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Hi, When modeling with negbin from the aod package, parameters for a given count y | lambda~Poisson(lambda) with lambda following a Gamma distribution Gamma(r, theta) are estimated. The intercept is called phi. Some other parameters may be also be estimated from factors in the data: the estimates returned for all these would be in accordance with the Value listing in the negbin entry in the aod

...86-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 9.0 year 2009 month 04 day 17 svn rev 48333 language R version.string R version 2.9.0 (2009-04-17) ------------------ Matthieu Lesnoff CIRAD Bamako, Mali E-mail: matthieu.lesnoff@cirad.fr [[alternative HTML version deleted]]

Information on package 'aod' Description: Package: aod Version: 1.1-2 Date: 2005-06-08 Title: Analysis of Overdispersed Data Author: Matthieu Lesnoff <matthieu.lesnoff at cirad.fr> and Renaud Lancelot <renaud.lancelot at cirad.fr> Maintainer: Renaud Lancelot <renaud.lancelot at cirad.fr> Depends: R (>= 2.0.0), methods, stats Suggests: MASS, nlme Description: This package provides a set of func...

Information on package 'aod' Description: Package: aod Version: 1.1-2 Date: 2005-06-08 Title: Analysis of Overdispersed Data Author: Matthieu Lesnoff <matthieu.lesnoff at cirad.fr> and Renaud Lancelot <renaud.lancelot at cirad.fr> Maintainer: Renaud Lancelot <renaud.lancelot at cirad.fr> Depends: R (>= 2.0.0), methods, stats Suggests: MASS, nlme Description: This package provides a set of func...

...When replying, please edit your Subject line so it is more specific > than "Re: Contents of R-help digest..." > > > Today's Topics: > > 1. Re: Changing gird marks in ggplot2 (ONKELINX, Thierry) > 2. Re: argument 'exclude' in function xtabs (Matthieu Lesnoff) > 3. Question of "Quantile Regression for Longitudinal Data" > (Helen Chen) > 4. Conditional plot labels (Christian Bustamante) > 5. simulate arima model (Rebecca1117) > 6. THE EQUIVALENT OF SQL INNER TABLE JOIN IN R (Nigel Birney) > 7. Scatterpl...

I have tried glm.nb in the MASS package, but many models (I have 250 models with different combinations of predictors for fish counts data) either fail to converge or even diverge. I'm attempting to use the negbin function in the AOD package, but am unsure what to use for the "random" term, which is supposed to provide a right hand formula for the overdispersion parameter.

...acter data 'John Fox [aut, cre], Liviu Andronic [ctb], Michael Ash [ctb], Milan Bouchet-Valat [ctb], Theophilius Boye [ctb], Stefano Calza [ctb], Andy Cha ng [ctb], Philippe Grosjean [ctb], Richard Heiberger [ctb], Kosar Karimi Pour [c tb], G. Jay Kerns [ctb], Renaud Lancelot [ctb], Matthieu Lesnoff [ctb], Uwe Ligg es [ctb], Samir Messad [ctb], Martin Maechler [ctb], Robert Muenchen [ctb], Dunc an Murdoch [ctb], Erich Neuwirth [ctb], Dan Putler [ctb], Brian Ripley [ctb], Mi roslav Ristic [ctb], Peter Wolf [ctb]' truncated to 255 bytes in column 'Author' Perl found. The follow...

I've submitted a new, and substantially enhanced, version (1.2-0) of the Rcmdr package to CRAN. Some highlights (from the CHANGES) file: o Added ability to import from Excel, Access or dBase files (contributed by Samir Messad, Renaud Lancelot and Matthieu Lesnoff). o Added ability to read data from the clipboard (suggested by Graham Smith). o Added "Data -> Active data set -> Stack variables in active data set" (suggested by Richard Heiberger). o Added many probability distributions, courtesy of Miroslav Ristic and G. Jay K...

I've submitted a new, and substantially enhanced, version (1.2-0) of the Rcmdr package to CRAN. Some highlights (from the CHANGES) file: o Added ability to import from Excel, Access or dBase files (contributed by Samir Messad, Renaud Lancelot and Matthieu Lesnoff). o Added ability to read data from the clipboard (suggested by Graham Smith). o Added "Data -> Active data set -> Stack variables in active data set" (suggested by Richard Heiberger). o Added many probability distributions, courtesy of Miroslav Ristic and G. Jay K...

Edward, you also can use the package aod on CRAN, see the help page of the function negbin. Best Matthieu An example: > library(aod) > data(dja) > negbin(y ~ group + offset(log(trisk)), ~group, dja, fixpar = list(4, 0)) Negative-binomial model ----------------------- negbin(formula = y ~ group + offset(log(trisk)), random = ~group, data = dja, fixpar = list(4, 0))

I have fitted the faults.data to glm.nb and to the function negbin from the package aod. The output of both is the following: summary(glm.nb(n~ll, data=faults)) Call: glm.nb(formula = n ~ ll, data = faults, init.theta = 8.667407437, link = log) Deviance Residuals: Min 1Q Median 3Q Max -2.0470 -0.7815 -0.1723 0.4275 2.0896 Coefficients:

Dear Lister, I am facing a strange problem fitting a GLM of the negative binomial family. Actually, I tried to estimate theta (the scale parameter) through glm.nb from MASS and could get convergence only relaxing the convergence tolerance to 1e-3. With warning messages: glm1<-glm.nb(nbcas~.,data=zonesdb4,control=glm.control(epsilon = 1e-3)) There were 25 warnings (use warnings() to see