[R-sig-eco] fourthcorner() with missing data

[Beth Atkinson]

Hi,

Thanks for your help. I tried imputeAFDM() in missMDA, but when I looked at 
completeObs the values of the original non-missing data were changed for 
the quantitative trait. This doesn't seem to be correct.

I'm new to trait analysis, so apologies if these are straightforward issues.

Beth

--On 09 January 2013 17:04 +0100 Stéphane Dray 
<stephane.dray at univ-lyon1.fr> wrote:

> Hello,
>
> the method does not consider missing values. The best solution would be
> to estimate missing values to fill the . For this estimation, you can
> either use the nipals method (nipals function in ade4 with rec = TRUE) or
> use the missMDA package. The second approach is better.
>
> Cheers.
>
> On 08/01/2013 16:40, Beth Atkinson wrote:
>>
>> Hello,
>>
>> I want to do a fourth corner analysis but I have missing data. I have
>> 169 species from 32 plots. There are 4 habitat types and I'm looking
>> at 8 traits. However, I don't have trait data for all species for each
>> trait (each trait has data for at least 80% of species).
>>
>> The function fourthcorner in ade4 returns an error message about NAs.
>> Is there a way around this? If I remove species that have data missing
>> for any trait, I lose around a third of the species.
>>
>> Thanks,
>>
>> Beth
>>
>> --------------------------------------------------------
>> Beth Atkinson
>>
>> PhD student
>> Community Ecology Group
>> School of Biological Sciences
>> University of Bristol
>> Woodland Road
>> Bristol
>> BS8 1UG
>>
>> http://www.bristol.ac.uk/biology/people/beth-atkinson/
>>
>> _______________________________________________
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>>
>
>
> --
> Stéphane DRAY (stephane.dray at univ-lyon1.fr)
> Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - Lyon I
> 43, Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
> Tel: 33 4 72 43 27 57       Fax: 33 4 72 43 13 88
> http://pbil.univ-lyon1.fr/members/dray/
>
>
>



--------------------------------------------------------
Beth Atkinson

PhD student
Community Ecology Group
School of Biological Sciences
University of Bristol
Woodland Road
Bristol
BS8 1UG

http://www.bristol.ac.uk/biology/people/beth-atkinson/