search for: reml

...quot;ML") mod2b<-lme(wthole~poly(nplants,2),data=d3,random=~1|field/subplot,method ="ML") > anova(mod2a,mod2b) Model df AIC BIC logLik mod2a 1 6 6698.231 6723.869 -3343.116 mod2b 2 6 6698.231 6723.869 -3343.116 However if I fit the two models by REML they are not considered to be the same and I get warned. > anova(mod2a.REML,mod2b.REML) Model df AIC BIC logLik mod2a.REML 1 6 6680.616 6706.219 -3334.308 mod2b.REML 2 6 6666.915 6692.518 -3327.457 Warning message: Fitted objects with different fixed effect...

Hi, I've been using gamm4 to build GAMMs for exploring environmental influences on genetic ancestry. Things have gone well and I have 2 very straightforward questions: 1. I've used method=REML. Am I correct that this is an alternative method for estimating the smooth functions in GAMMs rather than GCV that is often used for GAMs? I've read up on REML and it makes sense, but I'm confused about whether GCV is used for any part of the model formation of a GAMM with method=REML. I...

Hello. I am trying to determine whether I should be using ML or REML methods to estimate a linear mixed model. In the book by Pinheiro & Bates (Mixed-effects models in S and S-PLUS, page 76) they state that one difference between REML and ML is that « LME models with different fixed-effects structures fit using REML cannot be compared on the basis of their res...

Hi, I know that is not possible make a stepwise procedure using REML in R, I can use ML for this. For nested design it may be very dangerous due the difference in variance structure, mainly in a splitplot design. ML make significative variables that REML dont make. I read an article that is made a stepwise procedure using GENSTAT. from article: "Terms wer...

Hi, I am trying to use glmmPQL package for Generalized linear mixed models. This package works by repeated calls to lme. lme uses by default REML method for estimation. Then, does glmmmPQL use REML too? In contrast, how can I change it? I have tried it, writing : method="REML", but the program says: invalid method REML. If somebody can answer me....thanks, Sonja

Dear All, I have a question concerning the computation of the value of the Restricted Maximum Likelihood (REML) function evaluated at a given set of parameter estimates from the Maximum likelihood (ML) value. Following the book of Fitzmaurice, Laird and Ware (2004) "Applied Longitudinal Analysis" pp101, the REML likelihood can be computed by multiplying the ML likleihood by the square root of the...

Trying to use contrast to look at differences within an lme lme.fnl.REML <- lme(Max ~ S + Tr + Yr + Tr:Yr, random = ~1 |TID, method = "REML") I have three levels of Tr I'm trying to contrast among different years (R, T97, T98), years = 1997-1999, so I'm interested in contrasts of the interaction term. > anova(lme.fnl.REML) n...

..."ok", icon = c("error"), parent = 0) } ## ANOVA 2 facteurs Resultats=NULL Res=NULL i=0 while(i!=length(ions)) { i=i+1 myion=toto[,i] mixed=lme(myion ~ v1*v2, random= ~ 1 | Subject/v1,method="REML") ## effet al?atoire sujet(v1) #summary(mixed) #anova(mixed) zz=anova(mixed) Res <- data.frame(ions[i],toto1[i,2:(dim(toto1)[2]-n)],t(zz[-1,4]),toto1[i,c((dim(toto1)[2]-n+1):dim(toto1)[2])]) Resultats <- rbind(Resultats,Res)...

...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 structure and both are estimated with REML (I must admit I do not know exactly what REML is, although I do understand the concept of ML). The examples in Pinheiro & Bates 2000 deal with simple vs. complicated random-effects structures, both fitted with lme and method="REML". However, to fit a model without random effe...

Hi, In glmmPQL in the MASS library, the function uses repeated calls to the function lme(), using ML. Does anyone know how you can change this to REML? I know that in lme(), the default is actually set to REML and you can also specify this as 'method=REML' or 'method'ML' but this isn't applicable to glmmPQL(). I'd appreciate any help or advice! Thanks, Emma

hi I'm puzzled as to the relation between the REML score computed by gam and the formula (4) on p.4 here: http://opus.bath.ac.uk/22707/1/Wood_JRSSB_2011_73_1_3.pdf I'm ok with this for poisson, or for quasipoisson when phi=1. However, when phi differs from 1, I'm stuck. #simulate some data library(mgcv) set.seed(1) x1<-runif(500) x2&l...

