similar to: methods help and glmmPQL

Hi All, I would like to ask a question on fixed and random effecti in lme. I am fiddlying around Mick Crawley dataset "rats" : http://www.bio.ic.ac.uk/research/mjcraw/statcomp/data/ The advantage is that most work is already done in Crawley's book (page 361 onwards) so I can check what I am doing. I am tryg to reproduce the nested analysis on page 368:

Dear All, I would like to ask you how to accomplish a little tricky data manipulation. I have a large dataset, looking something like: temp line cage number 18 18 1 6678.63 18 18 1 7774.458 18 18 1 7845.902 18 18 1 9483.578 18 18 1 8983.555 18 18 1 9181.052 18 18 1 9458.696 18 18 1 8138.616 18 18 1 7981.994 18 18 1 7556.491 18 18 1 7672.137 18 18 1 6607.776 18 18 1 8383.65 18 18 1 7129.852 18 18

Dear All, is any way I can change the colours of the box and umbrella of a bwplot without having to go to the length of: box.rectangle<-trellis.par.get("box.rectangle") box.rectangle$col<-"black" trellis.par.set("box.rectangle", box.rectangle) etc... but straight from the call: bwplot(y ~ x | z, mydata) ? Regards, Federico Calboli

Dear All, using R is noticed that I would benefit by going back to the books and "refresh" my linear algebra and calculus. Has anybody suggestions on which books are better as reference on the two these two topics? I was thinking to get Lang's "A First Course in Calculus", but I I have no idea what could be a good one for linear algebra. Something detailed and clear

Dear All, I am analysing some data for a colleague (not my data, gotta be published so I cannot divulge). My response variable is the number of matings observed per day for some fruitlies. My factors are: Day: the observations were taken on 9 days Regime: 3 selection regimes Line: 3 replicates per selection regime. I have 81 observations in total The lines are coded A to I, so I do not need

Dear All, I am writing to ask a clarification on what R, and in particular lme, is doing. I have an experiment where fly wing area was measured in 4 selection lines, measured at 18 and 25 degrees. I am using a lme model because I have three replicated per line (coded 1:12 so I need not use getGroups to creat an orederd factor). The lines are called: "18"; "25";

Hi All, does anyone know if the package GLME by J. Pinheiro is available anywhere in any form? checking on the archive I got that it was at some point, as as a beta version (for S-Plus only, alas)... Cheers, Federico ========================= Federico C.F. Calboli Department of Biology University College London Room 327 Darwin Building Gower Street London WClE 6BT Tel: (+44) 020 7679 4395

Dear R community, I need to plot the results of some simulations I did using QTL Cartographer. I am plotting LOD scores over three chromosomes. The three plot have to be one next to the other. The procedure I am using is: par(mfrow=c(1,3)) plot(x$x, x$y, ylim=c(0,35), type="l", col="blue", las=1, xaxs="i", yaxs="i", xlab="X Chromosome",

Hi, R is very new for me, so excuse if my questions are too basic... BTW, are there any forum where new R users could get help without annoying this huge mailing list ? In following code, I'd like to choose the color for each of the curve diplayed. png(filename = filename, width = 950, height = 600, pointsize = 10, bg = "white") xyplot(HITS+MS1*3+FREQ~TIME

Hi, I just installed the last version of R taken from the CRAN mirron in University of Vi?osa, Brasil. Since I use Mandrake 9.1 I get the proper .rpm file. I installed fine and all the test runs OK. I tryied to install sevela packages ussing the install.packages("package.name") and the installation runs OK... apparently. However, when I try to use the new package I get the following

Hi all, I've been attempting to fit a logistic glmm using glmmPQL in order to estimate variance components for a score test, where the model is of the form logit(mu) = X*a+ Z1*b1 + Z2*b2. Z1 and Z2 are actually reduced rank square root matrices of the assumed covariance structure (up to a constant) of random effects c1 and c2, respectively, such that b1 ~ N(0,sig.1^2*I) and c1 ~

Dear All, I suspect this is kind of dumb, but when I was under the thrall of the dark lord (read, using a W2K box), all my work in R files came out as foo.RData. I moved on to GNU/Linux, and all the old .RData files keep on working as they used. No problems in loading and stuff. But I use R from the terminal. Assuming I decide to switch to emacs, do I need to save my work as foo.r? what about my

Dear list, I am having some problems with extracting Variance Components from a random-effects model: I am running a simple random-effects model using lme: model<-lme(y~1,random=~1|groupA/groupB) which returns the output for the StdDev of the Random effects, and model AIC etc as expected. Until yesterday I was using R v. 2.0, and had no problem in calling the variance components of the

Hi! Can anyone let me know how can I get the stdDev of the random intercept from the output of glmmPQL? Thanks Salom?

Dear All, when I try to: install.packages("Design"); install.packages("Hmisc") I get the following error messages: * Installing *source* package 'Design' ... ** libs g77 -mieee-fp -O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro -O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro -c lrmfit.f -o lrmfit.o make: g77: Command not found make: ***

I am using a two-factor ANOVA model with random factor effects including the interaction, i.e. the factors are crossed. I would like to be able to generate all four variance components along with approximate confidence intervals using the NLME package. However, I do not know how to specify the random option because of two problems. First, I do not know how to enter the interaction term into the

Dear All, I would like to ask a couple of questions on a LME model. I tested 4 selection lines at 4 food concentrations against a standard competitor stock. I had 3 replicate cages per selection line. In each cage I have 10 vials. I counted the number of wild type flies and competitor stock emerging in each vial. My main question is: is there any difference between selection lines? I did fit

If you are indeed using lme and not lmer then the needed function is VarCorr(). However, 2 recommendations. First, this is a busy list and better emails subject headers get better attention. Second, I would recommend using lmer as it is much faster. However, VarCorr seems to be incompatible with lmer and I do not know of another function to work with lmer. Hence, a better email subject header

Hi All, I woul like to ask you a couple of questions on chisq.test. First, I have 40 flies, 14 males and 26 females and I want to test for an a priori hypothesis that the sex ratio is 1:1 sex<-c(14,26) pr<-c(1,1)/2 chisq.test(se, p=pr, correct=TRUE) Chi-squared test for given probabilities data: sex X-squared = 3.6, df = 1, p-value = 0.05778 If my calculations are correct, this is

Dear All, recently, while setting me on the straight and narrow about linear contrasts for a linear mixed effect model, Prof Ripley pointed out that my interpertation of the call anova(mymodel.lme) was not correct, because I was meant to add type = "marginal", as in anova(mymodel.lme, type = "marginal") I tried to look deeper in the issue, asking people, checking on the