[R] glmmADMB

[Paul Johnson]

On Tue, May 8, 2012 at 5:16 PM, rbuxton <moyble at hotmail.com> wrote:
> http://r.789695.n4.nabble.com/file/n4618871/Data_for_list_serve.csv
> Data_for_list_serve.csv
>
> Here is my data, hope this helps.
>

> The "LESP CHUCKLE" , "FTSP FLIGHT", and "ANMU CHIRRUP" are the dependent
> variables, I want to run one model for each.
>

I've not succeeded in replicating your work, the data set has
something funny perhaps.

I saved  your file "data.csv" and ran this:

callsna <- read.table("data.csv", sep=",", header=T)

library(glmmADMB)

mod <- glmmadmb(LESP.CHUCKLE ~ Years.Erad + IS + Ref + Dist.Buldir +
Food+Moon+Wind.Speed + (1|SITE/ISLAND), data=callsna,
zeroInflation=TRUE, family="nbinom")

I don't get as far as you do.

> mod <- glmmadmb(LESP.CHUCKLE ~ Years.Erad + IS + Ref + Dist.Buldir + Food+Moon+Wind.Speed + (1|SITE/ISLAND), data=callsna, zeroInflation=TRUE, family="nbinom")
Error in II[, ii] = II[, ii] + REmat$codes[[i]] :
  number of items to replace is not a multiple of replacement length
In addition: Warning messages:
1: In glmmadmb(LESP.CHUCKLE ~ Years.Erad + IS + Ref + Dist.Buldir +  :
  NAs removed in constructing fixed-effect model frame: you should
probably remove them manually, e.g. with na.omit()
2: In II[, ii] + REmat$codes[[i]] :
  longer object length is not a multiple of shorter object length
> callsna <- na.omit(callsna)
> mod <- glmmadmb(LESP.CHUCKLE ~ Years.Erad + IS + Ref + Dist.Buldir + Food+Moon+Wind.Speed + (1|SITE/ISLAND), data=callsna, zeroInflation=TRUE, family="nbinom")
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) :
  contrasts can be applied only to factors with 2 or more levels


I wondered if the function you are using is supposed to be able to do
that.  I looked back at the web page for glmmADMB (note
capitalization), http://glmmadmb.r-forge.r-project.org/ and it says:

"Zero-inflation (currently only as a single constant term across all groups)"

But I'll try again if you post your R code that works with that CSV
file you posed, I may try again.

pj

> So, again the desired model is:
>
> mod <- glmmadmb(LESP.CHUCKLE~
> Years.Erad+IS+Ref+Dist.Buldir+Food+Moon+Wind.Speed+(1|SITE/ISLAND),
> data=callsna,
> zeroInflation=TRUE, family="nbinom")
>
> cheers!
> Rachel
>
>
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-- 
Paul E. Johnson
Professor, Political Science    Assoc. Director
1541 Lilac Lane, Room 504     Center for Research Methods
University of Kansas               University of Kansas
http://pj.freefaculty.org            http://quant.ku.edu