Hi everyone, I have been using REML to derive intercepts and coeficients for each individual in a growth study. So the code is m2 <- lmer(change.wt ~ newwt+(newwt|id), data = grow) Calling coef(model.lmer) gives a matrix with this information which is what I want. However, as a test I looked at each individual on its own and used...

Can you provide the summary(m2) results? > -----Original Message----- > From: Simon Pickett [mailto:S.Pickett at exeter.ac.uk] > Sent: Wednesday, August 16, 2006 7:14 AM > To: Doran, Harold > Cc: r-help at stat.math.ethz.ch > Subject: [SPAM] - RE: [R] REML with random slopes and random > intercepts giving strange results - Bayesian Filter detected spam > > Hi again, > Even stranger is the fact that the coefficeints (the slope) > and the intercepts are not independent, in fact they are > directly inversely proportional (r squared...

...;restricted maximum likelihood" for parameter estimation. ML has the advantage, that likelihood ratios can be computed even with changes in model structure. In addition, ML works with the stepAIC function from MASS-library which I am currently using for model-building. I am wondering, why REML is the default setting in NLME and therefore somehow preferred by the authors. What is the main reason to use REML? Maybe I am lacking here statistical knowledge. Any hint, including reference to literature would be very helpful. Best regards, Klaus Thul

...unit, it has measurement from about 25 sample site. I was trying to use lme function to discribe relationship between y and a few covariates. Both y and covariates were measured at the sample site level. My question is when I use exactlly the same model but choose different estimation method (ML vs REML), I got quite different coefficients esimate for fixed effect and variance estimate for random effect(see below). Can anyone here please help me to understand why? Thank you very much.       1) Using REML lme(y~ Region*(x1+x2+x3), random=~1|unit, data=temp)   Linear mixed-effects model fit by REML...

...hood in the expression for the (RE)ML score. I hadn't realised that this was possible before the paper was published. best, Simon ps. sorry for slow reply, the original message slipped through my filter for mgcv related stuff > hi > > I'm puzzled as to the relation between the REML score computed by gam and > the formula (4) on p.4 here: > http://opus.bath.ac.uk/22707/1/Wood_JRSSB_2011_73_1_3.pdf > > I'm ok with this for poisson, or for quasipoisson when phi=1. > > However, when phi differs from 1, I'm stuck. > > #simulate some data > librar...

Hello, I’m trying to perform a REML analysis using the lmer() function (lme4 package). Well, it seems to work well, except that I’m not getting any p-value (see example below). Can someone tell me what I did wrong? Thanks for your help, Amélie > library(gdata) > dive <- read.xls("C:/Documents and Settings/A...

...------------------------------------------------------ From: Joel Malard <JM.Malard at pnl.gov> Date: Sat, 01 May 2004 15:31:15 -0700 Subject: ACRE, Parallel Covariance Component Estimation Code A couple of people have asked recently for a copy of the parallel (restricted/residual) maximum (REML/ML) gradient algorithms from the paper: J.M. Malard, "Parallel Restricted Maximum Likelihood Estimation for Linear models with a Dense Exogenous Matrix", Parallel Computing, 28, pp343-53, 2002. The code has been upgraded to PETSc 2.2.0 and TAO 1.6 and is available by sendin...

Dear All, As you know, glmmADMB package use ML method for estimation. Is it possible to use REML estimation method for zero-inflated Poisson distribution? For ML method, poi_ML <- glmm.admb(los ~ psihigh + trt.mod + trt.high + psihigh*trt.mod + psihigh*trt.high + 1, random = ~1, group="site", family="poisson", data=edcap) summary(poi_ML) How can I control to use REML m...

...adratic terms for time.This took me a long time to figure out and I just wanted to make sure I did it correctly and I am interpreting it correctly. This is the code I ran Rtumor<-lmer(volume~Group+Time+(1|Subject), data=Rtumor)summary(Rtumor)Rtumor.null=lmer(volume~Time+(1|Subject), data=Rtumor, REML=FALSE)Rtumor.full=lmer(volume~Group+Time+(1|Subject), data=Rtumor, REML=FALSE)anova(Rtumor.null,Rtumor.full) Here is my output?Rtumor<-lmer(volume~Group+Time+(1|Subject), data=Rtumor)> summary(Rtumor)Linear mixed model fit by REML ['lmerMod']Formula: volume ~ Group + Time + (1 | Subje...