Hello, I'm trying to organize a dataset to run a multivariate mixed model in MCMCglmm. I have several response traits and since I have unequal number of replicates per individual for each trait, I have been suggested to arrange the data in a long format. I have 5 response traits. Three of them were recorded as follows: - Day 1: trait A - Day 2: trait A and trait B - Day 3: trait A and trait C - Day 4: trait A and trait B - Day 5: trait A and trait C During the following 6-7 days I didn' t measure anything. And then after that, the other two traits (trait D and trait E) were recorded weekly during 54 weeks. I want to run a multivariate model in MCMCglmm to estimate the random var-cov matrix and the residual var-cov matrix. The later however must have some constrains as for example, trait B and C do not covary at the residual (within-individual level) and traits A, B and C do not covary at the residual level with traits D and E. So the residual var-cov matrix should be something like: A B C D E A 1 B x 1 C x 0 1 D 0 0 0 1 E 0 0 0 x 1 Where x represents the covariances that should be estimated, and 0 the constrained covariances. Questions: - Is it possible to fit such a residual var-cov matrix in MCMCglmm? Maybe with an antedependence model? - How can I structure the dataset for the analysis? Do I need a "time" column? I could use "day" for the first three traits, but then what about traits D and E? - Does it make sense at all to run this model, or would it be more meaningful to get a mean value of traits A, B and C and used them as fixed effects, since I have a very low number of replicates of them? In that case I'd of course investigate the main effects of A, C and C on E and D, and not the covariation amontg them...but it could be ok as well. Thanks!
long format and residual covariance matrix in MCMCglmm
1 message · David Villegas Ríos