similar to: anova(mymodel.lme, type = "marginal")

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 would like to ask you to help me with my memeory. I remember using some function that would list all the possible methods I could apply to an object. Say, if I had an object of class=lme, it would tell me that that I could do stuff like qqnorm(myobjct), or VarCorr(myobject). In general, a very complete list. I though this list of all possible methods would pop out by typing

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, 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";

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 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

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 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 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: ***

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

Dear All, I would like to ask how to get the Sum of Squares from fitted lme model. I appreciate that lme maximises the likelihood (or REML) and uses likelihood ratio tests, but I just fail why I could not get the SS if I want them. I could use lm to calculate them, but it looks quite pointless to fit a second (and wrong in a way) model for something so trivial. I know that the issue has been

Hi everyone, I am confused on how to specify some nesting and interaction terma with lme(). I have a dataset where some flies where selected for accessory gland size, made to mate in presence/absence of another male and the level of some protein measured. Now the complex stuff. The selection has been replicated twice, so that the selection term has got two levels (large and small) with

>>>>> Ben Bolker >>>>> on Thu, 17 Jan 2019 12:32:20 -0500 writes: > tl;dr anova.lme() claims to provide sums of squares, but it doesn't. And > some names are misspelled in ?lme. I can submit all this stuff as a bug > report if that's preferred. > ?anova.lme says: > When only one fitted model object is present, a data

Is there a way to undo this? because mymodel wasn''t a model, but only a class... :)

tl;dr anova.lme() claims to provide sums of squares, but it doesn't. And some names are misspelled in ?lme. I can submit all this stuff as a bug report if that's preferred. ?anova.lme says: When only one fitted model object is present, a data frame with the sums of squares, numerator degrees of freedom, denominator degrees of freedom, F-values, and P-values The output of fm1

[ This was posted to the R-packages list (which I moderate), but definitely doesn't belong there. Martin Maechler ] ------- start of forwarded message ------- From: Federico Calboli <f.calboli at ucl.ac.uk> To: r-packages at stat.math.ethz.ch Subject: how to upload Date: 15 Jul 2004 18:30:26 +0100 Dear All, I just finished a add on lib called Malmig, to calculate Malecot

Check out textplot in the gregmisc package ... Federico Calboli <f.calboli@ucl.ac.uk> Sent by: r-help-bounces@stat.math.ethz.ch 07/13/2004 12:06 PM Please respond to f.calboli To: r-help <r-help@stat.math.ethz.ch> cc: Subject: [R] plotting a table together with graphs Dear All, I would like to ask how to add a table to a