[R] Nested model and variance partitioning

[bady at univ-lyon1.fr]

hi, hi all,

> I am not quite sure what you mean by "outcome" but I try to be more precise.
> I have 4 spatial scales with:
> - One sample per habitat (i.e. substratum)
> - Many habitats per site
> - One or many sites per river

maybe, you can use a more general variable “type of river” (?)

> - Many rivers per regions
> - Two regions
> Each scales is described by one or many variables:
> - Habitat: type of substratum
> - Site: altitude, distance from the source, slope, drainage area
> - River: drainage area, altitude of the source, slope, type of geology
> - Regions: 2 modalities
> First I could try a nested ANOVA such as:
> SR = habitat + Site / River / Region
> But I am rather interested by which variables in each scales explains the
> species richness variance. So something like this:
> SR = substratum + (alt+dfs+sl+da) / (da+as+s+geol) / Region

> But I don't know if i) if it is the good model and

I don’t know.
In your context, the organisation of the stratification is an ecological
problem.

> ii) how to proceed with the lmne package.

You can consult :

- the documentation of the package nlme

- http://zoonek2.free.fr/UNIX/48_R_2004/17.html (english version :
http://zoonek2.free.fr/UNIX/48_R/13.html). In this document, there is many
information about the procedure of variance decomposition with R.

- http://cran.r-project.org/doc/Rnews/Rnews_2005-1.pdf (see “Fitting linear
mixed models in R” by Douglas Bates)

- etc.


Regards,


Pierre




>
>
>
>
>
>
> Selon bady at univ-lyon1.fr:
>
> > hi, hi all,
> >
> >
> > > Dear R users,
> > > I face to a nested pattern and despite the numerous examples in the help
> I
> > am
> > > still confused.
> > > I sampled bugs in different habitats within sites which were within
> rivers
> > > themselves within different regions.
> > > The habitat correspond to different substrata (not systematically present
> > in
> > > all sites). For rivers and sites, I have environemental variables (e.g.
> > altitude
> > > and slope of the site, drainage area and geology of the river) and I have
> > > only 2 regions. Note that sometimes I have only one site per river.
> > > I would like to know the part of each spatial scale described by
> > > environmental
> > > data in the species richness variance. For instance is the drainage area
> > at
> > > the river scale that explains a large amount of species richness variance
> > or
> > the
> > > altitude of the site, or the substratum, etc.
> >
> >
> > The design of our data is complex. What is your outcome ?
> >
> >
> > > I looked into the nlme package but I did not found how to proceed

> >
> > The reference document about the package nlme is certainly “Pinheiro J. C.
> &
> > Bates D. M.  (2000) Mixed-effects models in S and S-plus. Springer Verlag,
> > New
> > York. 528 pp.”
> >
> > but there is many information about this subject on the WEB (see
> > http://www.google.fr/search?hl=fr&q=nlme&btnG=Recherche+Google&meta=)
> >
> >
> > Regards,
> >
> > Pierre
> >
> >
> >
> >
> > --------------------------------------------------------------------------
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> >
>
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