search for: downdat

Dear R-devel members, I am looking for a fast Cholesky update/downdate. The matrix A being symmetric positive definite (n, n) and factorized as A = L %*% t(L), the goal is to factor the new matrix A +- C %*% t(C) where C is (n, r). For instance, C is 1-column when adding/removing an observation in a linear regression. Of special interest is the case where A is s...

...dii: 1) with both random effects, 2+3) only one (each) random effect, and 4) none. I have tried to model the relationships using glm, glmer and lmer. The problem is that in the full model (all 7 variables) of some sets with random effects I get the following error: *Error in mer_finalize(ans) : Downdated X'X is not positive definite, 8.* The only record of this error I have found in the internet is for data with missing observation. This doesn't comply with my data set. I think it might be a singularity problem but I don't know how to check it, and as a result, I obviously don'...

...m3 <- lmer(.D ~ offset(log(.Y)) + (1|provn) +(1|bcohort) + x1 + x2 + z1 + z2 + x1:z1 + x2:z2, data, poisson, method="Laplace") Both model 1 and 2 run fine. For model 3, I got error message: ---------------------------------- Error in fn(par, ...) : Unable to invert singular factor of downdated X'X In addition: Warning messages: 1: optim or nlminb returned message ERROR: ABNORMAL_TERMINATION_IN_LNSRCH in: LMEopt(x = mer, value = cv) 2: Leading minor of size 1 of downdated X'X is indefinite ---------------------------------- What is going on here? Any workarounds? Thanks! B...

...measures and would like to include one (enclosure) random factor. I chose to use the glmer function (and tried the lmer as well). m1<-glmer(alive~treat*sex*trapping*ID+(1|enclosure),family=binomial,data=survadult) Both give the following error message: Error in mer_finalize(ans) : Downdated X'X is not positive definite, 49. Additionally: Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred I get that there is something wrong in my dataframe, but I don`t understand what and how I could change it. If I run a glm without the random factor m1<-...

...e model and code (same dataset) failed to run in lme4 and gave me the error message below. Any thoughts? lme(math~year, data=egsingle, random=~year|schoolid/childid) Error in lme(formula = math ~ year, data = egsingle, random = structure(list( : Unable to invert singular factor of downdated X'X Harold [[alternative HTML version deleted]]

Hey, I am having trouble with lmer. I am looking at the presence/absence of water shrews against habitat and other factors e.g so I used this: m1<-lmer(Presencebsence~Habitatype*Width+(1|Sitename))summary(m1) But i keep getting this error up Error in mer_finalize(ans) : Downdated X'X is not positive definite, 16.> summary(m1)Error in asMethod(object) : matrix is not symmetric [1,2] What does this mean and now can I fix it? Sophie [[alternative HTML version deleted]]

...Currently the simulations just stop and the output reads things like: Error in optim(.Call("lmer_coef", x, 2, PACKAGE = "Matrix"), fn, gr, method = "L-BFGS-B", : L-BFGS-B needs finite values of 'fn' In addition: Warning message: Leading minor of size 1 of downdated X'X is indefinite Error in .local(object, ...) : Leading 2 minor of Omega[[1]] not positive definite In addition: Warning messages: 1: optim or nlminb returned message ERROR: ABNORMAL_TERMINATION_IN_LNSRCH in: "LMEoptimize<-"(`*tmp*`, value = list(maxIter = 200, msMaxIter = 200,...

...ow per fish. Some results: lme4 (ver 0.98-1, R 2.1.1, Windows XP) ~~~~ > fish1.lmerPQL <- lmer(dead ~ Parasite * Bacteria + (1|Tank), data=fish.data, family=binomial) Error in lmer(dead ~ Parasite * Bacteria + (1 | Tank), data = fish.data, : Unable to invert singular factor of downdated X'X In addition: Warning message: Leading minor of size 4 of downdated X'X is indefinite > without the interaction: > fish3.lmerPQL <- lmer(dead ~ Parasite + Bacteria + (1|Tank), data=fish.data, family=binomial) > anova(fish3.lmerPQL) Analysis of Variance Table...

Hello, I'm trying to run an lmer model with family poisson but receive the following warning message: model<-lmer(count~tem+dat+alt+year+tem:dat+tem:alt+tem:year+dat:alt+dat:year+alt:year+(1|id),family=poisson) Error in objective(.par, ...) : Leading minor of order 2 in downdated X'X is not positive definite I'm using the newest version of R and recently installed the following libraries: (lme4, matrix, lattice). I don't understand what the warning message means or know how to fix it, please help! My response variable is a count variable (n=551); 212 with val...

...for nested designs but it does not work. model2 <- lmer(Growing ~ Seed + Species%in%Seed + Treatment +(Seed + Species + Treatment|Block%in%Treatment), data) I get the following error: Error en lmer(Growing ~ Seed + Species %in% Seed + Treatment + : .. Leading minor of order 5 in downdated X'X is not positive definite I would appreciate some help to fit this model. Thanks to everybody, Luis Luis Cayuela Departamento de Ecología Universidad de Alcalá Crta. de Barcelona km. 33,600 E-28871 Alcalá de Henares Madrid España Tlf: (+0034) 918856407 Fax: (+0034) 918854929 [[alt...

