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

2003 Apr 22

1

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

1

Differences between glmmPQL and lmer and AIC calculation

...re 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

1

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

1

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

1

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

1

GlmmPQL

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

1

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) -
https://www.routledge.com/Multilevel-Modeling-of-Categorical-Outcomes-Using-IBM-SPSS/Heck-Thomas-Tabata/p/book/9781848729568
I was wondering, which vari...

2006 Jan 10

1

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

1

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

1

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

1

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

0

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

1

variance functions in glmmPQL or glm?

...to 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

0

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

1

(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

1

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

0

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

1

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

1

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

1

glmmPQL

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'...