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Jos?? C. Pinheiro Training in UK - Analyzing Mixed-Effects Models with S-PLUS Mixed-effects models provide a powerful tool for analyzing grouped data. This course will overview the application of linear and nonlinear mixed-effects models in the analysis of grouped data, using the NLME software in S-PLUS to illustr...

All, Sorry for overly simplistic question, but I can't seem to remember how to create the basic plot shown in Figure 1.1 of Pinheiro & Bates (2004; p.4). The y-axis delineates a factor (Rail) while the x-axis displays the distribution of a continuous variable (time) according to each level of the factor. Didn't see it in archives but perhaps I'm not searching on correct key words, any help appreciated, David >...

Hello! could you give me some advice where i can finde out/recieve/download a GLME package, written by Jose Pinheiro. i couldn'ti find it in the package lists (probably becouse it is still in a beta version). thank you for your replay

Dear Mixed Effect Friends, Somehow, R(1021, Windows) seem to run differently from S Plus: The soybean example from Pinheiro/Bates on page 290 fails in R. (Soybean1 is Soybean with the NA and "critical" case removed. Same procedure with full Soybean). > fm1Soy.lis<-nlsList(weight~SSlogis(Time,Asym,xmid,scal),data=Soybean1) > fm1Soy.nlme<-nlme(fm1Soy.lis) Error: Singularity in backsolve at level 0,...

...quot; "factor" "numeric" "numeric" "numeric" Is there a way to change that? Thank you very much. PS: the levels for fruit and veget are intact or removed -- View this message in context: http://www.nabble.com/wroung-groupedData-despite-reading-Bates-and-Pinheiro-3-times-tp18548213p18548213.html Sent from the R help mailing list archive at Nabble.com.

Hello, I am interested in using nlme to model repeated measurements, but I don't seem to get good CIs. With the code below I tried to generate data sets according to the model given by equations (1.4) and (1.5) on pages 7 and 8 of Pinheiro and Bates 2000 (having chosen values for beta, sigma.b and sigma similar to those estimated in the text). For each data set I used lme() to fit a model, used intervals() to get a 95% CI for beta, and then checked whether the the CI contained beta. The rate at which the CI did not contain beta was 8...

Hi all, I'm trying to figure out the example about mixed models in the Pinheiro and Bates book (Mixed-Effects Models in S and S-Plus, 2000, pp. 135-137). One thing I don't understand is: When I run the command fm1Orth.lm <- lm( distance ~ age, Orthodont ) followed by fm2Orth.lm <- update( fm1Orth.lm, formula = distance ~ Sex*age ) and then do summa...

Dear all, This question may be too basic quesition for this list, but if someone has time to answer I will be happy. I have tried to find out, but haven't found a consice answer. As an example I use "Pinheiro, J. C. & Bates, D. M. 2000. Mixed-effects models in S and S-PLUS. Springer, New York." page 225, where rats are fed by 3 different diets over time, which body mass has been measured. Response: Body mass, fixed effects Time*Diet, random effect ~Time|Rat. The main question is if the interact...

...list members, I'm interested in showing that within-group statistical dependence is negligible, so I can use ordinary linear models without including random effects. However, I can find no mention of testing a model with vs. without random effects in either Venable & Ripley (2002) or Pinheiro and Bates (2000). Our in-house statisticians are not familiar with this, either, so I would greatly appreciate the help of this list. Pinheiro & Bates (2000:83) state that random-effect terms can be tested based on their likelihood ratio, if both models have the same fixed-effects stru...

Anybody know where I can get the Pinheiro/Bates book? I can't find a bookstore w/ stock and the publisher says they don't know when they'll have it again. Thanks. -Frank

...' make [2]: ** [all] Error 1 make [2]: Leaving directory `/ home / admcad / VMKit / lib / vmkit ' make [1]: ** [vmkit / .makeall] Error 2 make [1]: Leaving directory `/ home / admcad / VMKit / lib ' make: ** [all] Error 1 you must modify the file called? thanks, -- Anderson Boettge Pinheiro Grupo de Pesquisa em Paralelismo, Grafos e Otimização (Pargo) MDCC - Departamento de Computação - Mestrado em Computação Universidade Federal do Ceará -- Anderson Boettge Pinheiro Grupo de Pesquisa em Paralelismo, Grafos e Otimização (Pargo) MDCC - Departamento de Computação - Mestrado em C...

