similar to: When modeling with negbin from the aod package...

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.

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:

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))

Hello, After putting together interaction code that worked for a single pair of interactions, when I try to evaluate two pairs of interactions( flowers*gopher, flowers*rockiness) my computer runs out of memory, and the larger desktop I use just doesn't go anywhere after about 20 minutes. Is it really that big a calculation? to start: mle2(minuslogl = Lily_sum$seedlings ~ dnbinom(mu = a,

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 (>=

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 (>=

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

Hello, I'm trying to understand grofit's estimation of models, and fairly new to growth models generally. The data used by grofit consists of the vector of "experiments", that is the growth values for a vector of individuals measured at different times. Can I understand correctly that the program estimates parameters for the growth model based on a regression(linear or non

Hi, I wonder if predict.gam is supposed to work with family=negbin() definition? It seems to me that the values returned by type="response" are far off the observed values. Here is an example output from the negbin examples: > set.seed(3) > n<-400 > dat<-gamSim(1,n=n) > g<-exp(dat$f/5) > dat$y<-rnbinom(g,size=3,mu=g) >

Dear R people, I am not sure if this is the correct place to tell about problems in evolving programmes, but it seems that the `summary.negbin' function of the excellent `MASS' library is now broken, and gives the following error message: > summary(hm) Error in summary.negbin(hm) : subscript out of bounds `summary.negbin' calls `summary.glm' which seems to work and give the

Dear R-collegues, I'm getting an error message (Error in round) when summarising a glm.nb model, and when using anova.negbin (in R 1.3.1 for windows): > m.nb <- glm.nb(tax ~ areal) > m.bn Call: glm.nb(formula = tax ~ areal, init.theta = 5.08829537115498, link = log) Coefficients: (Intercept) areal 3.03146 0.03182 Degrees of Freedom: 283 Total (i.e. Null); 282

I am getting the following erro rmessage in ordistep. I have a number of similarly structured datasets using ordistep in a loop, and the message only occurs for some of the datasets. I cannot include a reproducible sample - the specific datasets where this is occur ing are fairly large and there are several pcnm's in the rhs of the formula. thanks for any pointers that may allow me to

Dear Clara, Thanks for the reply. I am forwarding your message to the list, ok. When I wrote was a way of get further information to help the helpers. happy holidays, milton ---------- Forwarded message ---------- From: Clara Brück <clara_brueck@web.de> Date: 2009/12/30 Subject: Re: [R] Negbin Error Warnings To: milton ruser <milton.ruser@gmail.com> Dear Milton, Thanks for

Hi, I ran a negative binomial regression (NBR) using the Zelig-package and the negbin model. When I then try to use the simumlation approach using the setx () and sim() functions to calculate expected values and first difference for different levels of one of my independent variables, I get 50 errors warnings, telling me that the calculation rpois produced NAs. However, the data I use

Dear R users, I am trying to use "gamm" from package "mgcv" to model results from a mesocosm experiment. My model is of type M1 <- gamm(Resp ~ s(Day, k=8) + s(Day, by=C, k=8) + Flow + offset(LogVol), data=MyResp, correlation = corAR1(form= ~ Day|Mesocosm), family=poisson(link=log)) where the response variable is counts, offset by the

Sorry Gentlemen and all. Now this is becoming a joke (to me). I repeated what I did earlier, with and without the option to set repos suggested by Duncan. Now it does not work. I wonder whether it is dependent on the mirror I chose, but I do not remember the one I chose earlier when it work. I need your help, gentlemen, as I need to use R-3.0.3 for my task. >

Thanks. You gentlemen please tell me what this means. In R (outside of RStudio) I ran: install.packages("aod") Received a warning (and installation did not seem to go through). Then I tried install.packages("aod",repos='https://cran-archive.r-project.org') Received a warning but it went on to try

Thanks for the help. I have a reason to continue with R-3.0.3. I used maxLik to estimate econometric models and some of them are better handled with R-3.0.3 (but not later)----a sad reality I do not like. Here is what I did. I downloaded https://cran-archive.r-project.org/bin/windows/contrib/3.0/aod_1.3.zip and installed the zip file, which worked in both RStudio and R (without RStudio). In

He didn't specify the RStudio repos, though it's probably implicitly specified in getOption("repos"). I wonder why install.packages() is looking there, when repos is given explicitly? On 08/10/2020 8:54 a.m., Uwe Ligges wrote: > Drop the RStudio repos. > > Best, > Uwe Ligges > > On 05.10.2020 11:10, Steven Yen wrote: >> Thanks. I did as suggested but

Dear all, I found a problem with 'lme4'. Basically, once you load the package 'aod' (Analysis of Overdispersed Data), the functions 'lmer' and 'glmer' don't work anymore: library(lme4) (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)) (gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd), family = binomial, data