[R-sig-eco] adonis to test difference in sums of squares partitioning across treatments?

[Etienne Laliberte]

Dear Andy,

For testing the null hypothesis of no land use effect, what you suggest does
not take into account the nested structure of your design (with land use
nested in location).

In ?adonis:

"If the experimental design has nestedness, then use strata to test
hypotheses. For instance, imagine we are testing the whether a plant
community is influenced by nitrate amendments, and we have two replicate
plots at each of two levels of nitrate (0, 10 ppm). We have replicated the
experiment in three fields with (perhaps) different average productivity. In
this design, we would need to specify strata = field so that randomizations
occur only within each field and not across all fields . See example below."

Which in your case translates to

adonis(bird.com  ~ land.use, strata = site.data$region, data = site.data)

Hope that helps,

Etienne


-----Original Message-----
From: r-sig-ecology-bounces at r-project.org
[mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of Andy Rominger
Sent: Friday, 17 December 2010 5:17 AM
To: r-sig-ecology at r-project.org
Subject: [R-sig-eco] adonis to test difference in sums of squares
partitioning across treatments?

Dear list,

We are working with a dataset of bird community composition across four
regions, each of which contain three land use treatments.  We are
interesting in understanding if the community dissimilarity within regions
and between regions differs according to land use treatment.  I understand
that multivariate analysis of variance (as implemented in adonis{vegan}) can
partition sums of squares between main effects and residuals, which I
understand would, for example, test the ratio (F-statistic) of between
versus within region dissimilarity.

What we'd like to know is effectively if this partitioning of sums of
squares within (residual) and between (main effects) regions changes
significantly under the different land use treatments.  So would the
following model to the trick?

adonis(bird.com~region*land.
use,data=site.data)

where...
bird.com is a sites by species matrix, and
site.data is a data.frame containing columns that indicate to which region
(column 'region') and land use (column 'land.use') each site belongs.

I appoligize for this simple question (and probably wrong model) I'm very
naive about these multivariate analyses.  We assumed that this approach was
probably wrong and so we are also working on a bootstrap method, which I
could post for your consideration if this use of adonis is incorrect, or if
no perMANOVA-based method would answer our question.

Thanks in advance for your help--
Andy Rominger

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