Re: [R] syntax for interactions in lme

Host (fixed) Sire (random) Dam nested within Sire (random) Host * Sire (random) Host * Dam within Sire (random) So without the interactions I have: hogmodel = lme(gain ~ host, random = ~1|sire/dam) If I understand correctly, that sire/dam term gives me both Sire and Dam within Sire

Re: [R] anova with models from glmmPQL

- Lorenz Gygax Centre for proper housing of ruminants and pigs Swiss Federal Veterinary Office agroscope FAT Tänikon, CH-8356 Ettenhausen / Switzerland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] interpretation output glmmPQL

. Cheers, Lorenz - Lorenz Gygax Centre for proper housing of ruminants and pigs Swiss Federal Veterinary Office agroscope FAT Tänikon, CH-8356 Ettenhausen / Switzerland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] The mathematics inside lme()

within group (and thus this value is certainly not independent). Cheers, Lorenz - Lorenz Gygax, Dr. sc. nat. Centre for proper housing of ruminants and pigs Swiss Federal Veterinary Office agroscope FAT Tänikon, CH-8356 Ettenhausen / Switzerland __ R-help

RE: [R] testing equality of variances across groups in lme?

|study.code, weights= varIdent (form= ~ 1 | CLnRGR)) with anova (fit3, fit4) you can test whether these weights improve the fits statistically. Lorenz - Lorenz Gygax, Dr. sc. nat. Centre for proper housing of ruminants and pigs Swiss Federal Veterinary Office agroscope FAT Tänikon, CH-8356

RE: [R] logistic regression 3D-plot

I tried to create a 3D surface showing the interaction between two continuous explanatory variables; the response variable is binary (0/1). The model is: model-glm(incidence~sun*trees,binomial) then I used wireframe to create a 3D plot:

RE: [R] random effects in lme

, (corrected) r-squared values might tell you something if you compare different models based on the same data (in a similar way as the AIC and BIC criteria) but not if you compare completely different data sets. Regards, Lorenz - Lorenz Gygax, Dr. sc. nat. Centre for proper housing of ruminants and pigs

RE: [R] Special paper for postscript

-user defined according to the bounding boxes in the postscript file. Thus, I am not sure what your problem is ... Regards, Lorenz - Lorenz Gygax, Dr. sc. nat. Centre for proper housing of ruminants and pigs Swiss Federal Veterinary Office agroscope FAT Tänikon, CH-8356 Ettenhausen / Switzerland

RE: [R] binomia data and mixed model

}, ADDRESS = {New York}, EDITION = {fourth} Regards, Lorenz - Lorenz Gygax, Dr. sc. nat. Centre for proper housing of ruminants and pigs Swiss Federal Veterinary Office agroscope FAT Tänikon, CH-8356 Ettenhausen / Switzerland __ R-help

RE: [R] Split-split plot ANOVA

transformation of your response might be enough. Regards, Lorenz - Lorenz Gygax, Dr. sc. nat. Centre for proper housing of ruminants and pigs Swiss Federal Veterinary Office agroscope FAT Tänikon, CH-8356 Ettenhausen / Switzerland __ R-help

RE: [R] lme and varFunc()

distribution do you have / do you expect? Regards, Lorenz - Lorenz Gygax, Dr. sc. nat. Centre for proper housing of ruminants and pigs Swiss Federal Veterinary Office __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

RE: [R] 3d bar plot

if a careful evaluation of alternatives was not promising success I would resign myself to using 3D graphs. Lorenz - Lorenz Gygax, Dr. sc. nat. Centre for proper housing of ruminants and pigs Swiss Federal Veterinary Office agroscope FAT Tänikon, CH-8356 Ettenhausen / Switzerland

RE: [R] Multiple comparisons following nlme

when you interpret your parameters and/or graphs of your data. ... and by the way, I guess your model is using lme (linear mixed effects model) in package nlme and not actually an nlme (non-linear mixed effects model) itself. Regards, Lorenz - Lorenz Gygax, Dr. sc. nat. Centre for proper housing

RE: [R] GLMM and crossed effects

the differences in the summary and VarCorr variance components... Here, you loose me completely. It is not clear to me what you compare and where you perceive a problem. Cheers, Lorenz - Lorenz Gygax, Dr. sc. nat. Centre for proper housing of ruminants and pigs Swiss Federal Veterinary Office

RE: [R] The hidden costs of GPL software?

projects that I supervise that people get started easily with a snippet of code that I provide and the insight of the usefulness of such a work approach is usually easily within reach. Lorenz - Lorenz Gygax, Dr. sc. nat. Tel: +41 (0)52 368 33 84 / [EMAIL PROTECTED] Centre for proper housing