Dear R users, I am building a hierarchical model on a large data set. It can take quite some time to finish one fit, I was just wondering whether it is possible to store the fit object (the result) to a file for later (offline) analysis. thanks Julia -- View this message in context: http://www.nabble.com/how-to-store-lme-lmer-fit-result-tp19910951p19910951.html Sent from the R help mailing

...# first fit a linear model with letter position nested in word length lm(rt ~ length + length:pos, data=df) # fit a mixed effects model, with subj (participant) as random effect lmer(rt ~ length + length:pos + (1 | subj), data=df) Using lmer() results in an error: Error in mer_finalize(ans) : Downdated X'X is not positive definite, 13. I don't experience any problems using lm(). Does anyone know where things go wrong? ~ Ben Meijering

Hello, I hope that you can bare with me. I am new to models, but I think I have a pretty godd understanding of how to run them now, including how to use AICc and Anova. The issue is that I have many factors that I wish to compare so doing each one at a time would take forever. I came across the MuMIn package and I was so excited, however I am getting an error message and i don't know why.

...+d+e+f+h+i, random = random = ~ e+f+h+i| group, data = mydata) # Using lmer mix.lmer <- lmer(DV ~a+b+c+d+(1|group)+(e|group)+(f|group)+(h|group)+(i|group), data = mydata) lme provided an output (fixed effects and random effects coefficients). lmer gave me an error: Error in mer_finalize(ans) : Downdated X'X is not positive definite, 10. I've rerun lmer with - but specifying the random effects for 2 fewer predictors. This time it ran and provided an output. (BTW, the random effects of lmer with 2 fewer predictors specified as random were very close to the output of lme). Question: Looks...

...ethods. Following the Oats example in chap. 1 of MEMSS, and adapting to lmer: <<2>>= require(lme4) gl.lmer <- lmer(rounds ~ method * physique + (1 | physique/team), data = gunload) mcmcsamp(gl.lmer) @ lmer runs as expected, but mcmcsamp() gives: Error: Leading minor of order 1 in downdated X'X is not positive definite Error in t(.Call(mer_MCMCsamp, object, saveb, n, trans, verbose, deviance)) : error in evaluating the argument 'x' in selecting a method for function 't' I tried: <<3>>= require(nlme) gl.lme <- lme(rounds ~ method * physique...

...d algorithms discovered over the years by a number of researchers (e.g. faster or more accurate eigenvalue and SVD algorithms, extra precise iterative refinement, recursive blocking for some linear solvers, etc.). We also know of a variety of other possible functions we could add (e.g. updating and downdating factorizations), but are uncertain of their impact. Please see http://icl.cs.utk.edu/lapack-survey.html for the survey. We would like to have your input by June 16th, 2004. Regards, Jack Dongarra, Jim Demmel, and Sven Hammarling

...e model: lmer_int_ageXdisc <- lmer(Concord ~ Age*Disc + (1|Subject), family="binomial", data=d, method="Laplace") In the actual data set the AgexDisc interaction should have 16 levels. This produces the error: Error in devLaplace(PQLpars) : Leading minor of order 7 in downdated X'X is not positive definite What does this mean? This error is not thrown for other interactions I specify from my data. Here is my session info: R version 2.4.1 (2006-12-18) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=En...

...What I want to do is to see if number of recruits (a) is dependent on the brood sex ratio (b) including brood identity (c) as random factor. However, I get the following error message; lmer(a~b + (1|c), family=poisson, data=tab) Error in devAGQ(PQLpars, 1) : Unable to invert singular factor of downdated X'X In addition: Warning messages: 1: optim or nlminb returned message singular convergence (7) in: LMEopt(x = mer, value = cv) 2: optim or nlminb returned message singular convergence (7) in: LMEopt(x = mer, value = cv) 3: optim or nlminb returned message singular convergence (7) in:...

...ng the matter with the code, hence I have not bored you with the details here).... however when I submit the job as a batch to a UNIX system it usually (but not always) fails and the execution is halted after an error message is produced: Error in objective (.par,...): Leading minor of order 1 in downdated X'X is not positive definite In addition: There were 12 warnings (use warnings() to see them) Error in logLik(model) : no applicable method for "logLik" Execution halted On windows when the execution of a single model run fails to estimate the logLik (an unstable model...) R just c...

...nsistent with my expectations. Earlier today, we updated to lme4 0.95-6 and R 2.1.0. When we try to use lmer to fit the same model, it complains bitterly: lmer(y ~ x1 + x2 + x3 + (1 + x3 | YEAR) + (1 | SITE), data=foo, family=poisson, offset=log(reps)) Error: Unable to invert singular factor of downdated X'X Simpler models still work (or at least return): lmer(y ~ x1 + x2 + x3 + (1 + x3 | YEAR), ...) lmer(y ~ x1 + x2 + x3 + (1 | YEAR) + (1 | SITE), ...) As I mentioned, the design is unbalanced. But, we get same "invert singular factor" Error using the balanced subset. Can any...