similar to: lme convergence failure within a loop

Dear R-help list readers, I am fitting mixed models with the lme function of the nlme package. If I get convergence depends on how the method (ML/REM) and which (and how much) parameters will depend randomly on the cluster-variable. How get the bist fit without convergence? I set the parameters msVerbose and returnObject to TRUE: lmeControl(maxIter=50000, msMaxIter=200, tolerance=1e-4,

I tried to use LME (on a fairly large dataset, so I am not including it), and I got this error message: Error in lme.formula(formula(paste(c(toString(TargetName), "as.factor(nodeInd)"), : nlminb problem, convergence error code = 1 message = false convergence (8) Is there any way to get more information or to get the potentially wrong estimates from LME? (Also, the page in the

Dear R-Users, Is it possible to get the covariance matrix from an lme model that did not converge ? I am doing a simulation which entails fitting linear mixed models, using a "for loop". Within each loop, i generate a new data set and analyze it using a mixed model. The loop stops When the "lme function" does not converge for a simulated dataset. I want to

Hi there, I've looked through the very helpful advice about adding fitted lines to plots in the r-help archive, and can't find a post where someone has offered a solution for my specific problem. I need to plot logistic regression fits from three differently-sized data subsets on a plot of the entire dataset. A description and code are below: I have an unbalanced dataset

Hi. I was wondering if anyone might have some suggestions about how I can overcome a problem of "iteration limit reached without convergence" when fitting a mixed effects model. In this study: Outcome is a measure of heart action Age is continuous (in weeks) Gender is Male or Female (0 or 1) Genotype is Wild type or knockout (0 or 1) Animal is the Animal ID as a factor

I want to make a log-log plot with a regression line, but I can't figure out what I'm doing wrong. What I'm trying is: plot(mass,area, log="xy", pch=as.numeric(food)) abline(lm(mass~area)) or plot(mass,area, log="xy", pch=as.numeric(food)) islands$logmass <- log(mass) islands$logarea <- log(area) attach(islands) abline(lm(logmass~logarea)) But that does

Hope one of you could help with the following question/problem: We would like to explain the spatial distribution of juvenile fish. We have 2135 records, from 75 vessels (code_tripnr) and 7 to 39 observations for each vessel, hence the random effect for code_tripnr. The offset (‘offsetter’) accounts for the haul duration and sub sampling factor. There are no extreme outliers in lat/lon. The model

Hello R-helpers, I have 10 dataframes (named data1, data2, ... data10) and I would like to add 5 new columns to each dataframe using the following code: data1$LogDepth<-log10(data1[,2]/data1[,4]) data1$LogArea<-log10(data1[,3]/data1[,5]) data1$p<-2*data1[,6]/data1[,7] data1$Exp<-data1[,2]^(2/data1[,8]) data1$s<-data1[,3]/data1[,9] ...but I would prefer not to repeat this chunk of

I have a question about the lme function in R. My question is: After I got the object from function lme, why the numIter value of the object is always NULL? Following is my code: jjww<-lme(y~x*zz,data=simul,random=~x|group, control=lmeControl(returnObject=TRUE)) attributes(jjww) jjww$numIter the first 20 observation of data simul are: > simul y

Dear R-help list readers, I am fitting a mixed model using the lme function (R V 2.3.1 for Windows). This is an example: dep<-c(25,40,33.33,60,70.83,72,71.43,50,40,53.33,64,54.17,60,53.57) yes<-c(0,1,2,3,4,5,6,0,1,2,3,4,5,6) treat<-c(1,1,1,1,1,1,1,0,0,0,0,0,0,0) #factor If I now fit a model with random slopes as well as intercepts: model1<-lme(dep~yes,random=yes|treat) R

Hello, all, I am running some simulations to estimate power for a complicated epidemiological study, and am using lme and lmer to get these estimates. I have to run a few thousand iterations, and once in a great while, an iteration will create fake data such that the model won't converge. I see from Google searches that this is not an uncommon situation. My question: is there a way to

Simply gooling for "writing ARFF file in R" gave the following as first hit, which is right on the WEKA page: Miscellaneous code [...] Function for reading ARFF files into the R statistical package (kindly provided by Dr Craig Struble). Function for writing ARFF files from the R statistical package (kindly provided by Nigel Sim).

Dear list members, In re-running with GLMM() from the lme4 package a generalized-linear mixed model that I had previously fit with glmmPQL() from MASS, I'm getting a warning of a convergence failure, even when I set the method argument of GLMM() to "PQL": > bang.mod.1 <- glmmPQL(contraception ~ as.factor(children) + cage + urban, + random=~as.factor(children) + cage +

Hello, I am working from a linux 64 machine on a server with R-2.12 (I can't update to 2.13). I am iterating through many linear mixed models for longitudinal data and I occasionally receive the following convergence error: > BI.lme <- lme(cd4 ~ time + genBI + genBI:time + C1 + C2 + C11 + C12, random =~ 1 + time | IID, data = d) Error in lme.formula(cd4 ~ time + genBI + genBI:time +

Hi, I have a question about the lme function in R. My question is: After I got the object from function lme, why the numIter value of the object is always NULL? Following is my code: jjww<-lme(y~x*zz,data=simul,random=~x|group, control=lmeControl(returnObject=TRUE)) attributes(jjww) jjww$numIter the first 20 observation of data simul are: > simul y

Dear all, I would like to estimate rainfall with the krige function. First, I produce a polygon of my region of interest (where poly_test.txt is a x,y suite of points defining a polygon, obtained with the grass v.out.ascii command) : user>border_limite<-read.table("/home/lionel/rwork/poly_test.txt",header=FALSE) user>polygone<-list(x=border_limite[,1],y=border_limite[,2])

Hello, This is what I am trying to do: I wrote a little function that takes addresses (coordinates) as input, and returns the road distance between every two points using Google Maps. Catch is, there are 2000 addresses, so I have to get around 2x10^6 addresses. On my first go, this is what I did: ######################################### getRoadDist = function(X,complete=F){ # X must be a

Tried to post this last night, but it doesn't seem to have appeared. Using R 2.0.1 on Windows XP + SP2. I am traveling, away from my usual references. I'm trying to make a 4-dimensional plot: a levelplot with overlaid contours, with different response variables represented by (1) colors on the levelplot and (2) the contour lines. First try was filled.contour + contour but the key

Hello all. I have been working on a (fairly simple) function for way too long. I’ve really hit a wall and I was hoping someone might be able to point me in the right direction. I have (attempted) to create a function that has an embedded while loop. The while loop works fine by itself, however, when the while loop is embedded in the function, the function fails. I’m not sure why this

> both "_ "and "<-" are assignment operators well, I've changed it in my script, but the result is the same. > what do you get if you call > > in.polygon(grid2.point$x,grid2.point$y,polygon$x,polygon$y) That's it ! In fact all my points in grid2.point where xy inverted. And I had no points in polygon. It was really a stupid mistake. Thanks for all !