Dear users, I'm trying to explain changes in tree vitality from 1 to 3 (1=green, 2=damage, 3=dry) using precipitation, diameter and tree species in an MCMCglmm model. I am struggling with two questions:1. How do I check if the model is correct??2. How do I interpret the summary of the MCMCglmm model in relation to my response variable (the three groups 1,2 and 3)? Data and R script can be found here?https://drive.google.com/drive/folders/1LmgEAssR5FfFw1CkYjygsaawg84dDAwk?usp=sharing?.?Details are posted here. ###MCMCglmm model, family= ordinal prior1<-list(R=list(V=diag(1),nu=0.002)) m1 <-MCMCglmm(VIT_2018~ pp18 +DBH+Species, family = "ordinal", data = comsp,prior=prior1,pr = TRUE, nitt = 60000, burnin =30000, thin = 50) summary(m1) Iterations = 30001:59951 Thinning interval = 50 Sample size = 600 DIC: -146008.7 R-structure: ~units post.mean l-95% CI u-95% CI eff.samp units 2697 1016 5304 6.075 Location effects: VIT_2018 ~ pp18 + DBH + Species post.mean l-95% CI u-95% CI eff.samp pMCMC (Intercept) 60.64229 31.71644 92.78733 11.49 < 0.002 ** pp18 -0.07020 -0.11518 -0.03556 15.47 < 0.002 ** DBH 0.17357 -0.01797 0.37281 58.26 0.06000 . SpeciesBetula pendula -12.88510 -29.42191 1.87807 58.40 0.08667 . SpeciesCarpinus betulus 15.57570 0.96439 30.89528 45.04 0.02000 * SpeciesCorylus avellana -3.81337 -18.31965 13.12771 600.00 0.59000 SpeciesCrataegus spec. -14.90077 -36.86880 4.24729 286.00 0.10333 SpeciesFagus sylvatica -15.03559 -29.04547 -2.07809 60.56 0.00667 ** SpeciesFrangula alnus 20.10817 -0.10598 38.66354 73.88 0.01333 * SpeciesQuercus spec. -9.09458 -24.52595 6.42502 293.33 0.26000 SpeciesSambucus nigra 24.29894 2.58339 46.29901 49.66 0.02333 * SpeciesSorbus aucuparia 39.56930 22.97282 63.15175 10.13 < 0.002 ** --- Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1 Cutpoints: post.mean l-95% CI u-95% CI eff.samp cutpoint.traitVIT_2018.1 80.46 55.38 117.9 4.204 #### Estimating Credible Intervals HPDinterval(mcmc(randomprior1$Sol[,"(Intercept)"])) # lower upper #var1 31.71644 92.78733 #attr(,"Probability") #[1] 0.95 Any suggestions/ideas would be really helpful. Thank you for your time and help! Mirela
How to check & interpret an MCMCglmm ordinal model in R?
1 message · Mirela Beloiu