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...(~ 0 + stim)), data=mydat1) When I check the approximate variance-covariance matrix, I get: > fm0$apVar [1] "Non-positive definite approximate variance-covariance" *However*, if I do the same on a Windows or a Mac OS X machine, I get: > fm0$apVar reStruct.subj1 reStruct.subj2 reStruct.subj3 reStruct.subj1 reStruct.subj1 1.952757e-01 3.130089e-01 5.766955e-01 -0.1034862377 reStruct.subj2 3.130089e-01 5.703211e-01 9.864047e-01 -0.1937902915 reStruct.subj3 5.766955e-01 9.864047e-01 1.861434e+00 -0.3303689957 reStruct.subj1 -1.0348...

Dear R users, I'm attempting to fit a GLM with random effects using the tweedie family for the error structure. I'm getting the error: iteration 1 Error in logLik.reStruct(object, conLin) : NA/NaN/Inf in foreign function call (arg 3) I'm running V2.1.0 I notice from searching the lists that the same error was reported in May 2004 by Spencer Graves, but no-one was able to offer any suggestions. Running the sample code that he provided also still produce...

...can try and understand why a particular model is failing to solve/converge from the verbose output one can generate when fitting a nonlinear mixed model. I am trying to understand this output and have not been able to find out much: **Iteration 1 LME step: Loglik: -237.4517 , nlm iterations: 22 reStruct parameters: subjectno1 subjectno2 subjectno3 subjectno4 subjectno5 subjectno6 -0.87239181 2.75772772 -0.72892919 -10.36636391 0.55290322 0.09878685 PNLS step: RSS = 60.50164 fixed effects:2.59129 0.00741764 0.57155 iterations: 7 Convergence: fixed reStruct 5.740688 2.15...

...s the d1 and d2 variables to the function as d1.1, d1.2, d1.3, and d2.1, d2.2, d2.3 to take into account the three grouping levels I have. The three d1's are then condensed into a single d1 column with respect to group. Same with the d2's. Thanks. John PS: Can anyone tell me what the reStruct parameter means? In looking at the verbose output, I obtain a reStruct parameter value of -0.8352462 (this is for my grouping factor for the random effect). Does anyone know what it means? The actual value of my single random effect is different, as is its variance.

Sorry if this is obvious, but my S skills aren't great and I haven't been able to find it documented anywhere. I want to write a new function for use with lme objects; the function will simply calculate an ICC (aka "rho") for each level of a mixed-effects model. What I need for this is pretty simple: (c(var1..varn, residual)) / sum(c(var1..varn, residual)) where var1..varn

Hi folks, I am tearing my hair out on this one. I am using an example from Pinheiro and Bates. ### this works data(Orange) mod.lis <- nlsList(circumference ~ SSlogis(age, Asymp, xmid, scal), data=Orange ) ### This works mod <- nlme(circumference ~ SSlogis(age, Asymp, xmid, scal), data=Orange, fixed = Asymp + xmid + scal ~ 1, start =

...weights=varPower(fixed=1)) (mydata has over 1000 records, so I won't reproduce it here). When I run this, I get the error: Error: dim<- length of dims do not match the length of object It turns out the error is being thrown by the statement: dim(work$pdFactor) <- dim(pdMatrix(nlmeSt$reStruct[[1]])) indeed: Browse[1]> length(work$pdFactor) [1] 72 Browse[1]> dim(pdMatrix(nlmeSt$reStruct[[1]])) [1] 6 6 It looks like work$pdFactor contains information about both levels of nesting, which is being ignored. Does someone have an idea for a fix (or am I abusing nlme)? I'm using :...

Hi, lme() users, Can some one tell me how to do this. I model Orthodont with the same G for random variables, but different R{i}'s for boys and girls, so that I can get sigma1_square_hat for boys and sigma2_square_hat for girls. The model is Y{i}=X{i}beta + Z{i}b + e{i} b ~ iid N(0,G) and e{i} ~ iid N(0,R{i}) i=1,2 orth.lme <- lme(distance ~ Sex * age, data=Orthodont, random=~age|Subject,

Dear all, Here is the question: For example, using the "petrol" data offered with R. pet3.lme<-lme(Y~SG+VP+V10+EP,random=~1|No,data=petrol) pet3.lme$sigma gives the residual StdDev. But I can't figure out how to extract the "(intercept) StdDev", although it is in the print out if I do "summary(pet3.lme)". In

...dom=list(code_tripnr=~1),family="poisson", niterPQL=200, control=lmeControl(returnObject=T)) Maximum number of PQL iterations: 200 iteration 1 iteration 2 Error in MEestimate(lmeSt, grps) : Singularity in backsolve at level 0, block 1 In addition: Warning messages: 1: In logLik.reStruct(object, conLin) : Singular precision matrix in level -1, block 1 2: In logLik.reStruct(object, conLin) : Singular precision matrix in level -1, block 1 3: In logLik.reStruct(object, conLin) : Singular precision matrix in level -1, block 1 4: In logLik.reStruct(object, conLin) : Singu...