RE: [R] grouping for lme with nested repeated measurements

= response ~ apparatus, data= XX, random= ~ 1 | Sample/Days) Lorenz - Lorenz Gygax, [EMAIL PROTECTED] Centre for proper housing of ruminants and pigs Swiss Federal Veterinary Office __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman

FW: [R] glmmPQL and random factors

the terrific book by Pinheiro Bates (Mixed Effects Modelling in S and S-Plus, Springer, 2000). Cheers, Lorenz - Lorenz Gygax Tel: +41 (0)52 368 33 84 / [EMAIL PROTECTED] Centre for proper housing of ruminants and pigs Swiss Federal Veterinary Office

RE: [R] drawing on axes

) axis (1, at= c (0, 3), labels= FALSE, tick= T, lwd= 5, tck= 0) axis (2, at= c (0.8, 1), labels= FALSE, tick= T, lwd= 5, tck= 0) Cheers, Lorenz - Lorenz Gygax Tel: +41 (0)52 368 33 84 / [EMAIL PROTECTED] Centre for proper housing of ruminants and pigs Swiss Federal Veterinary Office

RE: [R] multiple error strata in aov

Pinheiro Bates? Personally, I find it easier to work with lme and this should be an easy one. What about lme (fixed= Y ~ A, random= ~ 1 | B) or lme (fixed= Y ~ A, random= ~ A | B)? Regards, Lorenz - Lorenz Gygax, Dr. sc. nat. Tel: +41 (0)52 368 33 84 / [EMAIL PROTECTED] Center

RE: [R] mixed models question

one of the new lme packages or from MASS). Regards, Lorenz - Lorenz Gygax, Dr. sc. nat. Tel: +41 (0)52 368 33 84 / [EMAIL PROTECTED] Center for proper housing of ruminants and pigs Swiss Veterinary Office agroscope FAT Tänikon, CH-8356 Ettenhausen / Switzerland Fax : +41 (0)52 365 11 90

RE: [R] lme newbie question

aren't a trivial topic in R :) They never are. But, after having read most of Pinheiro and Bates' book 'Mixed effects modelling in S and S-PLUS' (Springer), it seems easier to me than ever, because they use a consistent, integrated and concise approach. Regards, Lorenz - Lorenz Gygax, Dr. sc. nat

[R] dfs in lme

Can anyone point me in the right direction on where and how to answer these questions? Many thanks and regards, Lorenz - Lorenz Gygax Tel: +41 (0)52 368 33 84 / [EMAIL PROTECTED] Center for proper housing of ruminants and pigs Swiss Veterinary Office agroscope FAT Tänikon, CH-8356

[R] bug in cor (..., use= ...)?

, y, use= 'pairwise.complete.obs', method= 'kendall') As I understand, the first one of this should result in an error which it does not. All the results are the same and seemingly treat the NA as if it was 0. Any ideas are appreciated. Thanks and regards, Lorenz - Lorenz Gygax, Dr. sc. nat. Tel

[R] glmmPQL - predict (..., type= 'response')?

Dear R users, Is there something like predict (..., type= 'response') for glmmPQL objects or how would I get fitted values on the scale of the response variable for the binomial and the poisson family? Any pointers are appreciated. Thanks, Lorenz - Lorenz Gygax, Dr. sc. nat. Tel: +41 (0)52

RE: [R] Repeated measures regression

Why not start with: @Book{Pin:00a, author = {Pinheiro, Jose C and Bates, Douglas M}, title ={Mixed-Effects Models in {S} and {S}-{P}{L}{U}{S}}, publisher ={Springer}, year = {2000}, address = {New York} } Regards, Lorenz -Original Message-

RE: [R] Mixed-effects model for nested design data

Bates? They explain well how to set up models. Regards, Lorenz - Lorenz Gygax, Dr. sc. nat. Tel: +41 (0)52 368 33 84 / [EMAIL PROTECTED] Tag der offenen Tür, 11./12. Juni 2004: http://www.fat.ch/2004 Center for proper housing of ruminants and pigs Swiss Veterinary Office agroscope FAT

RE: [R] modelling nested random effects with interactions in R

interactions togethter lead to a statistically better model: anova (lakernd, lakernd.int) I hope this helps to get you on the right track. Regards, Lorenz - Lorenz Gygax Tel: +41 (0)52 368 33 84 / [EMAIL PROTECTED] Center for proper housing of ruminants and pigs Swiss Veterinary Office agroscope FAT

[R] Hangup on save.image () / q ()

word)? Many thanks, Lorenz - Lorenz Gygax Tel: +41 52 368 33 84 / [EMAIL PROTECTED] Center for proper housing of ruminants and pigs Swiss Veterinary Office, FAT, CH-8356 Tänikon / Switzerland __ [EMAIL PROTECTED] mailing list https