search for: supernodal

Hello list, we have been running tinc to connect multiple nodes without problems for quite some time now. Thanks for this great piece of software! Our configuration is as follows: Two "supernodes" A and B running the tinc daemon are publicly reachable from the internet. Node A is running Linux and has a static public IP address. Node B is running Windows with port forwarding

Hi, I am getting a warning message when I am fitting a generalized linear mixed model (m1.2 below). CHOLMOD warning: matrix not positive definite Error in objective(.par, ...) : Cholmod error `matrix not positive definite' at file:../Supernodal/t_cholmod_super_numeric.c, line 614 Any idea? Thanks for your help, Reza > sessionInfo() 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=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_Un...

...model<-lmer(aphids~totmas+zone+(1|zone/site), family=quasipoisson) Totmas is also a continuous variable just like densroot, but in this case I receive the following message: CHOLMOD warning: &߆e Error in objective(.par, ...) : Cholmod error `matrix not positive definite' at file:../Supernodal/t_cholmod_super_numeric.c, line 613 Moreover, if I test yet another continuous variable "vitality", to my surprise R just crashes completely. This is a mystery to me, especially because the variables totmas or vitality don't give any problem when I build the exact same models in SA...

...(1|popu:amd) + + (1|gen) + (1|gen:nutrient) + (1|gen:amd) + + (1|gen:nutrient:amd), + data=datnm, family=binomial, method="AGQ") Error in lmer(yb ~ reg * nutrient * amd + (1 | rack) + (1 | status) + : method = "AGQ" not yet implemented for supernodal representation I would really appreciate any and all thoughts or leads. Cheers, Hank Stevens > version _ platform powerpc-apple-darwin8.6.0 arch powerpc os darwin8.6.0 system powerpc, darwin8.6.0 status major 2 minor 3.1 y...

Hello tinc users, I have been trying to work out how key exchange/hosts file sharing in tinc 1.1 works. My topology is straightforward, a "super" always-online node A to which remote nodes B, C, ... (and so on) ConnectTo = A, to discover each other via AutoConnect (that's on by default in tinc 1.1pre17) Only super A has host files with Ed25519 keys for every node on the network.

This is a "heads up" to those using the lmer function for fitting linear mixed models or generalized linear mixed models. In the next few days Martin and I will upload a new version of the Matrix package that employs a new representation of linear mixed models based on the supernodal Cholesky factorization provided by Tim Davis's CHOLMOD library of sparse matrix code. This representation will be incompatible with the current representation, which uses a class of blocked compressed sparse matrices called the dBCMatrix class. If you have an lmer object created with the curr...

...+(1|site)+(1|site/hab)) which also made R crashing. And, fm2<-lmer(data=NGud,family=poisson, seed~hab*seedtray +(1|site/hab)) and for this, I obtained : CHOLMOD warning: matrix not positive definite Error in devLaplace(PQLpars) : Cholmod error `matrix not positive definite' at file:../Supernodal/t_cholmod_super_numeric.c, line 614 J?r?me Lema?tre ?tudiant au doctorat Chaire de recherche industrielle CRSNG - Universit? Laval en sylviculture et faune & D?partement de biologie, Facult? des sciences et de g?nie Pavillon Alexandre-Vachon Universit? Laval Qu?bec, QC G1K 7P4 t?l : (418...

...f all the AIC of each model. For 1 of the models (the one in the [] above) I'm getting the following error message, which I don't know what it means: CHOLMOD warning: matrix not positive definite Error in objective(.par, ...) : Cholmod error `matrix not positive definite' at file:../Supernodal/t_cholmod_super_numeric.c, line 614 Could anybody give me some advice on using Tweedie distributions and does anybody have an idea what this error message means. Thanks a lot in advance, Cheers, Cristina.

This is a "heads up" to those using the lmer function for fitting linear mixed models or generalized linear mixed models. In the next few days Martin and I will upload a new version of the Matrix package that employs a new representation of linear mixed models based on the supernodal Cholesky factorization provided by Tim Davis's CHOLMOD library of sparse matrix code. This representation will be incompatible with the current representation, which uses a class of blocked compressed sparse matrices called the dBCMatrix class. If you have an lmer object created with the curr...

Hi! I get the following message trying to install the matrix pakcage, can anyone help me please? trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/Matrix_0.95-5.zip' Error in download.file(url, destfile, method, mode = "wb") : cannot open URL `http://cran.r-project.org/bin/windows/contrib/2.0/Matrix_0.95-5.zip' In addition: Warning message: cannot open: HTTP

i am using ipp2p module (v 0.6) from http://rnvs.informatik.uni-leipzig.de/ipp2p/index_en.html I have tried it on kazaa and e-donkey connections. Unfortunately, I am interesting in limiting kazaa traffic, which this modules seems not to work right with it. (Kazza traffic is not identified most of the cases....). Has anyone tried this kazza bandwidth control???

...: > residuals(reml.res) Error: 'residuals' is not implemented yet > resid(reml.res) Error: 'resid' is not implemented yet > names(reml.res) NULL > mcmcsamp(reml.res) Error in .local(object, n, verbose, ...) : mcmcsamp for GLMMs not yet implemented in supernodal representation I’m supposed to give a talk tomorrow and would be very grateful if someone can help me… I’m working with the following versions: Package: Matrix Version: 0.995-8 Date: 2006-03-21 Package: lme4 Version: 0.995-2 Date:...

I have been using lme from nlme to do a 3-way anova with all the effects treated as random. I was wondering if someone could direct me to an example of how to do this using lmer from lme4. I have 3 main effects, tim, trt, ctr, and all the interaction effects tim*trt*ctr. The response variable is ge. Here is my lme code: dat <-

Hi, this is not a new doubt, but is a doubt that I cant find a good response. Look this output: > m.lme <- lme(Yvar~Xvar,random=~1|Plot1/Plot2/Plot3) > anova(m.lme) numDF denDF F-value p-value (Intercept) 1 860 210.2457 <.0001 Xvar 1 2 1.2352 0.3821 > summary(m.lme) Linear mixed-effects model fit by REML Data: NULL AIC BIC

...;, mer, frame = if (model) fr$mf else data.frame(), terms = mt, call = mc)) } if (method %in% c("ML", "REML")) method <- "Laplace" if (method == "AGQ") stop("method = \"AGQ\" not yet implemented for supernodal representation") if (method == "PQL") cv$usePQL <- TRUE glmFit <- glm.fit(X, Y, weights = weights, offset = offset, family = family, intercept = attr(mt, "intercept") > 0) Y <- as.double(glmFit$y) mer <- .Call(me...

Hi all, Somehow I managed to mess with a RAID array containing an ext3 partition. Parenthesis, if it matters: I disconnected physically a drive while the array was online. Next thing, I lost the right order of the drives in the array. While trying to re-create it, I overwrote the raid superblocks. Luckily, the array was RAID5 degraded, so whenever I re-created it, it didn't go into sync;

Thanks to some help by Doug Bates (and the updated version of the Matrix package), I've refined my question about fitting nested and non-nested factors in lmer(). I can get it to work in linear regression but it crashes in logistic regression. Here's my example: # set up the predictors n.age <- 4 n.edu <- 4 n.rep <- 100 n.state <- 50 n <- n.age*n.edu*n.rep age.id

This concerns whether p-values from lmer can be trusted. From simulations, it seems that lmer can produce very small, and probably spurious, p-values. I realize that lmer is not yet a finished product. Is it likely that the problem will be fixed in a future release of the lme4 package? Using simulated data for a quite standard mixed-model anova (a balanced two-way design; see code for the