search for: glmmpql

Displaying 20 results from an estimated 99 matches for "glmmpql".

2003 Apr 22
glmmPQL and additive random effects?
I'm a bit puzzled by how to write out additive random effects in glmmPQL. In my situation, I have a factorial design on two (categorical) random factors, A and B. At each combination, I have a binary response, y, and two binary fixed covariates, C and D. If everything were fixed, I would use glm(y ~ A + B + C + D, family = binomial) My first thought was to use glm...
2013 Jul 11
Differences between glmmPQL and lmer and AIC calculation two different groups of fish (coded as 0 and 1 which should be the dependent variable) based on their swimming activity, habitat choice, etc. (independent variables). Each fish has several observations over time (repeated measurements) which I included as random factor in my models using library glmmPQL (package MASS). Because I have a binary data structure, I am using generalized linear mixed models. Using library glmmPQL the results reflect my descriptive analyses and the results are sound. However, we also want to rank several candidate models using AIC. And this is where the problems start. B...
2006 Apr 10
Weights in glmmPQL
Hello, I am using the R function glmmPQL to fit a logistic GLMM, with weights. I am finding that I get fairly different parameter estimates in glmmPQL from fitting the full dataset (with no "weight" statement) and an equivalent, shorter dataset with the weights statement. I am using the weights statement in the 'glmmPQL'...
2005 Oct 19
anova with models from glmmPQL
Hi ! I try to compare some models obtained from glmmPQL. model1 <- glmmPQL(y~red*yellow+I(red^2)+I(yellow^2)+densite8+I(densite8^2)+freq8_4 +I(freq8_4^2), random=~1|num, binomial); model2 <- glmmPQL(y~red*yellow+I(red^2)+I(yellow^2)+densite8+I(densite8^2)+freq8_4 , random=~1|num, binomial); anova(model1, model2) here is the answer : Erreur dan...
2006 Sep 25
glmmPQL in 2.3.1
Dear R-help, I recently tried implementing glmmPQL in 2.3.1, and I discovered a few differences as compared to 2.2.1. I am fitting a regression with fixed and random effects with Gamma error structure. First, 2.3.1 gives different estimates than 2.2.1, and 2.3.1, takes more iterations to converge. Second, when I try using the anova function...
2004 Jun 09
Dear all, I have two questions concerning model simplification in GlmmPQL, for for random and fixed effects: 1. Fixed effects: I don't know if I can simply specify anova(model) and trust the table that comes up with the p value for each variable in the fixed effects formula. I have read that the only way to test for fixed effects is to do approximate wald tests bas...
2018 Jan 31
What is the default covariance structure in the glmmPQL function (MASS package)?
Hello, currently I am trying to fit a generalized linear mixed model using the glmmPQL function in the MASS package. I am working with the data provided by the book from Heck, Thomas and Tabata (2012) - I was wondering, which vari...
2006 Jan 10
glmmPQL / "system is computationally singular"
Hi, I'm having trouble with glmmPQL from the MASS package. I'm trying to fit a model with a binary response variable, two fixed and two random variables (nested), with a sample of about 200,000 data points. Unfortunately, I'm getting an error message that is difficult to understand without knowing the internals of the...
2012 Jan 09
glmmPQL and predict
Is the labeling/naming of levels in the documentation for the predict.glmmPQL function "backwards"? The documentation states "Level values increase from outermost to innermost grouping, with level zero corresponding to the population predictions". Taking the sample in the documentation: fit <- glmmPQL(y ~ trt + I(week > 2), random = ~1 | ID,...
2012 Nov 15
confidence intervals with glmmPQL
Hi - I am using R version 2.13.0. I have run several GLMMs using the glmmPQL function to model the proportion of fish caught in one net to the total caught in both nets by length. I started with a polynomial regression full model with three length terms: l, l^2, and l^3 (l=length). The length terms and intercept were the fixed effects and the random effect was a paired ha...
2003 May 19
Syntax for random effect in glmmPQL
Dear R-listers I wonder if someone can help me with the syntax for the random effect in glmmPQL()? I have a data set with a response variable "y" (counts), two dependent variables: "treat" (4 levels) and "site" (2 levels). The latter, I want to use as a random variable. How do I specify this in the function? Is it like this: glmmPQL(y~treat,random=~1|site,family...
