search for: pdmat

I would like to be able to use lme to fit random effect models In which some but not all of the random effects are constrained to be independent. It seems as thought the pdMat options in lme are a promising avenue. However, none of the existing pdMat classes seem to allow what I want. As a specific example, I would like to fit a random intercept/slope mixed model to longitudinal observations in which the subjects are divided into 5 subgroups. There is good reason to sus...

Alguien tiene experiencia en escribir una pdMat. Para aquellos que no lo recuerden son las matrices de covarianzas de los efectos aleatorios que ajusta la función lme de la librería nlme Estas matrices tiene especial importancia en aplicaciones de genética de poblaciones y en particular en mapeo de asociación. Pinheiro y Bates dicen que el usua...

Dear members, I would like to switch from nlme to lme4 and try to translate some of my models that worked fine with lme. I have problems with the pdMat classes. Below a toy dataset with a fixed effect F and a random effect R. I gave also 2 similar lme models. The one containing pdLogChol (lme1) is easy to translate (as it is an explicit notation of the default model) The more parsimonious model with pdDiag replacing pdLogChol I cannot reproduc...

Hello. I want to specify a diagonal structure for the covariance matrix of random effects in the lme() function. Here is the call before I specify a diagonal structure: > fit2<-lme(Ln.rgr~I(Ln.nar-log(0.0011)),data=meta.analysis, + random=~1+I(Ln.nar-log(0.0011)|STUDY.CODE,na.action=na.omit) and this works fine. Now, I want to fix the covariance between the between-groups slopes

...e also # specify cov structure using value arg lme(response ~ 1, data=data.df, random=list( batch=pdSymm( value=batch.mat, form=~1, nam=batch.names) ) ) # throws error below ---snip--- Error in "Names<-.pdMat"(`*tmp*`, value = "(Intercept)") : Length of names should be 3 > traceback() 7: stop(paste("Length of names should be", length(dn))) 6: "Names<-.pdMat"(`*tmp*`, value = "(Intercept)") 5: "Names<-"(`*tmp*`, value = "(Inte...

...dual* ("within-group") variances for the two groups using varIdent. They also tantalizingly say, "The single-level variance function model (5.10) can be generalized to multilevel models" (page 206), which seems to suggest that a solution to the current problem might exist. The pdMat classes provide a way to *constrain* the dispersion matrix of the random effects, not make it more general. Of course, one way to test for unequal variances is to apply an F-test for equal variances to the random intercepts. If the data are as shown at the bottom of this email, the test can be imp...

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

...td=gnu99 -c nlme.c -o nlm e.o gcc -I"C:/pfs/R/R-2.11.1/include"???????? -O3 -Wall? -std=gnu99 -c nlmefit.c -o nlmefit.o gcc -I"C:/pfs/R/R-2.11.1/include"???????? -O3 -Wall? -std=gnu99 -c nls.c -o nls. o gcc -I"C:/pfs/R/R-2.11.1/include"???????? -O3 -Wall? -std=gnu99 -c pdMat.c -o pd Mat.o gcc -shared -s -static-libgcc -o nlme.dll tmp.def corStruct.o gnls.o init.o matr ix.o nlOptimizer.o nlme.o nlmefit.o nls.o pdMat.o -LC:/pfs/R/R-2.11.1/bin -lR installing to C:/pfs/R/R-2.11.1/library/nlme/libs ? ... done ** R ** data **? moving datasets to lazyload DB ** inst ** prepar...

...Identity-structure matrix. So i had, in symbols of nlme-package, and for only one cluster-variable my.Subject: random=list(my.Subject=pdBlocked(list(pdIdent(~var.a1+var.a2+var.a3,...),pdIdent(~var.b1+var.b2,...),pdIdent(~var.c1+var.c2+var.c3+var.c4),...))) As the lme4-package doesn't use the pdMat-classes for specification of the random-part in GLMM, i used, with advice of Douglas Bates, the explicit specification in the GLMM-call (this call can also been simplified, if i first attach the lme4 package and then the nlme-package): GLMM(....., random=list(my.Subject=~var.a1+var.a2+var.a3...

Folks: Suppose I have 3 random effects, A,B, and C. Using the older lme() function (in nlme) it was possible (using the pdMat classes) to specify that they are uncorrelated with identical variances. Is it possible to do this with lmer? My understanding is that if I specify them as lmer( y ~ ... + (A|Grp) + (B|Grp) + (C|Grp)) then they are uncorrelated but have different variances. Motivation: I'd like to use lmer i...

