[R-sig-ME] testing linear combinations of coefficients of an MCMCglmm model to be zero
vlagani at ics.forth.gr
vlagani at ics.forth.gr
Thu Jun 16 18:37:34 CEST 2011
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
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