[R] Contrast interaction effects in lmer object for reciprocal transplant experiment
Steven Brady
steven.brady at yale.edu
Mon Jun 21 20:47:08 CEST 2010
Dear All:
My apologies, but my formatting of the original message was poor.
Here it is again with more appropriate spacing for copying into the
terminal.
I am using lmer() {lme4} to analyze results from a reciprocal
transplant experiment where the response variable is modeled as a
function of two fixed effects and their interaction.
Example data follow:
#library(lme4)
#library(gmodels)
env=c("r","r","w","w","r","r","w","w","r","r",
"w","w","r","r","w","w")
#type of environment to where populations
#were transplanted (fixed effect)
origin=c("r","r","r","r","r","r","r",
"r","w","w","w","w","w","w","w","w")
#type of environment from where populations
#originated (fixed effect)
survival=c(rnorm(16,0.75, sd = 0.1))
#percent survival (response variable)
population=c("a","a","a","a","b","b","b","b",
"c","c","c","c","d","d","d","d")
#local population (random effect)
exp=data.frame(pond=pond, env=env,
origin=origin,survival=survival)
#make data frame
g<-lmer(survival~origin*env + (1|population),
data = exp)
# mixed model
pvals.fnc(g)
#evaluate fixed effects
My question is this:
How do I perform contrasts on the interaction of the fixed effects
using, say estimable() in the library {gmodels}? I have seen how to
do this for levels within a factor, however, I am unsure how to apply
these to levels among factors (i.e. the interaction terms).
Biologically speaking, I am interested in evaluating the difference in
survival between the two origin types in each of two types of
environments. In other words:
1. does origin r differ from origin w within env w? and,
2. does origin r differ from origin w within env r?
Part of my misunderstanding concerns the reporting of the fixed
effects of the model, which are named as the fixed term concatenated
with a level (e.g. originw). Does the way lmer names the fixed
effects influence the contrast matrix I should specify?
Many thanks in advance,
Steve Brady
__________________________________________
Steven P. Brady, Ph.D. Candidate
School of Forestry & Environmental Studies
Yale University
370 Prospect Street
New Haven, CT 06511
Email: steven.brady at yale.edu
Phone: 203-432-5321 Fax: 203-432-3929
Web: http://www.cbc.yale.edu/people/skelly/steveb.html
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