 0, niterEM = 15, EMverbose = FALSE, PQLmaxIt = 30, analyticGradient = TRUE, analyticHessian = FALSE)) This was generated by a call, in a previous session,to lmer() There m...

...fl <- FL$fl if (fltype < 0) { mer <- .Call(mer_create, fl, Zt, X, as.double(Y), method == "REML", nc, cnames) if (!is.null(start)) mer <- setOmega(mer, start) .Call(mer_ECMEsteps, mer, cv$niterEM, cv$EMverbose) LMEoptimize(mer) <- cv return(new("lmer", mer, frame = if (model) fr$mf else data.frame(), terms = mt, call = mc)) } if (method %in% c("ML", "REML")) method <- "Laplace" if (method == "AGQ") stop(&quot...

...lock, 4 Fixed effects: Estimate Std. Error t value (Intercept) 6.00000 0.92533 6.484 Treatment 2.00000 0.07795 25.658 Correlation of Fixed Effects: (Intr) Treatment -0.168 Warning message: Estimated variance-covariance for factor 'Block' is singular in: `LMEoptimize<-`(`*tmp*`, value = list(maxIter = 200, tolerance = 1.49011611938477e-08, Charmy _________________________________________________________________ Communicate instantly! Use your Hotmail address to sign into Windows Live Messenger now. http://get.live.com/messenger/overview

Dear All, Can anyone give me some hints about how to set starting values for a lmer model? For complicated models like this, good starting values can help the numerical computation and make the model converge faster. Thanks! Shige [[alternative HTML version deleted]]

...esults, whereas the third (which I think perhaps is the one that best represents the data generated by the simulation) differs slightly. In running the simulations, warnings like this are occasionally generated: Warning message: optim or nlminb returned message false convergence (8) in: "LMEoptimize<-"(`*tmp*`, value = list(maxIter = 200, tolerance = 1.49011611938477e-08, They seem to derive from the third of the lmer models. Perhaps there is some numerical issue in the lmer function? From running SimMixed() several times, I have noticed that large p-values (say, larger than 0.5...

dear R experts: sorry, I have to ask this again. I know that the answer is in section 7.2 of "S Programming," but I don't have the book (and I plan to buy the next edition---which I hope will be titled S/R programming ;-) ). I believe the following yields a standard fixed-effects estimation: fixed.effects = as.factor( as.integer( runif(100)*10 ) ) y=rnorm(100); x=rnorm(100);

Dear list members, the following hlm was constructed: hlm <- groupedData(laut ~ design | grpzugeh, data = imp.not.I) the grouped data object is located at and can be downloaded: www.anicca-vijja.de/lg/hlm_example.Rdata The following works: library(nlme) summary( fitlme <- lme(hlm) ) with output: ... AIC BIC logLik 425.3768 465.6087 -197.6884 Random effects:

Dear R-users, I did some more research and I'm still not sure how to set up an ANCOVA with nestedness. Specifically I'm not sure how to express chicks nested within boxes. I will be getting Pinheiro & Bates (Mixed Effects Models in S and S-Plus) but it will not arrive for another two weeks from our interlibrary loan. The goal is to determine if there are urbanization (purban)