similar to: A problem about the package "lme4" in R-2.11.1

> I would assume that > library(Matrix, include.only="isDiagonal") > implies that only `isDiagonal` ends up on the search path This could also be a reasonable behavior, but neither does that happen today. > I think a far better approach to solve Michael's problem is simply to use > fac2sparse <- Matrix::fac2sparse This does not fully simulate attachment, e.g.

? "form" -> "from". Diff against latest SVN: Index: sparse.model.matrix.Rd =================================================================== --- sparse.model.matrix.Rd??? (revision 3336) +++ sparse.model.matrix.Rd??? (working copy) @@ -4,7 +4,7 @@ ?\alias{fac2sparse} ?\alias{fac2Sparse} ?\description{Construct a sparse model or \dQuote{design} matrix, -? form a formula

I think we should try to advance and hopefully finalize this thread before we forget about it .. >>>>> Michael Chirico n Thu, 11 Apr 2024 09:10:11 -0700 writes: >> I would assume that >> library(Matrix, include.only="isDiagonal") >> implies that only `isDiagonal` ends up on the search path > This could also be a reasonable

Hi, I wanted to check the difference in results (using lme4) , if I treated a particular variable (beadchip) as a random effect vs if I treated it as a fixed effect. For the first case, my formula is: lmer.result <- lmer(expression ~ cancerClass + (1|beadchip)) For the second case, I want to do: lmer.result2 <- lmer(expression ~ cancerClass + beadchip) However, I get an error in

Dear R users, I'm trying to use function 'refit' from lme4 and I get this error that I can't understand: > refit(dolo4.model4,cbind(uu,50-uu)) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "refit", for signature "mer", "matrix" if I try: > refit(dolo4.model4,uu) Error in asMethod(object) :

I mistakenly left a write in "/tmp" in the rockchalk package (version 1.8.109) that I uploaded last Friday. Kurt H wrote and asked me to fix today. While uploading a new one, I became aware of a problem I had not seen. The version I uploaded last Friday, 1.8.109, has OK status on all platforms except r-release-windows-ix86+x86_64. I get OK on oldrel-windows and also on devel-windows.

Hi: I was trying to use apply on a sparse matrix from package Matrix, and I get the error: Error in asMethod(object) : Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 106 Is there a way to apply a function to all the rows without bumping into this problem? Here is a simplified example: > dim(sm) [1] 72913 43052 > class(sm) [1] "dgCMatrix"

Dear R and lme4 users- I am trying to fit a mixed-effects model, with the glmer function in lme4, to right-skewed, zero-inflated, non-normal data representing understory grass and forb biomass (continuous) as a function of tree density (indicated by leaf-area). Thus, I have tried to specify a Gamma distribution with a log-link function but consistently receive an error as follows: >

Hi, Calling gdistance::shortestPath gives me the error Error in asMethod(object) : not a symmetric matrix; consider forceSymmetric() or symmpart() The output of dput(.traceback()) is pairlist("stop(\"not a symmetric matrix; consider forceSymmetric() or symmpart()\")", "asMethod(object)", "as(Laplacian,\"symmetricMatrix\")",

Dear all, I want to estimate a crossed-random-effects model (i.e., measurements, students, schools) where students migrate between schools over time. I'm interested in the fixed effects of "SES", "age" and their interaction on "read" (reading achievement) while accounting for the sample design. Based on a previous post, I'm specifying my model as: fm1 <-

I have a pretty large sparse matrix of integers: > dim(tasa) [1] 91650 37651 I need to add one to it in order to take logs, but I'm getting the following error: > tasa = log(tasa + 1) CHOLMOD error: problem too large Error in asMethod(object) : Cholmod error `problem too large' I have 2 Gb of RAM, and the current workspace is barely 300mb. Is there any workaround to this?

I have a pretty large sparse matrix of integers: > dim(tasa) [1] 91650 37651 I need to add one to it in order to take logs, but I'm getting the following error: > tasa = log(tasa + 1) CHOLMOD error: problem too large Error in asMethod(object) : Cholmod error `problem too large' I have 2 Gb of RAM, and the current workspace is barely 300mb. Is there any workaround to this?

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

I have a data in the following form : CIN TRN_TYP 9079954 1 9079954 2 9079954 3 9079954 4 9079954 5 9079954 4 9079954 5 9079954 6 9079954 7 9079954 8 9079954 9 9079954 9 . . . . . . there are 100 types of CIN (9079954,12441087,15246633,...) and respective TRN_TYP first of all, I want this data to be

Right now, attaching the same package with different include.only= has no effect: library(Matrix, include.only="fac2sparse") library(Matrix) ls("package:Matrix") # [1] "fac2sparse" ?library does not cover this case -- what is covered is the _loading_ behavior of repeated calls: > [library and require] check and update the list of currently attached packages and

Dear all, My code is presented as the following. library(MASS) library(rmutil) library(repeated) library(lme4) library(arm) #install.packages("Zelig", repos = "http://gking.harvard.edu") library(Zelig) rm(list = ls()) beta0<-2.5 beta1<--0.3 sigs2<-0.5 I<-4 #numberpatients<-c(40,100,160,200,400,600) numberpatients<-c(1000) #numberpatients<-3 times<-1

Hi, We've observed rather strange behavior related to as(). When as() is used to make a conversion to a super class, an invalid entry is inserted into the table of methods. > setClass("A", contains="list") > get(".MTable", environment(coerce))[["list#A"]] NULL > as(list(), "A") > get(".MTable",

Dear R users I have built several glmm models using glmmPQL in the following structure: m1<-glmmPQL(dev~env*har*treat+dens, random = ~1|pop/rep, family = Gamma) (full script below, data attached) I have tried all the methods I can find to obtain some sort of model fit score or to compare between models using following the deletion of terms (i.e. AIC, logLik, anova.lme(m1,m2)), but I

I've got a problem with "mcmcsamp" used with glmer objects produced with "lmer" from the lme4 package. When calling mcmcsamp, I get the error Error in if (var(y) == 0) { : missing value where TRUE/FALSE needed This does not occur with all models, but I can't find anything wrong with the dataset. If the error is in my data, can someone tell me what I am looking

Dear colleagues, each time I use htmlParse, R crashes or hangs. The url I'd like to parse is included below as is the results of a series of basic commands that describe what I'm experiencing. The results of sessionInfo() are attached at the bottom of the message. The thing is, htmlTreeParse appears to work just fine, although it doesn't appear to contain the information I need (the