Displaying 20 results from an estimated 500 matches similar to: "glmm.admb - bug and possible solution??"
2008 Jul 14
0
Question regarding lmer vs glmmPQL vs glmm.admb model on a negative binomial distributed dependent variable
Hi R-users,
I intend to apply a mixed model on a set of longitudinal data, with a negative binomial distributed dependent variable, and after following the discussions on R help list I saw that more experienced people recommended using lmer (from lme4 pack), glmmPQL (from MASS) or glmm.admb (from glmmADMB pack)
My first problem: yesterday this syntax was ok, now I get this weird message (I
2005 Mar 23
1
Negative binomial GLMMs in R
Dear R-users,
A recent post (Feb 16) to R-help inquired about fitting
a glmm with a negative binomial distribution.
Professor Ripley responded that this was a difficult problem with the
simpler Poisson model already being a difficult case:
https://stat.ethz.ch/pipermail/r-help/2005-February/064708.html
Since we are developing software for fitting general nonlinear random
effects models we
2009 Jan 07
0
fixed effect significance_NB mixed models_further pursuit
7 Jan 09
Hello,
I am using R version 2.7.0 in a Windows XP context.
I am also using the glmm.admb package (created by Dave Fournier, Hans
Skaug, and Anders Nielson) to run mixed-effects negative binomial
models.
To the best of my knowledge and ability, I have searched and studied
the R-help, R-sig-mixed models, and ADMB NBMM for R (through Otter
Research Ltd) list servs; R help
2008 Mar 29
0
AD-MB problem in package:glmmADMB
Hi here,
i recently notice the software built by otter company know as AD-MB
tools . i explore a little bit this tools under the R Package for mixed
logistics model. it is a very interesting tool. but i get several questions.
first question: i tried the R code below, and have the error , i can run
the code for switching the setting to impSamp=0 , it means i can only
run the code under
2005 Dec 14
3
glmmADMB: Generalized Linear Mixed Models using AD Model Builder
Dear R-users,
Half a year ago we put out the R package "glmmADMB" for fitting
overdispersed count data.
http://otter-rsch.com/admbre/examples/glmmadmb/glmmADMB.html
Several people who used this package have requested
additional features. We now have a new version ready.
The major new feature is that glmmADMB allows Bernoulli responses
with logistic and probit links. In addition there
2011 Sep 03
1
help with glmm.admb
R glmmADMB question
I am trying to use glmm.admb (the latest alpha version
from the R forge website 0.6.4) to model my count data
that is overdispersed using a negative binomial family but
keep getting the following error message:
Error in glmm.admb(data$total_bites_rounded ~
age_class_back, random = ~food.dif.id, :
Argument "group" must be a character string specifying
the
2006 May 23
2
glmmADMB and the GPL -- formerly-- How to buy R.
Dear List,
Some of you have been following the discussion of the GPL and its inclusion
in the glmmADMB package we created for R users. I would like to provide
a bit of background and include an email we received from
Prof. Ripley so that everyone can be aware of how some might use the
GPL to try to force access to proprietary software. I think this is
interesting because many have voiced the
2005 Oct 12
0
Mixed model for negative binomial distribution (glmm.ADMB)
Dear R-list,
I thought that I would let some of you know of a free R package, glmm.ADMB, that
can handle mixed models for overdispersed and zero-inflated count data
(negativebinomial and poisson).
It was built using AD Model Builder software (Otter Research) for random effects
modeling and is available (for free and runs in R) at:
http://otter-rsch.com/admbre/examples/glmmadmb/glmmADMB.html
I
2006 Dec 19
2
Problem with glmmADMB
library(glmmADMB)
#Example for glmm.admb
data(epil2)
glmm.admb(y~Base*trt+Age
+Visit,random=~Visit,group="subject",data=epil2,family="nbinom")
Gives:
Error in glmm.admb(y ~ Base * trt + Age + Visit, random = ~Visit,
group = "subject", :
The function maximizer failed
******************
R version 2.4.1 RC (2006-12-14 r40181)
powerpc-apple-darwin8.8.0
locale:
C
2005 Jun 17
0
glmmADMB: Mixed models for overdispersed and zero-inflated count data in R
Dear R-users,
Earlier this year I posted a message to this list regarding
negative binomial mixed models in R. It was suggested that
the program I had written should be turned into an R-package.
