[R] A question on modeling brain growth using GAM

Leon Lee bhamlion78 at gmail.com
Thu Mar 30 15:56:55 CEST 2017


Thank you for your reply. I apologize if I posted in the wrong forum, as I
really couldn't decide which forum is the best place for my question and I
saw similar questions asked before in this forum.

I agree that a sample of ~30 subjects (70 scans in total), the model can be
too complicated. Based on that, I did the following:
(1) ignored the gender effect, as we have less females than males.
(2) corrected chronological age based on their gestational age, that is, we
subtracted an infant's chronological age by 2 weeks, if the infant's
gestational age is 38 weeks instead of 40weeks.

When I ran the model with corrected age, gestational age and their
interactions modeled, I found the main effect of gestational age and the
interaction between the two are gone.

So, my final model will look something like this:
gamObj=gam(brainVolume~ s(correctedAge) +  s(subjIndexF, bs="re"),
method="REML", data=mydata)

Does this look more reasonable? Yes, I am relatively new to the mixed
model. We originally applied functional data analysis (PACE) on the data,
but want to see the results using a different approach. Also, I couldn't
find the Mixed Models list, do you mind sending me a link?

Thank you!

On Tue, Mar 28, 2017 at 4:28 PM, David Winsemius <dwinsemius at comcast.net>

> > On Mar 28, 2017, at 9:32 AM, Leon Lee <bhamlion78 at gmail.com> wrote:
> >
> > Hi, R experts
> >
> > I am new to R & GAM toolbox and would like to get inputs from you all on
> my
> > models. The question I have is as follows:
> > I have 30 subjects with each subject being scanned from one to three
> times
> > in the first year of life. The brain volume from each scan was measured.
> > The scan time was randomly distributed from birth to 1 year.
> > Each subject has different gestational age ranging from 38 to 41 weeks
> > Each subject has chronological age from birth to 1 year old
> > Each subject has gender category.
> > Now, I want to look at how predictors, such as subject's chronological
> age,
> > gestational age and gender will explain the changes in brain volume. I
> also
> > want to include interactions between gender and age, gestational and
> > chronological age. Random effects are also included in the model to
> account
> > for subject variability. My model looks like the follows:
> >
> > gam=gam(brainVolume~ s(age) + ti(age, gestationalAge) + gestationalAge +
> > sex + s(age, by=sex) +  s(subjIndexF, bs="re"), method="REML",
> data=mydata)
> >
> > Are there any obvious mistakes in the model? Any suggestions will be
> > greatly appreciated!
> I'm not seeing mistakes in the syntax but I would question whether 30
> subjects is sufficient to adequately support estimates in a a model of this
> complexity. I would also think that the 's(age)' and 'sex' terms would get
> aliased out in a model with "+ s(age, by=sex)". Most R regression functions
> handle removal of over-parametrization automatically.
> You also have a variable number of measurements per subject. I am unable
> to comment on the effort to account for the implicit and variably measured
> correlation and auto-correlation of values within subjects using a "smooth"
> on subjIndexF, since that is not an approach I was familiar with.  But I am
> getting concerned whether you are also new to statistical modeling in
> addition to your use of R and GAM being "new to you"?
> (Perhaps Simon or one of the mixed-effects experts can correct the gaps in
> my understanding of how to model repeated measures in the context of small
> numbers of subjects and irregular emasurements.)
> Please read the Posting Guide and the pages of candidate mailing lists.
> Rhelp is not really the place to go when you need statistical advice. I'm
> not sure if this is really in the center of concerns that get discussed on
> the Mixed Models list, but to my eyes it would be a better fit there.
> --
> David.
> >
> > L
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> David Winsemius
> Alameda, CA, USA

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