Hi,

I'm currently running an MCMCglmm for a data set of male and female fitness within 100 genetic fly lines.

For each line, I have 4 female data points and 6 male data points.

Each data point represents the average fitness of that sex in each replicate (note that reps are labelled 1-4 for females and 1-6 for males, and each rep for the sexes was carried out at different times - i.e. rep 1 female was done at a different time to rep 1 male).

For the model, I therefore need to incorporate replicate by sex as a random effect:

prior.model.2<-list(R=list(V=matrix(c(400,0,0,600),2,2), nu=0.01),G=list (G1=list(V=matrix(c(400,0,0,600),2,2), nu=2, alpha.mu=c(0,0), alpha.V=matrix(c(400,0,0,600),2,2), G2=list(V=matrix(c(400,0,0,600),2,2), nu=2, alpha.mu=c(0,0), alpha.V=matrix(c(400,0,0,600),2,2))))


model.2 <- MCMCglmm(S_relative_fec ~ sex-1, random=~us(sex):line + us(sex):rep,rcov=~idh(sex):units, family="gaussian", nitt = 100000, burnin = 30000, thin=30, data = h100newdata, prior = prior.model.2, verbose = FALSE)


However, when I run this model I get the following warning message: 'some combinations in us(sex):rep do not exist and 2 missing records have been generated'

The autocorrelation for female rep and units is also very high

Does anyone know how I can correct the model or prior to change this?

Many thanks,
Tanya



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