Dear R-help, I am trying to create groupedData objects using the nlme library. I'm missing something basic, I know: Here is the first example in ch.1 of Pinheiro & Bates (2000): library(nlme) x2=Rail$travel;x1=Rail$Rail;eg1=data.frame(x1,x2);eg1gd=Rail print(eg1gd) x11();print(plot(eg1gd)) femodel=lm(x2~x1-1,data=eg1gd) print(femodel$coefficients) Result: x12 x15 x11 x16 x13 x14 31.66667 50.00000 54.00000 82.66667 84...

...data.frame with data <- read.table("Orthodont.dat",header=T) attach(data) and created the objects Orthodont.fit1 <- lme(fixed=distance~age,random=~age) Orthodont.fit2 <- lme(fixed=distance~age*Sex,random=~age) which appear to be the R equivalent of the objects created in Pinheiro and Bates 1995 (lme and nlme). The code fm1 <- lmList(distance~age|Subject,data) generated the error message Error: couldn't find function "restart" without 'data' it doesn't run. The code plot(Orthodont.fit1) generated the error message Error: couldn't...

...tribution. The larger model would allow the boys' and girls' random intercepts (or more generally their random effects) to come from separate normal distributions with possibly unequal variances. There must be some straightforward obvious way to fit the larger model, but I do not see it. Pinheiro and Bates, chapter 5.2, show how to model unequal *residual* ("within-group") variances for the two groups using varIdent. They also tantalizingly say, "The single-level variance function model (5.10) can be generalized to multilevel models" (page 206), which seems to suggest t...

All, I'm trying to create an augPred plot in the nlme library, similar to the plot on p.43 of Pinheiro & Bates (Mixed Effects Models in S and S-Plus) for their Pixel data. My data structure is the same as the example but I still get the error msg below. > comp.adj.UKV <- groupedData(adj.UKV ~ Time | Patient_no/Lisinopril, data = comp.adj.UKV.frm, order.groups = F) > fm1comp = l...

Dear R users, I would like to exactly reproduce a figure like the 1.5 or 1.9 or 4.13 from the book Mixed effects models in S and S-Plus. Not for the sake of it, but because I have my own data I would like to plot in that fashion (no colors) If I write plot(ergoStool) I can get a good informative plot with colors, but I would like to have a B&W one instead. I've played a little with

...package, following R-exts, I realised that if I use only one 'citEntry' I got both a text description and a BibTex entry for the package, as for the 'nlme' package: -------------------------- citation('nlme') To cite package 'nlme' in publications use: Jose Pinheiro, Douglas Bates, Saikat DebRoy, Deepayan Sarkar and the R Development Core Team (2012). nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1-105. A BibTeX entry for LaTeX users is @Manual{, title = {nlme: Linear and Nonlinear Mixed Effects Models}, author = {Jo...

...d how to use some R feature. Instead, I often provide the same answer multiple times to different posts. I can think of two changes off the top of my head that I'd like to see: First, many if not all of the helps page in the nlme and lme4 packages should, I believe, include a reference Pinheiro and Bates. This is not the place for modesty on the part of Pinheiro, Bates, and co-workers. I believe that many requests for help might be eliminated if such references were added. Failing that, it would be easier for people like me to suggest someone read that book, because I wouldn't...

I am trying to understand the proper way to encode the nesting structure for data in the context of nlme, in the specific case of individuals nested within species for which each individual is unique. I have searched through Pinheiro & Bates and also past postings, but without success. Take the Wafer data set which has 2 levels: Wafer (8 values) and Site nested within Wafer (10 values for each value of Wafer) (Pinheiro & Bates book). The data set has Sites coded as values from 1 to 8 for Wafer 1, values 1 to 8 for...

Hi, I was trying to run the example of Indomethacin kinetics from the book: ## From Pinheiro/Bates, Mixed-Effects-Models in S and S-Plus, ## Springer, Second Printing 2001, Section 6.2 library(nlme) plot(Indometh) fm1Indom.nls <- nls(conc~SSbiexp(time,A1,lrc1,A2,lrc2), data=Indometh) summary(fm1Indom.nls) plot(fm1Indom.nls,Subject~resid(.),abline=0) ## .... the last plot command gives...