similar to: Help with lmer

Hi, I am having problems trying to assess the significance of random terms in a generalized linear mixed model using lme4 package. The model describes bird species richness R along roads (offset by log length of road log_length) as a function of fixed effects Shrub (%shrub cover) and Width (width of road), and random effect Site (nested within Site Cluster). >From reading answers to previous

When using drag and drop, the browser window will not scroll if you move the mouse off the page. This makes it very difficult, if not impossible to create certain types of web applications. I know this has been mentioned before and is on the Wish List, but it''s very frustrating. If you look at this other Javascript library called "Drag''nDrop & DHTML Library"

Hi, I would like to compare differences in AUC from 2 different models, glm and gam for predicting presence / absence. I know that in theory the model with a higher AUC is better, but what I am interested in is if statistically the increase in AUC from the glm model to the gam model is significant. I also read quite extensive discussions on the list about ROC and AUC but I still didn't find

Hi All - Where I work uses the Shrew Soft VPN client to access remote resources. I have found pre-built rpms for EL5, various versions of Fedora, and appropriate packages for non-rpm based distros but no rpm for EL6. I have downloaded the source from Shrew Soft and built "my own" which built and installed with no errors but then didn't work. I'm finally taking the lack of

Dear R Users, I am having trouble with lmer. I am looking at recombinant versus non recombinant individuals. In the response variable recombinant individuals are coded as 1's and non-recombinant as 0's. I built a model with 2 fixed factors and 1 random effect. Sex (males/females) is the first fixed effect and sexual genotype (XY, YY, WX and WY) the second one. Sexual Genotype is

Hi. Some time ago I posted some prototype-"extensions", which could come in handy. I''ve been updating them a bit and added a few more and I think its time to share it again. Feel free to use it. The code should be rather self explaining, but heres a quickguide. - new Geometry.Size(width,height) - Creates a new instance of size - new Geometry.Position(x,y) - Creates a new

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 All, I have conducted an experiment in order to examine predation pressure in the surroundings of potential wildlife road-crossing structures. I have documented predation occurrence (binary?) in these structures and calculated several possible explanatory variables describing the spatial heterogeneity in several scales. At the landscape scale I have calculated the percentage of different

Hi (again), let's say I want to create a class Matrix that extends the class matrix, but I can't get it to work. I define the class as > setClass("Matrix", "matrix") > getClass("Matrix") No Slots, prototype of class "matrix" Extends: Class "matrix" directly. Class "structure" by class "matrix".

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"

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, After playing with lmer for couple of days, I have to say that I am amazed! I've been using quite some multilevel/mixed modeling packages, lme4 is a strong candidate for the overall winner, especially for multilevel generzlized linear models. Now go back to my two-level poisson model with cross-classified model. I've been testing various different model specificatios for the

Hi, I'm having trouble writing .pnm images which I think is due to a problem with my colour space. The pixmap object seems to be looking for 72 of 8 colours (one per cell?) which doesn't seem healthy... > library(pixmap) > x <- pixmapIndexed(rep(1:8, 9), nrow=6, col=rainbow(8)) > x Pixmap image Type : pixmapIndexed Size : 6x12 Resolution : 1x1

Dear list, I am new to this list and I am new to the world of R. Additionally I am not very firm in statistics either but have to deal. So here is my problem: I have a dataset (which I attach at the end of the post) with a binomial response variable (alive or not) and three fixed factors (trapping,treat,sex). I do have repeated measures and would like to include one (enclosure) random factor. I

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?

Dear all R-users, When I install the package "lme4" in R-2.11.1, and use it to run the simulation on the Linux system, it appears the following problem. Attaching package: 'lme4' The following object(s) are masked from 'package:stats':     AIC Error in names(argNew)[1] <- names(formals(new))[[1]] :   replacement has length zero Calls: initial ... lmerFactorList

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

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) :

Dear List: I was able to run the following in nlme successfully, but the same 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