Displaying 20 results from an estimated 3000 matches similar to: "extracting residual variance from glmmPQL"
2008 Oct 10
1
glmmPQL
Dear all,
I am experiencing problems with glmmmPQL. I am trying to analyze
binomial data with some spatial autocorrelation. Here is my code and
some of the outputs
> colnames(d.glmm)
[1] "BV" "Longitude" "Latitude" "nb_pc_02" "nb_expr_02"
[6] "pc_02" "nb_pc_07" "nb_expr_07"
2008 Mar 19
1
analyzing binomial data with spatially correlated errors
Dear R users,
I want to explain binomial data by a serie of fixed effects. My problem is
that my binomial data are spatially correlated. Naively, I thought I could
found something similar to gls to analyze such data. After some reading, I
decided that lmer is probably to tool I need. The model I want to fit would
look like
lmer ( cbind(n.success,n.failure) ~ (x1 + x2 + ... + xn)^2 ,
2007 Jun 25
1
degrees of freedom in lme
Dear all,
I am starting to use the lme package (and plan to teach a course based on it
next semester...). To understand what lme is doing precisely, I used balanced
datasets described in Pinheiro and Bates and tried to compare the lme outputs
to that of aov. Here is what I obtained:
> data(Machines)
> summary(aov(score~Machine+Error(Worker/Machine),data=Machines))
Error: Worker
2009 Nov 22
0
glmmPQL random effects model
Dear R-helpers,
I'd like to use glmmPQL to predict binary responses based on a data.frame
data1
containing N entries (N<1000):
target covariate1 covariate2 covariate3 ... covariateM
cluster
134131 1 -0.30031885 0 0 -2.886870e-07
1
38370 1 -0.04883229 0 1 -1.105720e-07
1
19315 1 -0.11084267
2009 Oct 21
1
odd evaluation within correlation argument of glmmPQL
[I think I've seen this reported before but can't locate it any more.
I believe this oddity (glitch? feature?) is behind a query that
Jean-Baptiste Ferdy asked a year ago
<http://finzi.psych.upenn.edu/Rhelp08/2008-October/176449.html>]
It appears that glmmPQL looks in the global workspace, not
within the data frame specified by the "data" argument, for
the variables
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,sig.1^2*I) and
c1 ~
2005 Dec 27
2
glmmPQL and variance structure
Dear listers,
glmmPQL (package MASS) is given to work by repeated call to lme. In the
classical outputs glmmPQL the Variance Structure is given as " fixed
weights, Formula: ~invwt". The script shows that the function
varFixed() is used, though the place where 'invwt' is defined remains
unclear to me. I wonder if there is an easy way to specify another
variance
2007 Oct 01
0
Interpretation of residual variance components and scale parameters in GLMMs
Dear R-listers,
I am working with generalized linear mixed models to quantify the
variance due to two nested random factors, but have hit a snag in the
interpretation of variance components. Despite my best efforts with
Venables & Ripley 2002, Fahrmeir & Tutz 2001, R-help archives, Google,
and other eminent sources (i.e. local R gurus), I have not been able
to find a definitive answer
2002 Sep 05
0
ape 0.1 is released
Ape is an R package for "analyses of phylogenetics and evolution". The
first version (0.1) has been released on 27 August 2002 and is available on
CRAN.
>From the 'Description' file of version 0.1:
Ape provides functions for reading, and plotting
phylogenetic trees in parenthetic format (standard Newick
format), analyses of comparative data in a
2006 Sep 20
1
variance functions in glmmPQL or glm?
Hello R users-
I am new 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
2009 Jan 30
1
Fitted values and residuals from glmmPQL (MASS package)
Dear All,
I would like to analyse the residuals from a generalized linear mixed model (GLMM) that I estimated, with random effects, by means of the command glmmPQL, from the MASS package.
It is not very clear to me what the actual residuals to analyse are (Y - Yhat): I obtain two columns of residuals, of which the first are population residuals, and the second refer to the grouping used in the
2006 Oct 29
1
glmmPQL in 2.3.1
I have come across the previous communication on this list in September
(copied below) because I had received the same error message.
I understand from Brian Ripley's reply that anova should not be used
with glmmPQL because it is not an adequate method, and that this is now
shown with an error message.
My question is, what method *should* be used? Using summary does not
give me the result
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
glmmPQL(y ~ A + B, random
2005 Oct 17
0
pdIdnot / logLik in glmmPQL
Dear R users,
I have been using the pdMat class "pdIdnot" (from the mgcv
package)instead of "pdIdent" to avoid overflow in GLMM fits with
the MASS package function glmmPQL, of the following form:
fit1 <- glmmPQL(fixed=y0~-1+xx0, random=list(gp=pdIdent(~-1+zz0)),
family=binomial) # vulnerable to overflow
fit2 <- glmmPQL(fixed=y0~-1+xx0,
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 dans anova.lme(model1, model2) : Objects must
2005 Aug 20
1
glmmPQL and Convergence
I fit the following model using glmmPQL from MASS:
fit.glmmPQL <-
glmmPQL(ifelse(class=="Disease",1,0)~age+x1+x2,random=~1|subject,family=binomial)
summary(fit.glmmPQL)
The response is paired (pairing denoted by subject), although some
subjects only have one response. Also, there is a perfect positive
correlation between the paired responses. x1 and x2 can and do differ
within each
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' function exactly as in the 'glm'
function. I
2007 Mar 28
2
what is the difference between survival analysis and (...)
Hi everybody,
recently I had to teach a course on Cox model, of which I am
not a specialist, to an audience of medical epidemiologists.
Not a good idea you might say.. anyway, someone in the
audience was very hostile. At some point, he sayed that
Cox model was useless, since all you have to do is count
who dies and who survives, divide by the sample sizes
and compute a relative risk, and if there
2006 Mar 24
1
predict.glmmPQL Problem
Dear all,
for a cross-validation I have to use predict.glmmPQL() , where the
formula of
the corresponding glmmPQL call is not given explicitly, but constructed
using as.formula.
However, this does not work as expected:
x1<-rnorm(100); x2<-rbinom(100,3,0.5); y<-rpois(100,2)
mydata<-data.frame(x1,x2,y)
library(MASS)
# works as expected
model1<-glmmPQL(y~x1, ~1 | factor(x2),
2003 May 20
0
Problem on model simplification with glmmPQL
Hi all,
I try to make a split-plot with poisson errors using glmmPQL, but I
have some doubts about the model simplification.
Look my system:
Block = 3 blocks
Xvar1 = 2 levels
Xvar2 = 13 levels
Yvar = Count data Response
I need know about the behaviour of Var1, Var2 and interaction
Var1:Var2.
Look the levels:
> levels(Xvar1)
[1] "A" "B"
> levels(Xvar2)
[1]