search for: varexp

...for the lme() or nlme() macros. I want to write my own specification for the variance function and am following homework problem 4, Chapter 5, page 268 of Pinheiro and Bates book on mixed effect. I'm up to point where I've created a new class using an existing variance function class, varExp as a template. Next I need to write an initialize method. The book suggests that I use the inialize method for one of the exisiting variance functions for lme(), eg varExp. What I want is the syntax of the initialize.varExp method so that I can edit it to create an initialize method for my new...

Hello. I am trying my hand at modifying the varFunc class varExp, but I must be missing a step. All I want to do right now is make a working copy of varExp, call it varExp2, and then later change it. coef.varExp2, coef<-.varExp2, and Initialize.varExp2 all seem to work properly after I construct them. I can successfully use the commands: v2 <- varExp2(...

Hi, I am trying to add multiple variance structures such as the first example below: vf1 <- varComb(varIdent(form = ~1|Sex), varPower()) However my code below will not work can anybody please advise me? VFcomb<-varComb(varExp(form=~depcptwithextybf),varFixed(form=~FebNAO)) also if you have two variables with the same weights function would you write that as: VFcomb<-varComb(varExp(form=~depcptwithextybf),varExp(form=~FebNAO)) thanks Rebecca -- View this message in context: http://www.nabble.com/Dealing-with-het...

...f male attempts increases with female quality Q1. When including the method weights in the function lmer, I get the message that variables' length varies and the model does not run. lmer(MatingAttempts~Q1+Q2+(1|Group),data=file,family="poisson",na.action=na.omit, REML=FALSE, weights=varExp(form=~Q1)) If I run the same model (fixed effects and random effects) with lme, it works properly, which shows that there is no problem with data structure. lme(MatingAttempts~Q1+Q2,random=~1|Group,data=file,na.action=na.omit, method="ML", weights=varExp(form=~Q1)) I saw on the forum t...

...heteroscedasticity. The variance function is exp(c0+nu0*W +nu1*W^2) where W is a covariate. Initially I want to use varFunc to define my own variance function following the instruction in the Pinheiro and Bates (2000), but I could not make it work. Then I used varComb in gls with weights=varComb(varExp(form=~W), varExp(form=~I(W^2))))). But the estimated variance parameters seems to have a large discrepancy from the true values (I used the simulated data). This makes me wonder if it is a right way to model variance function exp(c0+nu0*W +nu1*W^2) using "varComb". The codes and ou...

...heteroscedasticity. The variance function is exp(c0+nu0*W +nu1*W^2) where W is a covariate. Initially I want to use varFunc to define my own variance function following the instruction in the Pinheiro and Bates (2000), but I could not make it work. Then I used varComb in gls with weights=varComb(varExp(form=~W), varExp(form=~I(W^2))))). But the estimated variance parameters seems to have a large discrepancy from the true values (I used the simulated data). This makes me wonder if it is a right way to model variance function exp(c0+nu0*W +nu1*W^2) using "varComb". The codes and out...

...atomic vectors, returning NULL in: control$nlmStepMax What is new for me is the warning message. It appears when I try to specify different settings using the control statement.For example: > hm02<-gnls(ht~a1*hd*(1-a2*exp(-a3*(dbh/dq2))),data=hdat, + start=c(a1=1.04,a2=1.38,a3=2.88),weights=varExp(), + control=c(minFactor=1/2048)) Any comment will be appreciate Thanks PM

...ginal data with the line of the model using the predict function. I want to add SE to the graph, but not sure how to get them out as the predict function for gls does not appear to allow for SE=TRUE argument. Here is my code so far: f1<-formula(MaxNASC40_50~hu3+flcmax+TidalFlag) vf1Exp<-varExp(form=~hu3) B1D<-gls(f1,correlation=corGaus(form=Lat~Lon, nugget=TRUE),weights=vf1Exp , data=ocean) ochu3<-seq(from=2.9,to=4,length=120) ocflc<-seq(from=0,to=0.8,length=120) tidal1<-rep(c("1"),length=120) mydata1<-data.frame(TidalFlag=factor(tidal1),hu3=ochu3,flcmax=ocflc...

...velopmental series of two capuchin monkey species. I'm interested in whether the rate of bone length scaling to body mass (i.e., growth) differs between species. My call to lme looks like this: model=lme(lghumlen ~ species + lgbmkg, random= ~ lgbmkg | id, correlation=corCAR1(), weights=varExp()) where lghumlen is the log of humerus length and lgbmkg is the log of body mass. If I ask for a summary of my model, I get this from the table of fixed effects: Fixed effects: lghumlen ~ species + lgbmkg Value Std.Error DF t-value p-value (Intercept) 3...

...nts should be constructed separate from the model statement (not sure how this is supposed to work). Generally, I believe my model in lme4 should look like this: gm1 = glmer(cbind(#successes,#trials) ~ A*B + covariate + (1|B/C), family = binomial, link="logit", data=mydata, weights=varExp(form = ~covariate)) where #trials is the number of subjects at the beginning of the experiment in each experimental unit, #successes is the number of survivors, A and B are fully crossed fixed categorical factors, C is a categorical random factor nested within B (i.e. random site within year),...

Hello everybody. I am trying to upgrade from R-1.9.0 to R-1.9.1 on a RedHat linux 2.4.18 system. I get the following error after "tar -xvzf R-1.9.1.tgz ; cd ./R-1.9.1/ ; ./configure" and "make" : [make works for 10 minutes ... snip ...] varExp text html latex varFixed text html latex varFunc text html latex varIdent text html latex varPower text html latex varWeights...

...effect. I am not interested in a time effect. Is is still appropriate to use the AR1 auto-correlation structure? If M.AR1 is OK, should I be worried about non-homogeneity in the residuals? If so, how should I go about dealing with it? Could I add a new variance structure to the model (e.g., varExp). The approach outlined here is drawn from my interpretation of chapters 4 and 6 of Zuur et al. 2009. Mixed effects models and extensions in ecology with R. Thanks, Jake Research Ecologist US EPA [[alternative HTML version deleted]]

  Hola,   Por favor, ¿podríais indicarme qué recursos (librerías o ideas) pueden resultar de utilidad para crear un gráfico del estilo del de la figura 3.8 del siguiente link?   http://www.tsc.uvigo.es/BIO/Bioing/ChrLDoc3.html#3.5   Actualmente estoy utilizando funciones muy básicas y la verdad es que no me encuentro muy satisfecha con el resultado.   Muchas gracias.   Eva [[alternative HTML

...velopmental series of two capuchin monkey species. I'm interested in whether the rate of bone length scaling to body mass (i.e., growth) differs between species. My call to lme looks like this: model=lme(lghumlen ~ species + lgbmkg, random= ~ lgbmkg | id, correlation=corCAR1(), weights=varExp()) where lghumlen is the log of humerus length and lgbmkg is the log of body mass. If I ask for a summary of my model, I get this from the table of fixed effects: Fixed effects: lghumlen ~ species + lgbmkg Value Std.Error DF t-value p-value (Intercept) 3...