r - Repeated measures in MCMCglmm -


i'm analyzing data given, set follows:

  • 2 sites
  • 30 trees in each site (tree nested in site)
  • 12 branches per tree (a branch each direction - n,s,e,w in each of crown level - up, mid, low) (repeated measure)
  • dependent variable shoot damage insect (proportion of shoots damaged per branch)

the goal determine if insect damage varies within tree (from data see no effect of cardinal direction , clear effect of crown level)

i want model these data using mcmcglmm, i've nested tree in site coding follows (where df data frame):

 df$tr<-df$site:df$tree  

my mcmcglmm model follows:

prior1 = list(r = list(v = 1, nu = 0.002), g = list(g1 = list(v =  1, nu = 0.002)))  fit1<-mcmcglmm(cbind(damage,no.dam) ~ crown+dir+site, random = ~tr, family="multinomial2", prior = prior1, data=df,verbose=f) 

i'm confused on how specify repeated measures in model. think need use rcov~units or rcov~idh(tr):units

however, i'm not sure correct (or off track altogether). i'm graduate student i'm still learning stats , there nobody in department works these types of models , i'm finding difficult find need.

thanks in advance advice!


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