Message-ID: <6f8e9df7-c871-a048-dd1f-3f47168ed91f@uni-bremen.de>
Date: 2019-06-06T15:17:46Z
From: Tim Richter-Heitmann
Subject: forward selection of significant eigenvectors
In-Reply-To: <1b91003a-5a2a-6b23-d47c-c8ca25cf95b5@univ-lyon1.fr>
Hi Stephane,
thank you for this very useful information.
As for the global test, the tutorial of Benoit Gendreau-Berthiaume (as
linked in my mail) does start the analysis with anova.cca on a RDA
fitting all available dbMEM before doing variable selection.
Does this satisfy the requirement of a global test?
Cheers, Tim
Am 06.06.2019 um 17:03 schrieb St?phane Dray:
> Hi,
>
> we introduced a new function mem.select in adespatial (that used
> forward.sel)? based on the work by Bauman et al
> (https://onlinelibrary.wiley.com/doi/abs/10.1111/ecog.03380)
> Basically, we showed that you should use a global test before
> performing forward selection (this step is suggested by Blanchet et al
> but rarely performed? in ecological studies).
>
> Cheers
>
>
> Le 06/06/2019 ? 16:41, Tim Richter-Heitmann a ?crit?:
>> Dear Irene,
>>
>> i found this tutorial very useful:
>>
>> https://sites.ualberta.ca/~ahamann/teaching/renr690/Lab9.pdf
>>
>> You basically do a forward selection (forward.sel() from packfor
>> package) using the adjusted R-square (RsquareAdj() from vegan package).
>>
>> Hope this helps, Tim
>>
>> Am 06.06.2019 um 16:34 schrieb Irene Adamo:
>>> Dear all,
>>>
>>> I am trying to run a variaion partitioning in using the varpart
>>> function in
>>> vegan. I would like to include the geographic coordinates as
>>> explanatory
>>> variables so I calculated the principle coordinates of neighbour
>>> matrices.
>>> Now I would like to perform a selection of the significant spatial
>>> eigenvectors but I don`t know how to do it in R. Could anybody help me?
>>>
>>> data(mite.xy)
>>> pcnm1 <- pcnm(dist(mite.xy))
>>>
>>> then I get the pcnm vectors and I would like to select only the
>>> significant ones.
>>>
>>> Thanks a lot!
>>>
>>> ????[[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-sig-ecology mailing list
>>> R-sig-ecology at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>
>
--
Dr. Tim Richter-Heitmann
University of Bremen
Microbial Ecophysiology Group (AG Friedrich)
FB02 - Biologie/Chemie
Leobener Stra?e (NW2 A2130)
D-28359 Bremen
Tel.: 0049(0)421 218-63062
Fax: 0049(0)421 218-63069
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