R help - Jun 2014 - ANOVA for proportions with large mass on an extreme of [0, 1]

I am trying to perform an ANOVA on a dependent variable that has large mass
on the 1 side of the (0, 1] interval. I decided to use Fractional Regression
Models, as implemented in the package frm. This package seems well-suited for
my problem, but I don't see how to perform model comparisons of nested frm
models. Please, see data and code below.

I would like to do:

anova(model1, model2)

There is a function frm.ptest(model1, model2), but does not work with nested
models.

Are there alternatives to the frm package to perform ANOVAs on proportions
(with large mass on an extreme of [0, 1])?

Is there a way to model repeated measures (as in package lme4) when the
dependent variable is a  proportion?

Data and code
-------------

con <-
url("http://sccn.ucsd.edu/~rapela/avshift/anovaDataFrame.RData")
myData <- get(load(con))
close(con)

myData <- myData[!is.na(myData$alternationRate),]
y <- myData$alternationRate

library(frm)

model1 <- frm(y=y, x=model.matrix(~modality*condition+clusterID,
data=myData)[, -1], linkfrac="logit", linkbin="logit",
type="2P", inflation=1)
model2 <- frm(y=y, x=model.matrix(~modality+condition+clusterID,
data=myData)[, -1], linkfrac="logit", linkbin="logit",
type="2P", inflation=1)

# this works
frm.ptest(model2, model3)

# but this does not
# frm.ptest(model1, model2)
#
# Error in frm.ptest(model1, model2) : 
# object 2 is nested in object 1 - no need to use the P test

Thanks, Joaquin

Although your queries certainly intersect R, they are primarily about
statistical modeling, which is OT for this list. Your issues also
appear to be complex. I would therefore suggest that you eschew remote
Internet advice and consult a local statistical expert for help.

Cheers,
Bert

Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374

"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
Clifford Stoll




On Fri, Jun 20, 2014 at 8:54 PM, Joaquin Rapela <rapela at ucsd.edu>
wrote:
>
> I am trying to perform an ANOVA on a dependent variable that has large mass
> on the 1 side of the (0, 1] interval. I decided to use Fractional
Regression
> Models, as implemented in the package frm. This package seems well-suited
for
> my problem, but I don't see how to perform model comparisons of nested
frm
> models. Please, see data and code below.
>
> I would like to do:
>
> anova(model1, model2)
>
> There is a function frm.ptest(model1, model2), but does not work with
nested
> models.
>
> Are there alternatives to the frm package to perform ANOVAs on proportions
> (with large mass on an extreme of [0, 1])?
>
> Is there a way to model repeated measures (as in package lme4) when the
dependent variable is a  proportion?
>
> Data and code
> -------------
>
> con <-
url("http://sccn.ucsd.edu/~rapela/avshift/anovaDataFrame.RData")
> myData <- get(load(con))
> close(con)
>
> myData <- myData[!is.na(myData$alternationRate),]
> y <- myData$alternationRate
>
> library(frm)
>
> model1 <- frm(y=y, x=model.matrix(~modality*condition+clusterID,
data=myData)[, -1], linkfrac="logit", linkbin="logit",
type="2P", inflation=1)
> model2 <- frm(y=y, x=model.matrix(~modality+condition+clusterID,
data=myData)[, -1], linkfrac="logit", linkbin="logit",
type="2P", inflation=1)
>
> # this works
> frm.ptest(model2, model3)
>
> # but this does not
> # frm.ptest(model1, model2)
> #
> # Error in frm.ptest(model1, model2) :
> # object 2 is nested in object 1 - no need to use the P test
>
> Thanks, Joaquin
>
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