[R-sig-eco] mvpart alternatives and machine learning multivariate analysis

Sat Jul 1 19:14:17 CEST 2017

If you want to stick with or at least compare a mulivariate tree with
other approaches (like CCA or mvabund or boral) then the partykit
package provides an implementation of a multivariate tree model, using
conditional inference trees (i.e. you use conditional inference to
decide if spits are "significant" and stop splitting when they aren't
rather than the classic build a big tree and prune it back with
cost-complexity pruning and cross-validation.

An illustration with the classic hunting spider data set (which was
used in the mvpart paper too IIRC) can be found at the end of one of
the vignettes supplied with partykit:
https://cran.r-project.org/web/packages/partykit/vignettes/ctree.pdf

When I used this recently to replicate an analysis from a book chapter
I wrote a few years back, the partykit implementation worked well
after a little fiddling, but some of the plot options for the terminal
nodes don't work so well if your species response matrix has many
columns in it (i.e. lots of species).

HTH

Gavin

On 24 June 2017 at 10:35, Manuel Spínola <mspinola10 at gmail.com> wrote:
> Thank you very much Ralf.
>
> I am looking for alternatives to the classic CCA community analysis, and I
> was thinking into machine learning techniques.
>
> Manuel
>
> 2017-06-24 10:10 GMT-06:00 Ralf Schäfer <senator at ecotoxicology.de>:
>
>> Indeed! To expand on this: if you need a tutorial for mvabund, we once
>> analysed some categorical multivariate data and provided a tutorial:
>> http://dx.doi.org/10.1007/s10646-015-1421-0
>> Paper and tutorial are freely available on researchgate
>>
>> There are also many other methods, but to point you to some, it would be
>> good if you were more specific than „community- environment relationships“.
>>
>> Best regards
>> Ralf
>>
>>
>> Am 24.06.2017 um 18:02 schrieb Torsten Hauffe <torsten.hauffe at gmail.com>:
>>
>> As far as I remember, on Windows you will need to download and install the
>> Rtools first (https://cran.r-project.org/bin/windows/Rtools/) because
>> some parts of mvpart need to be compiled.
>>
>> You can analyse multiple species-environment relationships with the
>> mvabund package. This is not fancy machine-learning but solid likelihood
>> statistic.
>>
>> HTH,
>> Torsten
>>
>> On 24 June 2017 at 11:57, Ralf Schäfer <senator at ecotoxicology.de> wrote:
>>
>>> Manuel,
>>>
>>> I just checked, it is currently still compatible. So you can download
>>> from the archive and install from source - at least on Linux and OS X, nut
>>> sure about Windows.
>>> See Session information below:
>>>
>>> > R version 3.4.0 (2017-04-21)
>>> > Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>> > Running under: macOS Sierra 10.12.5
>>> >
>>> > Matrix products: default
>>> > BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/
>>> libRblas.0.dylib
>>> > LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/
>>> libRlapack.dylib
>>> >
>>> > locale:
>>> > [1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8
>>> >
>>> > attached base packages:
>>> > [1] stats     graphics  grDevices utils     datasets  methods   base
>>> >
>>> > other attached packages:
>>> > [1] mvpart_1.6-2
>>> >
>>> > loaded via a namespace (and not attached):
>>> > [1] compiler_3.4.0
>>>
>>>
>>> However, there are certainly other packages that can partition
>>> multivariate ecological data, though I am not aware of other packages for
>>> use with multivariate regression trees.
>>>
>>> Regards
>>> Ralf
>>>
>>>
>>>
>>> > Am 24.06.2017 um 17:47 schrieb Manuel Spínola <mspinola10 at gmail.com>:
