[R-sig-ME] interpretation of covariate effect on traits in multinomial mixed model (MCMCglmm)
Dominique CARVAL
dominique.carval at cirad.fr
Tue Oct 7 23:42:32 CEST 2014
Hi everybody,
I want to assess the possible effect of the density of 3 plants strata (herbaceous, ligneous, and banana plant; continuous variables) on the probability of 6 ant species to be the (numerically) dominant species.
The data come from samplings on 500 sites in plantain agrosystems in Cameroun, with 2 replicates per site.
The multinomial response variable is composed of the 6 following categories : DomSpecies1,DomSpecies2, DomSpecies3, DomSpecies4, DomSpecies5, DomSpecies6.
I used the DomSpecies5 as the baseline category.
I followed the instructions of J. Hadfield (MCMCglmm Course Notes)to specify covariance matrix and I specified the following random effect : siteid, which is the identification number of each of the 500 sampled sites.
I suppose that each ant species may respond differently to the density of each stratum.
Therefore, I used the following model:
bayesId<-MCMCglmm(DomSpecies~trait + herbaceous:trait + banana:trait + ligneous:trait - 1, rcov = ~idh(trait):units, random=~siteid, nitt=nbiterations, burnin=burning, prior=priors1, family="categorical", data=Dominance, pr = TRUE, pl = TRUE, saveX=TRUE, saveZ = TRUE,thin=10)
Here is the location effects part summary of the model:
Location effects: DomSpecies ~ trait + herbaceous:trait + banana:trait + ligneous:trait - 1
post.mean l-95% CI u-95% CI eff.samp pMCMC
traitDomSpecies.1 -0.40504 -0.67616 -0.18239 32.804 <0.001 **
traitDomSpecies.2 -1.56674 -1.84566 -1.27239 18.023 <0.001 **
traitDomSpecies.3 -2.68457 -3.24824 -2.02872 4.320 <0.001 **
traitDomSpecies.4 -0.57887 -0.87424 -0.28980 21.054 <0.001 **
traitDomSpecies.6 -0.34739 -0.58999 -0.11550 28.079 <0.001 **
traitDomSpecies.1:herbaceous -0.12314 -0.36278 0.08398 36.442 0.2300
traitDomSpecies.2:herbaceous -0.81781 -1.12423 -0.45659 13.293 <0.001 **
traitDomSpecies.3:herbaceous -0.79766 -1.79822 0.20292 1.548 0.2225
traitDomSpecies.4:herbaceous 0.06787 -0.17180 0.25493 18.361 0.5375
traitDomSpecies.6:herbaceous -0.38589 -0.67043 -0.10492 13.041 0.0050 **
traitDomSpecies.1:banana -0.55612 -0.97868 -0.08495 20.617 0.0100 **
traitDomSpecies.2:banana -0.35302 -0.74533 0.04908 19.673 0.0875 .
traitDomSpecies.3:banana -0.31290 -1.21542 0.57856 4.051 0.7075
traitDomSpecies.4:banana 0.09981 -0.24120 0.47918 23.943 0.5850
traitDomSpecies.6:banana -0.36227 -0.76133 -0.02808 33.856 0.0350 *
traitDomSpecies.1:ligneous 1.15269 0.79352 1.55125 32.402 <0.001 **
traitDomSpecies.2:ligneous 0.85504 0.26285 1.42060 9.794 0.0125 *
traitDomSpecies.3:ligneous 1.30803 0.83209 1.92698 12.474 <0.001 **
traitDomSpecies.4:ligneous -0.19435 -1.10642 0.42893 3.782 0.8575
traitDomSpecies.6:ligneous 1.09109 0.68030 1.53037 20.792 <0.001 **
I understand that the probability of being in the categories 1,2,3,4 and 6 are significantly lower than the probability of being in the baseline category 5 (which is consistent with observed data).
I am more confused to interpret the effect of covariates. For instance, the 7th line of this summary dispalys:
post.mean l-95% CI u-95% CI eff.samp pMCMC
traitDomSpecies.2:herbaceous -0.81781 -1.12423 -0.45659 13.293 <0.001 **
I understand that the hebaceous stratum affect negatively (and significantly) the probability of being in the trait category 2.
If I look at the 6th line:
post.mean l-95% CI u-95% CI eff.samp pMCMC
traitDomSpecies.1:herbaceous -0.12314 -0.36278 0.08398 36.442 0.2300
I understand that the hebaceous stratum does not affect the probability of being in the trait category 1.
My first question is then: Am I right?
My second question: where do I found the effect of covariates on the baseline category 5?
Third and fourth questions: Is it correct to select the best models using only difference in DIC (delta DIC)? How to decide if the delta DIC is sufficiently large to be considered?
Thanks for answering,
Cheers,
Dom
Dominique Carval (PhD) - Ecologue
UR26 Système de Culture à base de Bananiers, Plantain et Ananas
CIRAD
Campus Agro-environnemental Caraïbes
Quartier Petit Morne – BP214
97285 Le Lamentin Cedex 2
Tel : (+596) 0596 42 30 28
Fax : (+596) 0596 42 30 01
More information about the R-sig-mixed-models
mailing list