2004 Mar 22
solved mystery of difference between glmmPQL and lme
I asked a few days ago about the difference in results I saw between the MASS function glmmPQL (due to Venables and Ripley) and the lme function from the package nlme (due to Pinheiro and Bates). When the two tools apply to the same model (gaussian, link=identity, correlation=AR1), I was getting different results and wondered if there was an argument in favor of one or the other. Sever...
2006 Sep 20
variance functions in glmmPQL or glm? R, and tried searching the archives and literature for an answer to this - please be patient if I missed something obvious. I am fitting a logistic regression model, and would like to include variance functions (specifically the varIdent function). I cannot figure out how to do this either in glmmPQL (or something similar) for the model with random effects, or in glm for the model without random effects. Is it possible to fit a varIdent function in a generalized linear model? If so, what are the appropriate packages/functions to use? Any help would be appreciated. Thank you, Gretchen An...
2008 Oct 18
extracting residual variance from glmmPQL
Dear all, I am trying to simulate data sets from a model fitted with glmmPQL, in order to compute the distribution of a summary statistics. My data are binomial and I have a correlation term in my model. My model is structured in the following way m <- glmmPQL( fixed = cbind(sucess,failure) ~ x1 + x2 + ... , random = ~ 1 | bidon, correlation...
2010 Jan 23
(nlme, lme, glmmML, or glmmPQL)mixed effect models with large spatial data sets
...a spatial data set with many observations (~50,000) and would like to keep as much data as possible. There is spatial dependence, so I am attempting a mixed model in R with a spherical variogram defining the correlation as a function of distance between points. I have tried nlme, lme, glmmML, and glmmPQL. In all case the matrix needed (seems to be (N^2)/2 - N) is too large for my machine to handle even when maxed (memory.limit and virtual memory in vista). Past the range of my variogram (which I have a good estimate of), the matrix that R is trying to allocate will have 0 values (I believe)....
2006 Jan 13
glmmPQL: Na/NaN/Inf in foreign function call
I'm using glmmPQL, and I still have a few problems with it. In addition to the issue reported earlier, I'm getting the following error and I was wondering if there's something I can do about it. Error in logLik.reStruct(object, conLin) : Na/NaN/Inf in foreign function call (arg 3) ... Warnings...
2012 Nov 27
Variance component estimation in glmmPQL
Hi all, I've been attempting to fit a logistic glmm using glmmPQL in order to estimate variance components for a score test, where the model is of the form logit(mu) = X*a+ Z1*b1 + Z2*b2. Z1 and Z2 are actually reduced rank square root matrices of the assumed covariance structure (up to a constant) of random effects c1 and c2, respectively, such that b1 ~ N(0,si...
2003 May 28
Bradley Terry model and glmmPQL
Dear R-ers, I am having trouble understanding why I am getting an error using glmmPQL (library MASS). I am getting the following error: iteration 1 Error in MEEM(object, conLin, control$niterEM) : Singularity in backsolve at level 0, block 1 The long story: I have data from an experiment on pairwise comparisons between 3 treatments (a, b, c). So a typical run of an exp...
2010 Jan 04
glmer (lme4), glmmPQL (MASS) and xtmepoisson (Stata)
...of counts in different regions. My aim is to fit subject-specific curves, modelling a non-linear trend for each region through random effects for linear splines components (see Durban et al, Stat Med 2005, or " Semiparametric regression" by Ruppert et al, 2003). I use the command 'glmmPQL' in the MASS package and replicated the analysis with Stata's 'xtmepoisson'. I obtained very different results, so I would like to try 'glmer' in the lme4 package. I guess the default correlation for the random effects in 'glmer' is unstructured, but this choice is...
2002 Jul 01
Dear R users, can anybody explain me why the function glmmPQL(.) behaves in different ways, depending on the number of measurements/individuals you use? To show you this, I generated two examples. The first one includes 20 indivduals with each 100 repeated measurements (binary response), the second one includes 40 individuals. The 'individuals'...