My apologies if this is obvious: Is there a simple way (other than simulation or bootstrapping) to obtain a (approximate)confidence interval for the ratio of 2 variance components in a fitted lme model? -- In particular, if there are only 2 components (1 grouping factor). I'm using nlme but lme4 would be fine, too. -- Bert Gunter Genentech Non-Clinical Statistics South San Francisco, CA

...don't really represent any meaningful gradient, slip is a random effect. There are also an unequal number of slips at each dock. I'm having syntactical issues, however. When I try dock.lme<-lme(X.open ~ Dock, random=Slip|~Dock, data=my.data) I get Error in inherits(object, "reStruct") : Object "Slip" not found I'm uncertain as to what this means, as Slip most certainly is there (yes, I checked) - any pointers, or pointers about syntax for this as a general topic. And while I'm on it, is there a way to fit models with random effects using least squar...

...om=~1+y|id,na.action=na.omit)) #Error in chol.default((value + t(value))/2) : # the leading minor of order 2 is not positive definite I also tried fitting the same model with a diagonal covariance structure, which resulted in convergence failure. m3.lme<-with(data,lme(y~x1+x2+x3+factor,random=reStruct(object=~1+y|id,pdClass="pdDiag"),na.action=na.omit)) #Error in lme.formula(y ~ x1 + x2 + x3, random = reStruct(object = ~y | : #nlminb problem, convergence error code = 1 #message = false convergence (8) However, changing lmeControl gets this model to run, but I can't make sense of...

Hi, I've got a question regarding the restructering of a data set. What I have are municipality zip-codes and the names of 5'000 built-up areas within municipalities. The following example shows, what I would like to do: Input (Zip-Codes and Names): # CODE NAME #1 3 aaa #2 3 aab #3 3 aac #4...

Greetings, 1) Is there a nice way of extracting the variance estimates from an lme fit? They don't seem to be part of the lme object. 2) In a series of simulations, I am finding that with ML fitting one of my random effect variances is sometimes being estimated as essentially zero with massive CI instead of the finite value it should have, whilst using REML I get the expected value. I guess

...ber of Groups: 119 > When I try to get the contrast I get one of two errors each time. Trying for a paired contrast... tst <- contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr="R"), b=list (Yr=levels(Yr, Tr="T97"))) Error in gendata.default(fit = list(modelStruct = list(reStruct = list ( : not enough factors Trying to include the other factor to make R happy.... > tst <- contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr="R"), b=list (Yr=levels(Yr, Tr="T97")), c=list(Yr=levels(Yr, Tr="T98")) + ) Error in contrastCalc(fit, ...) : argum...

...= fgdata.df[coded.resource,], + na.action=na.omit, + niter=50, + family=binomial(link=probit)) iteration 1 iteration 2 iteration 3 iteration 4 iteration 5 iteration 6 iteration 7 iteration 8 Error in logLik.reStruct(object, conLin) : NA/NaN/Inf in foreign function call (arg 3) The traceback() output is very long, so I won't post it, but you can see it here: http://www.unc.edu/~aperrin/stuff/diagnostics Thanks, Andy Perrin ---------------------------------------------------------------------- An...

Hi all, I'm trying to build from source on Linux and getting the following error when it tries to build the help for 'nlme': <snip> ranef.lme text html latex example reStruct text html latex example /home/sfalcon/sw/R-related/R-1.8.1/bin/INSTALL: line 1: 8133 Segmentation fault ${R_CMD} perl "${R_HOME}/share/perl/build-help.pl" ${build_help_opts} "${pkg_dir}" "${lib}" "${R_PACKAGE_DIR}" &quot...

...ually and reset j in for-loop every time error returned. Doing this manually would be very tedious. m1<-matrix(ncol=3,nrow=0) for (j in 1:1000){ fit<-lme(Expression~1,random=~1|MonkeyID, data=mydata1,subset=Probes==as.character(Probes_Blood_sub[j,"probe"])) ci<-intervals(fit)$reStruct$MonkeyID^2 m1<-rbind(m1,ci)} Thanks,Sityee _________________________________________________________________ The i’m Talkathon starts 6/24/08.  For now, give amongst yourselves. [[alternative HTML version deleted]]

I'm using glmmPQL, and I still have a few problems with it. In addition to the issue reported earlier, I'm getting the following error and I was wondering if there's something I can do about it. Error in logLik.reStruct(object, conLin) : Na/NaN/Inf in foreign function call (arg 3) ... Warnings: 1: Singular precistion matrix in level -1, block 4 (...) 4: "" The interaction terms are primed ~ log(dist) * role random = ~ dist | target.utt / prime.utt The family is binomial (logit). I ensured that log...