[R-sig-ME] summary fn zero-inflated MCMC models.

[Hodsoll, John]

Great. Thanks for the work-around!! 
Bw
John
-----Original Message-----
From: Jarrod Hadfield [mailto:j.hadfield at ed.ac.uk] 
Sent: 31 March 2014 17:39
To: Hodsoll, John
Cc: 'r-sig-mixed-models at r-project.org'
Subject: Re: [R-sig-ME] summary fn zero-inflated MCMC models.

Hi,

That's annoying. The bug happens with print.summary, and will occur for all zero-inflated, hurdle and multinomial models with idh residual structure. I will upload a fix ASAP. For now,

cf.za.1$Residual$nrt<-2

should work when using summary(cf.za.1).

Cheers,

Jarrod



Quoting "Hodsoll, John" <john.hodsoll at kcl.ac.uk> on Mon, 31 Mar 2014
13:04:03 +0000:

> Dear all / Jarrod
>
> Have just updated to the latest version of MCMCglmm but am now unable 
> to produce model info using the summary function for zero inflated 
> models. It doesn't work on hurdle models fitted on the previous 
> version either (but these do on an older version I have on my laptop).
>
> Error is
>
> Error in rep(rep(1:length(object$Residual$nrt), object$Residual$nrt),  :
>   invalid 'times' argument
>
> Unless something was wrong with my model specification previously and 
> something in the update is now showing that?
>
> Best wishses
> John Hodsoll
>
> prior and model definitions..
>
> #### Define prior  #####
> zal2.prior <-  list(B= list (mu = matrix(c(rep(0,20)),20),V = diag(20)*(20)),
>                     R = list(V = diag(2), n = 0.002, fix = 2),
>                     G = list(G1 = list(V = diag(2), n = 0.002)))
>
>
> zal2.prior$B$mu[9] <- 1
> diag(zal2.prior$B$V)[9]<-1e-9
>
> zal2.prior$B$mu[10] <- 1
> diag(zal2.prior$B$V)[10]<-1e-9
>
> #Level 2 models with complementary log log link.
>
> system.time(
>   cf.za.1 <- MCMCglmm(totflct ~ trait-1 + trait:(expcon.r*period.x + 
> log.beds + nshift + cday),
>                       data = rswAll.df, family = "zapoisson",
>                       random = ~us(trait):wardn,
>                       rcov = ~idh(trait):units,
>                       prior = zal2.prior,
>                  #     nitt = 300000, burnin = 50000, thin = 250,
>                       verbose = TRUE, pr = TRUE, pl = FALSE)
> )
>
> summary(cf.za.1)
> save(cf.za.1, file="cf.za.1.rda")
>
> 	[[alternative HTML version deleted]]
>
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>



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