testing linear combinations of coefficients of an MCMCglmm model to be zero
Dear Listmembers,
I am interested in testing linear combinations of coefficients in a
MCMCglmm model to be zero. Here an example based on the anova.lme
function for performing this type of tests:
#loading libraries and data
library(nlme)
data(BodyWeight)
#setting the contrasts
contrasts(BodyWeight$Diet) = contr.sum(3);
#fitting the model
model.nlme = lme(weight ~ Time * Diet, BodyWeight, random = ~ Time);
summary(model.nlme)
#is the coefficient Time:Diet3 equal to zero? Given the contrasts we chose,
#we must calculate and test the quantity -1*(Time:Diet1 + Time:Diet2)
anova(model.nlme, L = c("Time:Diet1" = -1, "Time:Diet2" = -1))
Given my quite limited knowledge about MCMC models, I suppose that a
similar test can be performed in a MCMC setting as follows:
#loading libraries and data
library(MCMCglmm)
data(BodyWeight, package= 'nlme')
set.seed(1234);
#setting the contrasts
contrasts(BodyWeight$Diet) = contr.sum(3);
#fitting the model
model.mcmc = MCMCglmm(weight ~ Time * Diet, data = BodyWeight, random
= ~ Time, verbose = FALSE);
summary(model.mcmc)
#is the coefficient Time:Diet3 equal to zero?
HPDinterval(-model.mcmc$Sol[, "Time:Diet1"] - model.mcmc$Sol[,
"Time:Diet2"], 0.95)
Is this the correct way to test the linear combination of two
coefficients in a MCMCglmm model?
Please notice that this question is closely related to one my previous post:
http://permalink.gmane.org/gmane.comp.lang.r.lme4.devel/6205
Again, I am trying to understand how to replicate some of the
functionalities of the nlme package within an MCMC framework.
Thanks in advance,
Vincenzo
Vincenzo Lagani Visiting Researcher BioInformatics Laboratory Institute of Computer Science Foundation for Research and Technology - Hellas