Dear all,

I am trying to model mackerel egg abundance in the North Sea. The egg abundance information comes from triennial surveys and contains a lot of 0 values (e.g. samples without any mackerel eggs). The idea was hence to build a zero-inflated or a zero-altered model using MCMCglmm. Fixed terms should be Sea Surface Temperature (sst), Longitude, Latitude and years as random factor.

The first problem or question I ran into is that of course the number of eggs within a sample is a simple integer, although normally I would define an offset : Egg abundance = Counted Eggs x Correction Factor x Sampling Depth / Filtered Volume (Ce*R*SD/VolFilt), but as far as I understand it this is not an option in MCMCglmm? My easy solution for now was to simply round volume the corrected  egg counts, which introduces a minor error.

Based on some online readings etc. I came up with a model and a prior, but I am not feeling very confident about it, could you please indicate if this model makes sense?

prior0 <- list(B=list(mu = matrix(0,10,2),
V  = diag(10)*1e+6),
                            R  = list(V=diag(2),n=2,fix=2),
                            G  = list(G1=list(V=diag(c(1, 1e-6)),n=2, fix=2)))

m.zip <-  MCMCglmm(AE ~ trait + trait:(LONGITUDE*LATITUDE) + trait:sst,
                            random = ~idh(trait):YEAR,
family = "zipoisson",
rcov = ~ idh(trait):units,
                            prior = prior0,
nitt = 100000,
burnin = 10000,
thin = 25,
data = eggs)

m.zap <-MCMCglmm(AE ~ trait + trait:(LONGITUDE*LATITUDE) + trait:sst,
                            random = ~idh(trait):YEAR,
family = "zapoisson",
rcov = ~ idh(trait):units,
                            prior = prior0,
nitt = 100000,
burnin = 10000,
thin = 25, data = eggs)


Plotting and looking at the summary both models works fine, but I cannot figure out how to predict the data. I tried the following, but get an Error message (which I do not understand):
predict(m.zip, marginal = ~idh(trait):YEAR, type = "response", interval = "confidence")
Error in M[, which(rm.v), ] <- 0 : incorrect number of subscripts

Any help is greatly appreciated and many thanks in advance,

Sven Gastauer

IMARES
Fisheries Acoustician
Email: sven.gastauer@wur.nl<mailto:sven.gastauer@wur.nl>
Mobile: +31 (0)61 005 71 03

P.O. Box 68
Haringkade, 1 (0.23)
1970AB IJMUIDEN


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