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

[Manuel Spínola]

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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>
>


-- 
*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/>

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