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interaction and nested notation in lmer

2 messages · Mashitah Jusoh, Ben Bolker

Original
Mashitah Jusoh
# 
Hi,

I would like to ask about the notation to indicated nested and interaction
when using lmer function.

Here is my experiment look like:

I have 95 genotypes with 2 replications that were conducted in two years.
Some of the observation were missing, making the dataset unbalance. So, I
decided to use lmer function to fit the data to get the variance component
and will treat all components as random. The model that I am going to fit
is:

Y=mean + year + genotype + rep (nested in year)  + genotype*year + error

I am wondering how to write the command for nested and interaction term in
R using lmer function for this model? As far as I search in the internet,
the command for nested and interaction seems like using similar notation,
for example (1|year:rep) to show rep is nested within year (for random
effect) the same notation is used to indicate the interaction (for other
variables, such as genotype:year). Correct me if i am wrong. And, can you
give some clarification about this and also how lmer/ R works with
interaction and nested data?

Thank you
1 day later
Ben Bolker
#
On Mon, Sep 21, 2015 at 6:24 PM, Mashitah Jusoh <mashitahj at gmail.com> wrote:
If you have samples from only 2 years, it's not going to be
particularly practical to fit
a model with year as random effect.  Setting that aside for the moment,
the distinction between (1|year/rep) and (1|year:rep) is that the
former expands to
(1|year) + (1|year:rep)  (i.e., effect of year and effect of rep
within year), while the latter
is just rep within year -- i.e. no main effect of year.

  However, nesting syntax doesn't really doesn't work well for fixed
effects (partly
due to the way R handles the formulae, and partly for conceptual reasons) -- in
your model, year:rep would give 4 fixed-effect parameters, as would
year+rep+year:rep
or year*rep (two ways of specifying crossed effects)

  I think I would recommend

Y  ~ 1 + year*rep + (1|genotype) + (1|genotype:year)

With unbalanced data, it may be hard to get a unique decomposition of
variance ...

 Ben Bolker