>>> >
>>> > Thank you Ralf,
>>> >
>>> > But I guess is not going to be newer versions and could be incompatible
>>> with newer version of R, so at some moment there will be no accessibility
>>> to the package.
>>> >
>>> > Manuel
>>> >
>>> > 2017-06-24 5:25 GMT-06:00 Ralf Schäfer <senator at ecotoxicology.de
>>> <mailto:senator at ecotoxicology.de>>:
>>> > Dear Manuel
>>> >
>>> > despite it has been removed, it should still work.
>>> > At least I used it last year - just install the version from the
>>> archive manually:
>>> > https://cran.r-project.org/src/contrib/Archive/mvpart/ <
>>> https://cran.r-project.org/src/contrib/Archive/mvpart/>
>>> >
>>> > Best regards
>>> > Ralf
>>> >
>>> >
>>> >> Date: Fri, 23 Jun 2017 13:59:13 -0600
>>> >> From: Manuel Sp?nola <mspinola10 at gmail.com <mailto:
>>> mspinola10 at gmail.com>>
>>> >> To: "r-sig-ecology at r-project.org <mailto:r-sig-ecology at r-project.org>"
>>> <r-sig-ecology at r-project.org <mailto:r-sig-ecology at r-project.org>>
>>> >> Subject: [R-sig-eco] mvpart alternatives and machine learning
>>> >>      multivariate    analysis
>>> >> Message-ID:
>>> >>      <CABkCotRiCwJjsh=_hsONMsh+OE52rC7L6E3Q4ssOUM=6w3DXTw at mail.
>>> gmail.com <mailto:CABkCotRiCwJjsh=_hsONMsh+OE52rC7L6E3Q4ssOUM=6w3DXTw@
>>> mail.gmail.com>>
>>> >> Content-Type: text/plain; charset="UTF-8"
>>> >>
>>> >> Dear list members,
>>> >>
>>> >> As mvpart has been removed form the CRAN repository, Is there any r
>>> package
>>> >> that do similar analysis (multivariate partitioning)?
>>> >>
>>> >> Also, is there any other machine learning technique to do multivariate
>>> >> analysis as done in ecology to asses multiple species-environment
>>> >> relationships?
>>> >>
>>> >> Thank you very much in advance,
>>> >>
>>> >> Manuel
>>> >>
>>> >> --
>>> >> *Manuel Sp?nola, Ph.D.*
>>> >> Instituto Internacional en Conservaci?n y Manejo de Vida Silvestre
>>> >> Universidad Nacional
>>> >> Apartado 1350-3000
>>> >> Heredia
>>> >> COSTA RICA
>>> >> mspinola at una.cr <mailto:mspinola at una.cr> <mspinola at una.ac.cr <mailto:
>>> mspinola at una.ac.cr>>
>>> >> mspinola10 at gmail.com <mailto:mspinola10 at gmail.com>
>>> >> Tel?fono: (506) 8706 - 4662
>>> >> Personal website: Lobito de r?o <https://sites.google.com/site
>>> /lobitoderio/ <https://sites.google.com/site/lobitoderio/>>
>>> >> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/ <
>>> http://www.icomvis.una.ac.cr/>>
>>> >
>>> >
>>> >
>>> > --
>>> > Manuel Spínola, Ph.D.
>>> > Instituto Internacional en Conservación y Manejo de Vida Silvestre
>>> > Universidad Nacional
>>> > Apartado 1350-3000
>>> > Heredia
>>> > COSTA RICA
>>> > mspinola at una.cr <mailto:mspinola at una.ac.cr>
>>> > mspinola10 at gmail.com <mailto:mspinola10 at gmail.com>
>>> > Teléfono: (506) 8706 - 4662
>>> > Personal website: Lobito de río <https://sites.google.com/site
>>> /lobitoderio/>
>>> > Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>>>
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>>>
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>>
>>
>>
>
>
> --
> *Manuel Spínola, Ph.D.*
> Instituto Internacional en Conservación y Manejo de Vida Silvestre
> Universidad Nacional
> Apartado 1350-3000
> Heredia
> COSTA RICA
> mspinola at una.cr <mspinola at una.ac.cr>
> mspinola10 at gmail.com
> Teléfono: (506) 8706 - 4662
> Personal website: Lobito de río <https://sites.google.com/site/lobitoderio/>
> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
>
>         [[alternative HTML version deleted]]
>
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-- 
Gavin Simpson, PhD