[R-sig-ME] Model for Preference analysis

[Evan Palmer-Young]

Dear Colleagues,
I am trying to analyze an experiment comparing consumption of 2 food types
in a choice-type design. Subjects were offered a choice of 2 food types,
and their daily consumption of each food type was recorded. Each subject
also was assigned to one of 2 Infection treatments.
We want to know-- "
*How does infection affect preference for one food type over another?*

I am wondering if it is acceptable to model this like a repeated measures
design, with 2 observations per subject and timepoint-- one for each food
type. Or is that not acceptable because the 2 food types were given at the
same time?

I attached my actual data and script, and also paste a code to generate a
random data set, to show the general data structure.

####choice analysis for list###
Df<-expand.grid(Time=seq(0,10,1),
        Subject=c("Honeybunch","Buttercup","Rosy",
                          "Sting", "Buzz", "Bumble"))
View(Df)
Df$Infection<-NULL
Df$Infection[1:33]<-"Infected"
Df$Infection[34:66]<-"Uninfected"
Df$Infection

Df$Consumption.Food.A<-rnorm(n=length(Df$Time),mean=30, sd=6)
Df$Consumption.Food.B<-rnorm(n=length(Df$Time),mean=25, sd=8)

library(lme4)
##Analysis with consumption of other food type as covariate
ModelA<-lmer(Consumption.Food.A~ Time + Infection + Consumption.Food.B +
               (1|Subject),data=Df)
ModelB<-lmer(Consumption.Food.B~ Time + Infection + Consumption.Food.A +
             (1|Subject), data=Df)

#option to convert data to long format
library(tidyr)
Df_long<-gather(data=Df, key=Foodtype, value=Amt.eaten,
                Consumption.Food.A,Consumption.Food.B)
View(Df_long)
#Is this model legal, because both foods offered simulateneously
Fullmodel<-lmer(Amt.eaten ~ Foodtype * Infection + Time +
                  (1|Subject) + (1|Time), data=Df_long)



(Originally I was planning to model proportions of the 2 food types eaten,
but there a lot of values close to zero that could make the proportion
estimates highly variable. And the proportional analysis would not account
for the strong trends of decreasing with (a) time and (b) infection
treatment)

Thanks very much for your advice!
Evan



-- 
Department of Biology
221 Morrill Science Center
611 North Pleasant St
Amherst MA 01003
https://sites.google.com/a/cornell.edu/evan-palmer-young/