Re: [R-sig-eco] RDA

[Richards, Christina]

Hello!

That is very helpful and seems to work! Thank you!!

I did not realize we could use raw data in capscale, is this true only because 
it is 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 
Sent: Wednesday, November 25, 2015 3:28 AM
To: Richards, Christina; r-sig-ecology@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]]
>
> ___
> R-sig-ecology mailing list
> R-sig-ecology@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>

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Re: [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 
Sent: Wednesday, November 25, 2015 3:28 AM
To: Richards, Christina; r-sig-ecology@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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Re: [R-sig-eco] RDA

[Jari Oksanen]

> On 26 Nov 2015, at 20:05 pm, Marcelino de la Cruz  
> wrote:
> 
> 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
> 
Yes, this is true: current and *future* implementations of capscale/rda/cca 
(and future dbrda) will only have one data= argument. However, in addition to 
variables in the data frame given in data=, you can mix variables in the work 
environment in your formula. If you think you need to have several data frames 
for the data= argument, please consider cbind(). 

cheers, Jari Oksanen

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Re: [R-sig-eco] RDA

[Jari Oksanen]

> On 26 Nov 2015, at 17:27 pm, Richards, Christina  wrote:
> 
> Hello!
> 
> That is very helpful and seems to work! Thank you!!
> 
> I did not realize we could use raw data in capscale, is this true only 
> because it is 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.
> 
If you supply raw community matrix (observations times species), capscale() 
will internally turn it into dissimilarities using specified distance= method 
(defaults “euclidean”). You should verify that the selected distance= method is 
the one you need. The variables on the right-hand-side of the formula must be 
in “raw” (observations times variables) format. They cannot be distances. 

Cheers, Jari Oksanen

> ___
> From: Marcelino de la Cruz 
> Sent: Wednesday, November 25, 2015 3:28 AM
> To: Richards, Christina; r-sig-ecology@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]]
>> 
>> ___
>> R-sig-ecology mailing list
>> R-sig-ecology@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>> 
> 
> ___
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Re: [R-sig-eco] RDA

[Richards, Christina]

Thank you! that is exactly what we need.

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: Jari Oksanen 
Sent: Thursday, November 26, 2015 1:24 PM
To: Richards, Christina
Cc: Marcelino de la Cruz; r-sig-ecology@r-project.org; Robertson, Marta; 
Verhoeven, Koen; Alvarez, Mariano; Foust, Christy
Subject: Re: [R-sig-eco] RDA

> On 26 Nov 2015, at 17:27 pm, Richards, Christina  wrote:
>
> Hello!
>
> That is very helpful and seems to work! Thank you!!
>
> I did not realize we could use raw data in capscale, is this true only 
> because it is 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.
>
If you supply raw community matrix (observations times species), capscale() 
will internally turn it into dissimilarities using specified distance= method 
(defaults “euclidean”). You should verify that the selected distance= method is 
the one you need. The variables on the right-hand-side of the formula must be 
in “raw” (observations times variables) format. They cannot be distances.

Cheers, Jari Oksanen

> ___
> From: Marcelino de la Cruz 
> Sent: Wednesday, November 25, 2015 3:28 AM
> To: Richards, Christina; r-sig-ecology@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]]
>>
>> ___
>> R-sig-ecology mailing list
>> R-sig-ecology@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>
>
> ___
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> R-sig-ecology@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

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Re: [R-sig-eco] RDA

[Richards, Christina]

Hi Dr. Oksanen!

Its very gracious of you to respond. On another important note, this is the 
citation suggested for the vegan package:

Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'Hara RB, Simpson GL, 
Solymos P, Stevens MHH, Wagner H. (2015) vegan: Community Ecology Package. R 
package version 2.2-1. http://CRAN.R-project.org/package=vegan 

Is this the most appropriate for our purposes (using Adonis and capscale in 
Vegan)?

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: Jari Oksanen 
Sent: Thursday, November 26, 2015 1:15 PM
To: Marcelino de la Cruz
Cc: Richards, Christina; r-sig-ecology@r-project.org; Robertson, Marta; 
Verhoeven,  Koen; Alvarez, Mariano; Foust, Christy
Subject: Re: [R-sig-eco] RDA

> On 26 Nov 2015, at 20:05 pm, Marcelino de la Cruz  
> wrote:
>
> 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
>
Yes, this is true: current and *future* implementations of capscale/rda/cca 
(and future dbrda) will only have one data= argument. However, in addition to 
variables in the data frame given in data=, you can mix variables in the work 
environment in your formula. If you think you need to have several data frames 
for the data= argument, please consider cbind().

cheers, Jari Oksanen

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Re: [R-sig-eco] RDA

[Gavin Simpson]

Yes, that is the appropriate citation for the software/implementation (and
in the case of capscale() the method, I think; there are other variants of
the idea around). `adonis()` is based on the permutational MANOVA
(PERMANOVA) references to the papers that introduced this method are in
`?adonis`, which you may choose to cite also.

HTH

Gavin

On 26 November 2015 at 14:13, Richards, Christina  wrote:

> Hi Dr. Oksanen!
>
> Its very gracious of you to respond. On another important note, this is
> the citation suggested for the vegan package:
>
> Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'Hara RB,
> Simpson GL, Solymos P, Stevens MHH, Wagner H. (2015) vegan: Community
> Ecology Package. R package version 2.2-1.
> http://CRAN.R-project.org/package=vegan
>
> Is this the most appropriate for our purposes (using Adonis and capscale
> in Vegan)?
>
> 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: Jari Oksanen 
> Sent: Thursday, November 26, 2015 1:15 PM
> To: Marcelino de la Cruz
> Cc: Richards, Christina; r-sig-ecology@r-project.org; Robertson, Marta;
> Verhoeven,  Koen; Alvarez, Mariano; Foust, Christy
> Subject: Re: [R-sig-eco] RDA
>
> > On 26 Nov 2015, at 20:05 pm, Marcelino de la Cruz <
> marcelino.delac...@upm.es> wrote:
> >
> > 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
> >
> Yes, this is true: current and *future* implementations of
> capscale/rda/cca (and future dbrda) will only have one data= argument.
> However, in addition to variables in the data frame given in data=, you can
> mix variables in the work environment in your formula. If you think you
> need to have several data frames for the data= argument, please consider
> cbind().
>
> cheers, Jari Oksanen
>
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>



-- 
Gavin Simpson, PhD

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[R-sig-eco] Morisita horn similarity index

[moses selebatso]

 Hello 
I am trying to analyse diet overlap (level of similarity) between two species. 
I have diet composition in %. I have tried to find the best tool, and thought 
Morisita horn will do, but I cant find the right package for. Is this the best 
tool?
Thank you,
Moses 
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