[R-sig-eco] RDA

[Marcelino de la Cruz]

El 26/11/2015 a las 16:27, Richards, Christina escribió:
> Hello!
>
> That is very helpful and seems to work! Thank you!!
>
> I did not realize we could use raw data in capscale,
We could and we should! Currently, it is the only way to achieve it.

  is this true only because it is conditioning variables?
It seems that the current implementation of capscale only accepts a 
single *data.frame* for both explanatory and conditioning variables

  At any rate it recapitulates our analysis using partial mantel in 2 
species with 2 different results (one significant, the other not), so 
I'm inclined to believe its doing something similar.


>
> Christina Richards, Ph.D.
> University of South Florida
> Department of Integrative Biology
> 4202 East Fowler Avenue SCA 127
> NES 107 (shipping)
> Tampa, FL 33620
> (813)974-5090
> (813)974-3263 FAX
> http://www.ecologicalepigenetics.com
> Twitter: @EcolEpig
> Facebook: Ecological Epigenetics
> ________________________________________
> From: Marcelino de la Cruz <marcelino.delacruz at upm.es>
> Sent: Wednesday, November 25, 2015 3:28 AM
> To: Richards, Christina; r-sig-ecology at r-project.org
> Subject: Re: [R-sig-eco] RDA
>
> Hi Christina,
>
> I think this could work:
>
> You should combine the *raw* y and z (i.e.not the Euclidean matrices) in
> the same data.frame (e.g. "yz"), and call capscale like this:
>
> capscale (x ~y1+y2+...+yn + Condition(z1+z2+...+z80), data=xy)
>
>
> Cheers!
>
> Marcelino
>
>
>
> --
> Marcelino de la Cruz Rot
> Depto. de Biología Y Geología
> Universidad Rey Juan Carlos
> Móstoles España
>
>
> El 24/11/2015 a las 22:11, Richards, Christina escribió:
>>
>>
>> Hello!
>>
>>
>> We are trying to do a partial RDA with 3 matrices but our x matrix has a lot of missing data. We could use instead distance matrices which imputed missing data, but when we try to use capscale and the euclidean matrices, it seems we have to use the formula x~y + condition (z) and we cannot use a matrix of values for z.  We would like to identify the the effect of y on x with z partitioned out where:
>>
>>
>> x= dataframe of dna methylation with individuals listed in column 1 and 0/1 data across ~80 columns
>>
>> y= habitat for each individual
>>
>> z= dataframe of genetic loci with individuals listed in column 1 and 0/1 data across ~80 columns
>>
>>
>> Christina Richards, Ph.D.
>> University of South Florida
>> Department of Integrative Biology
>> 4202 East Fowler Avenue SCA 127
>> NES 107 (shipping)
>> Tampa, FL 33620
>> (813)974-5090
>> (813)974-3263 FAX
>> http://www.ecologicalepigenetics.com
>> Twitter: @EcolEpig
>> Facebook: Ecological Epigenetics
>>
>>        [[alternative HTML version deleted]]
>>
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>>
>
>