Re: [R] What happen for Negative binomial link in Lmer fonction?

2009-11-20 Thread Emmanuelle Robardet

Dear R users,
As I have no answer to my las reply i try again.
If the binomal negative link has never been implemented in the lmer
fonction, 
and as it was working when I did it some months ago,
What kind of result did I get?

This is the exemple of the answer of R when i was using lmer with negative
binomal family:

m1a-lmer(atpos~ninter+saison+milieu*zone+(1|code),family=neg.bin(0.429),method=Laplace,data=manu)
summary(m1a)
Generalized linear mixed model fit using Laplace 
Formula: atpos ~ ninter + saison + milieu * zone + (1 | code) 
   Data: manu 
 Family: Negative Binomial(log link)
   AIC   BIC logLik deviance
 125.1 147.6 -54.57109.1

Thank you for your answers,
Best Regards
Emmanuelle



E. Robardet wrote:
 
 Thank you for your answers,
 
 I have an exemple of that i was using:
 
 m1a-lmer(atpos~ninter+saison+milieu*zone+(1|code),family=neg.bin(0.429),method=Laplace,data=manu)
 summary(m1a)
 Generalized linear mixed model fit using Laplace 
 Formula: atpos ~ ninter + saison + milieu * zone + (1 | code) 
Data: manu 
  Family: Negative Binomial(log link)
AIC   BIC logLik deviance
  125.1 147.6 -54.57109.1
 
 I think It was the version lme4 0.9975-10.
 Unfortunately, I have this version no more available on my computer..
 I wonder if this old results are still valid..
 
 
 Ben Bolker wrote:
 
 
 
 ROBARDET Emmanuelle wrote:
 
 Dear R users,
 I'm performing some GLMMs analysis with a negative binomial link.
 I already performed such analysis some months ago with the lmer()
 function but when I tried it today I encountered this problem:
 Erreur dans famType(glmFit$family) : unknown GLM family: 'Negative
 Binomial'
 
 Does anyone know if the negative binomial family has been removed from
 this function?
 I really appreciate any response.
 Emmanuelle
 
 
 
 I would be extremely surprised if this worked in the past; to
 the best of my knowledge the negative binomial family has
 never been implemented in lmer.  One could in principle
 do a glmmPQL fit with the negative binomial family
 (with a fixed value of the overdispersion parameter).
 glmmADMB is another option.
 Can you say which version etc. you were using???
 
 Follow-ups should probably be sent to r-sig-mixed-mod...@r-project.org
 
 
 
 

-- 
View this message in context: 
http://old.nabble.com/What-happen-for-Negative-binomial-link-in-Lmer-fonction--tp26013041p26439076.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


Re: [R] What happen for Negative binomial link in Lmer fonction?

2009-10-29 Thread E. Robardet

Thank you for your answers,

I have an exemple of that i was using:

m1a-lmer(atpos~ninter+saison+milieu*zone+(1|code),family=neg.bin(0.429),method=Laplace,data=manu)
summary(m1a)
Generalized linear mixed model fit using Laplace 
Formula: atpos ~ ninter + saison + milieu * zone + (1 | code) 
   Data: manu 
 Family: Negative Binomial(log link)
   AIC   BIC logLik deviance
 125.1 147.6 -54.57109.1

I think It was the version lme4 0.9975-10.
Unfortunately, I have this version no more available on my computer..
I wonder if this old results are still valid..


Ben Bolker wrote:
 
 
 
 ROBARDET Emmanuelle wrote:
 
 Dear R users,
 I'm performing some GLMMs analysis with a negative binomial link.
 I already performed such analysis some months ago with the lmer()
 function but when I tried it today I encountered this problem:
 Erreur dans famType(glmFit$family) : unknown GLM family: 'Negative
 Binomial'
 
 Does anyone know if the negative binomial family has been removed from
 this function?
 I really appreciate any response.
 Emmanuelle
 
 
 
 I would be extremely surprised if this worked in the past; to
 the best of my knowledge the negative binomial family has
 never been implemented in lmer.  One could in principle
 do a glmmPQL fit with the negative binomial family
 (with a fixed value of the overdispersion parameter).
 glmmADMB is another option.
 Can you say which version etc. you were using???
 
 Follow-ups should probably be sent to r-sig-mixed-mod...@r-project.org
 
 

-- 
View this message in context: 
http://www.nabble.com/What-happen-for-Negative-binomial-link-in-Lmer-fonction--tp26013041p26113408.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


[R] What happen for Negative binomial link in Lmer fonction?

2009-10-22 Thread ROBARDET Emmanuelle
Dear R users,
I'm performing some GLMMs analysis with a negative binomial link.
I already performed such analysis some months ago with the lmer() function but 
when I tried it today I encountered this problem:
Erreur dans famType(glmFit$family) : unknown GLM family: 'Negative Binomial'

Does anyone know if the negative binomial family has been removed from this 
function?
I really appreciate any response.
Emmanuelle




[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


Re: [R] What happen for Negative binomial link in Lmer fonction?

2009-10-22 Thread Ben Bolker



ROBARDET Emmanuelle wrote:
 
 Dear R users,
 I'm performing some GLMMs analysis with a negative binomial link.
 I already performed such analysis some months ago with the lmer() function
 but when I tried it today I encountered this problem:
 Erreur dans famType(glmFit$family) : unknown GLM family: 'Negative
 Binomial'
 
 Does anyone know if the negative binomial family has been removed from
 this function?
 I really appreciate any response.
 Emmanuelle
 
 

I would be extremely surprised if this worked in the past; to
the best of my knowledge the negative binomial family has
never been implemented in lmer.  One could in principle
do a glmmPQL fit with the negative binomial family
(with a fixed value of the overdispersion parameter).
glmmADMB is another option.
Can you say which version etc. you were using???

Follow-ups should probably be sent to r-sig-mixed-mod...@r-project.org 
-- 
View this message in context: 
http://www.nabble.com/What-happen-for-Negative-binomial-link-in-Lmer-fonction--tp26013041p26015140.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


Re: [R] What happen for Negative binomial link in Lmer fonction?

2009-10-22 Thread Douglas Bates
On Thu, Oct 22, 2009 at 1:39 PM, Ben Bolker bol...@ufl.edu wrote:

 ROBARDET Emmanuelle wrote:

 Dear R users,
 I'm performing some GLMMs analysis with a negative binomial link.
 I already performed such analysis some months ago with the lmer() function
 but when I tried it today I encountered this problem:
 Erreur dans famType(glmFit$family) : unknown GLM family: 'Negative
 Binomial'

 Does anyone know if the negative binomial family has been removed from
 this function?
 I really appreciate any response.
 Emmanuelle



 I would be extremely surprised if this worked in the past; to
 the best of my knowledge the negative binomial family has
 never been implemented in lmer.

I too would be extremely surprised if it had worked in the past,
considering that I have never implemented it.

I did exchange email with Bill Venables about it and we formulated
what seems to be a reasonable approach but it hasn't made it to the
top of the To Do list yet.  Right now the big push is on code to
profile the log-likelihood with respect to the parameters so we can
actually get confidence intervals and, the holy grail of
mixed-modeling, p-values.
 One could in principle
 do a glmmPQL fit with the negative binomial family
 (with a fixed value of the overdispersion parameter).
 glmmADMB is another option.
 Can you say which version etc. you were using???

 Follow-ups should probably be sent to r-sig-mixed-mod...@r-project.org 
 --
 View this message in context: 
 http://www.nabble.com/What-happen-for-Negative-binomial-link-in-Lmer-fonction--tp26013041p26015140.html
 Sent from the R help mailing list archive at Nabble.com.

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.