similar to: possible bug in plot.intervals.lmList

Dear List, I am plotting lmList objects using plot(intervals()) in nlme package. I want to make changes to the y-axis labels. When I try to change cex of y-axis labels using the following: fm1 <- lmList(distance ~ age | Subject, Orthodont) plot(intervals(fm1), scales=list(y=list(cex = .7))) I receive: Error in bwplot(formula = group ~ intervals | what, data = structure(list( : formal

Dea-R community. I'd like to draw your attention to an issue I have recently encountered while doing my current data analysis. I've got an unexpected (to me) result from the command: > augPred(lmList(my.object)), 'my.object' being a grouped data frame of class: > class(my.object) [1] "nfnGroupedData" "nfGroupedData" "groupedData"

I am using rw0641. In my continuing quest to understand repeated measures analysis, I again return to lme. I exported the Potthoff and Roy data Orthodont.dat from S-PLUS 4.5 to avoid capture errors and ran the examples in the R help. I imported the data.frame with data <- read.table("Orthodont.dat",header=T) attach(data) and created the objects Orthodont.fit1 <-

I want to compute confidence intervals for the random effect estimates for each subject. From checking on postings, this is what I cobbled together using Orthodont data.frame as an example. There was some discussion of how to properly access lmer slots and bVar, but I'm not sure I understood. Is the approach shown below correct? Rick B. # Orthodont is from nlme (can't have both nlme and

Hi Folks, I'm trying to understand the model specification formalities for 'lme', and the documentation is leaving me a bit confused. Specifically, using the example dataset 'Orthodont' in the 'nlme' package, first I use the invocation given in the example shown by "?lme": > fm1 <- lme(distance ~ age, data = Orthodont) # random is ~ age Despite the

dear all, I would like to get the lme call without fitting the relevant model. library(nlme) data(Orthodont) fm1 <- lme(distance ~ age, random=list(Subject=~age),data = Orthodont) To get fm1$call without fitting the model I use call(): my.cc<-call("lme.formula", fixed= distance ~ age, random = list(Subject = ~age)) However the two calls are not the same (apart from the data

Hi r-helpers! I need to save the output of summary() function that I?ve runned like this: z<- lmList(y~x1+x2| x3, na.action=na.omit,data1,subset=year==1999) w<-summary(z) The output (w) is something like this: Call: Model: y ~ x1 + x2 | x3 Data: data1 Coefficients: (Intercept) Estimate Std. Error t value Pr(>|t|) 1 0.081110514 1.141352e-01

Hi all, To follow up on an older thread, it was suggested that the following would produce confidence intervals for the estimated BLUPs from a linear mixed effect model: OrthoFem<-Orthodont[Orthodont$Sex=="Female",] fm1OrthF. <- lmer(distance~age+(age|Subject), data=OrthoFem) fm1.s <- coef(fm1OrthF.)$Subject fm1.s.var <- fm1OrthF. at bVar$Subject fm1.s0.s <-

Hi, I'm having some problems regarding the packages lme4 and nlme, more specifically in the denominator degrees of freedom. I used data Orthodont for the two packages. The commands used are below. require(nlme) data(Orthodont) fm1<-lme(distance~age+ Sex, data=Orthodont,random=~1|Subject, method="REML") anova(fm1) numDF DenDF F-value p-value (Intercept) 1

Hello, How do I get the standard deviations for the random effects out of the lme object? I feel like there's probably a simple way of doing this, but I can't see it. Using the first example from the documentation: > fm1 <- lme(distance ~ age, data = Orthodont) # random is ~ age > fm1 Linear mixed-effects model fit by REML Data: Orthodont Log-restricted-likelihood:

Hi using this code example: library(nlme) fm1 <- lme(Orthodont, random = ~1) plot(augPred(fm1)) is there any way to have the plots in each cell labelled and ordered according to Orthodont$Sex? I.e. in addition to the bar with the label for Orthodont$Subject there is another bar labelling the Sex of the subject? thanks a lot christoph --

Hello, I am looking for a way to obtain standard errors for emprirical Bayes estimates of a model fitted with lmer (like the ones plotted on page 14 of the document available at http://www.eric.ed.gov/ERICDocs/data/ericdocs2/content_storage_01/0000000b/80/2b/b3/94.pdf). Harold Doran mentioned (http://tolstoy.newcastle.edu.au/~rking/R/help/05/08/10638.html) that the posterior modes' variances

Dear R developers, first of all let me join the chorus of congratulations for the release of R 1.0.0. Well, done! Unfortunately, I find it necessary to e-mail in a bug report regarding the `nlme' package. On my office machine I experience the following trouble: bossiaea:/opt/R$ R CMD check -c nlme Checking package `nlme' ... Massaging examples into `nlme-Ex.R' ... Running

Dear R-help, I can't plot nls objects for some reason. The following example, taken from help(plot.nls) illustrates the problem: > data(Orthodont) > fm1 <- lme(distance ~ age, Orthodont, random = ~ age | Subject) > plot(fm1, resid(., type = "p") ~ fitted(.) | Sex, abline = 0) Error in do.call(plotFun, as.list(args)) : couldn't find function

Dear friends. I tried the session below with 10 MB in both vsize and nsize but didn't get the example work. Is this a problem in LME or in me or both or somewhere else or undefined ? R : Copyright 1999, The R Development Core Team Version 0.64.0 Patched (May 3, 1999) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type

Hi everyone, I have a quick and probably easy question about lme for this list. Say, for instance you want to model growth in pituitary distance as a function of age in the Orthodont dataset. fm1 = lme(distance ~ I(age-8), random = ~ 1 + I(age-8) | Subject, data = Orthodont) You notice that there is substantial variability in the intercepts (initial distance) for people at 8 years, and that

Hello, I am trying to use lmLists in the lme4 package and copying over very standard code from the nlme package given in 'Mixed-Effects Models in S and S-Plus'. It appears to not accept an 'I(age-11)' in the formula, though it will accept the formula with out the subtraction of 11 from age. This seems like it would be a bug, since this is standard formula syntax, unless

Hi, I'm new at this, I'm very confused, and I think I'm missing something important here. In our pet example we have this: > fm <- lme(Orthodont) > plot(Orthodont) > plot(augPred(fm, level = 0:1)) which gives us a trellis plot with the females above the males, starting with "F03", "F04", "F11", "F06", etc. I thought the point of

Hello: Let me rephrase my question to attract interest in the problem I'm having. When I appply anova() to two equations estimated using glmmPQL, I get a complaint, > anova(fm1, fm2) Error in anova.lme(fm1, fm2) : Objects must inherit from classes "gls", "gnls" "lm","lmList", "lme","nlme","nlsList", or "nls"

Dear r-helpers, After successfully running require(nlme) vfr.lmL <- lmList( estimate ~ (slant + respType + visField + hand)^2 | subject, vfr ) pairs(vfr.lmL, id = 0.01, adj = -0.5) # Pinheiro & Bates (p. 141) produces the following error: Error in sprintf(gettext(fmt, domain = domain), ...) : object "form" not found Any guesses as to what I may have done wrong?