This has now been done, in collaboration with David Fournier
and Anders Nielsen.
The R-package glmmADMB provides the following GLMM framework:
- Negative binomial or Poisson responses.
- Zero-inflation
2012 Sep 04
1
ADMB error- function maximizer failed (couldnt find STD file)
Greetings glmmADMB function users,
I am trying to run a series of models using the glmmADMB function with several different distribution families (e.g., poisson, negbinom). I am using a Optiplex 790 PC with Windows 7, 16.0 GB of RAM and a 64-bit operating system. I am running R version 2.15.0 and started out using the most recent version of glmmADMB (I believe version 7.2.15).
My data is zero
2006 May 16
0
Course in AD Model Builder; integrating ADMB with R
For those of you who want to learn how to integrate AD Model Builder with R,
and are going to the JSM in Seattle, the following course may be of interest:
Statistical and ecological modeling in AD Model Builder
Date: August 5, 2006 (the day before the Joint Statistical Meetings open)
For more information see:
http://www.mi.uib.no/~skaug/admb/seattleworkshop.html
Regards,
hans
2006 Feb 24
1
SE of parameter estimates in glmm.admb
Dear R users,
Does anyone know how to get standard errors of the
parameter estimates in glmm.admb?
Thanks,
Istvan
2008 Mar 29
0
AD-model builder under R for mix logistics model, a problem.
the code is list below , i can run this code for laplace approximation
but not importance sampling. the code work properly if use impSamp=0 ,
but error for any other number >0 .
could you guys help me out.
thanks so much !
source("http://www.mi.uib.no/~skaug/cash/lesaffre_dat.s")
library(glmmADMB)
fit_glmmADMB_ip <-
2006 Jan 26
1
Automatic differentiation (was: Re: D(dnorm...)?)
Dear Alberto,
There are fisheries people also in Europe using AD Model Builder (Denmark and England for instance),
but you are probably right that it is more widespread in North America. There is also effort
going on where people try to make assessment models written in ADMB callable from R.
best regards,
hans
> think AD Model Builder is mainly used for fisheries assessment in North
2005 Apr 13
0
Summary: GLMMs: Negative Binomial family in R
Here is a summary of responses to my original email (see my query at the
bottom). Thank you to Achim Zeileis , Anders Nielsen, Pierre Kleiber and Dave
Fournier who all helped out with advice. I hope that their responses will help
some of you too.
*****************************************
Check out
glm.nb() from package MASS fits negative binomial GLMs.
2006 Jan 05
1
Understanding and translating lme() into lmer() model
I am newbie in R, trying to understand and compare syntax in nlme and
lme4. lme() model from the nlme package I am interested in is:
lme.m1.1 = lme(Y~A+B+C,random=~1|D/E,data=data,method="ML")
(for simplicity reason, I am giving generic names of factors)
If I understand well, there are three fixed factors: A, B and C, and two
random factors: D and E. In addition to that, E is nested in
2010 May 31
1
running admb from R using system()
Hi
I'm trying to run an admb model from R by using the system () command.
The admb model runs fine when running it from the admb command line or
when using emacs. However when I try it with system() then R crashes
every time.
And I tried using the R command line and RGui and in both it crashes. I
also tried it from different computers.
What I do is I first set the directory where I keep
2011 Nov 17
2
RV: Reporting a conflict between ADMB and Rtools on Windows systems
De: Rubén Roa
Enviado el: jueves, 17 de noviembre de 2011 9:53
Para: 'Users@admb-project.org'
Asunto: Reporting a conflict between ADMB and Rtools on Windows systems
Hi,
I have to work under Windows, it's a company policy.
I've just found that there is a conflict between tools used to build R packages (Rtools) and ADMB due to the need to put Rtools compiler's
2012 Jan 30
1
mgcv bam() with grouped binomial data
Hello,
I'm trying to use the bam() function in the R mgcv package for a large set of grouped binary data. However, I have found that this function does not take data in the format of cbind(numerator, denominator) on the left hand side of the formula. As an example, consider the following
dat1 <- data.frame(id=rep(1:6, each=3), num=rbinom(18, size=10, prob=0.8), den=rbinom(18, size=5,