...that Iwant to evaluate randomness in the interaction x*z (i.e intercept, slope, interaction) grouped by by a general nesting structure that sets factorA1 and factorA2 as same level effects (hence non nested) and factorB as nested in both. I also must express my momentaneous sheer ignorange on the pdMat objects, thing that prabably is not helping me in the process Kindly Regards Federico Bonofiglio [[alternative HTML version deleted]]

...clustering variable. The code above returns separate variances for the random effects associated with x1-x4, as well as the correlation between them. What I really want is the random effects to all have the same variance (i.e. multiple of an identity). It doesn't seem that you can use the pdMat classes, like with lme. Can glmer do what I need it to do, or is there another command that I should be using? Any guidance would be great. Cheers, Kris Kris Jamsen Research Fellow Centre for Molecular, Environmental, Genetic and Analytic (MEGA) Epidemiology Level 1, 723...

..., Z(Dk)Z+sigmak), so I need to extract D0 and D1 form the lme object. I've looked in Pinheiro and Bates but was unable to identify how to fit this type of covariance matrix from the examples provided in the book - perhaps it is there expressed in a different form? I looked in section 4.2.2 (pdMat) of teh book but I'm still not sure how to pass it on in the call. Any help would be greatly appreciated, Regina Regina Rendas-Baum Graduate Student Brown University Biostatistics

Hi, When installing "nlme" from CRAN on Solaris 5.3.1 by doing install.packages("nlme") I get: [clip] gcc -G -o nlme.so corStruct.o gnls.o matrix.o nlOptimizer.o nlme.o nlmefit.o nls.o pdMat.o -L/usr/local/lib R data inst /usr/local/lib/R/bin/INSTALL: /bin/perl: not found help /usr/local/lib/R/bin/INSTALL: /usr/local/lib/R/bin/build-help: not found /usr/local/lib/R/bin/INSTALL: /usr/local/lib/R/bin/Rd2contents: not found DONE (nlme) I wonder why I have never encountered this di...

The print method for lme *prints out* the fitted correlation matrix for the random effects. Is there any way to get these values as an object in R? I have examined the components of the lme object (called "junk" in the example below) and the components of summary(junk) without finding these numbers. (How I did this: I dumped the entire lme object to a text file and then used egrep to

...lot.HoltWinters* [19] plot.intervals.lmList* plot.isoreg* plot.lm [22] plot.lme* plot.lmList* plot.medpolish* [25] plot.mlm plot.nffGroupedData* plot.nfnGroupedData* [28] plot.nls* plot.nmGroupedData* plot.pdMat* [31] plot.ppr* plot.prcomp* plot.princomp* [34] plot.profile.nls* plot.ranef.lme* plot.ranef.lmList* [37] plot.shingle* plot.simulate.lme* plot.spec [40] plot.stepfun plot.stl* plot.table*...

Dear R-list, I?m trying to use the lmer of the lme4 package to fit a linear mixed model of the form Y = Xb + Zu + e and I can?t figure out how to control the covariance structure of u. I want u ~ N(0,sigma^2*I). More precisely I?m trying to smooth a curve through data using the "Penalized Splines as BLUPs" method as described in Ruppert, Wand & Carroll (2003). So I have Z = [Z1

...NULL) : Object must be a list or a formula I also tryed creating a function fun <- function(a,b,c,d) a+b+c+d Then tryed fit <- nlme(Y ~ fun(A,B,C,D), fixed=list(A,B,C,D),random=list(Z)). I got this error message: Error in FUN(X[[1]], ...) : Elements in object must be formulas or pdMat objects Please help me! Thank you, Debbie __________________________________________________ Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. http://geocities.yahoo.com/ps/info1 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing...

.../2) incidence matrix using the lme and lmer packages. The closest I got was with the lmer package, where I tried using the doFit=FALSE flag and manually setting the 'Zt' matrices but that doesn't seem to work. With the lme package, I'm not sure if it's possible to create a new pdMat class or if I can manually set the Z design matrix. I tried using the model.matrix commands but that only reads the current design. Thanks in advance to whoever can help out. ~Jimmie [[alternative HTML version deleted]]

Dear R users, I have been using the pdMat class "pdIdnot" (from the mgcv package)instead of "pdIdent" to avoid overflow in GLMM fits with the MASS package function glmmPQL, of the following form: fit1 <- glmmPQL(fixed=y0~-1+xx0, random=list(gp=pdIdent(~-1+zz0)), family=binomial) # vulnerable to...