Re: [R-sig-eco] DCCA in R?

2020-11-11 Thread Peter Solymos 
You are right, Attila, I missed the canonical part. It is either detrended
& unconstrained (decorana) or plain & constrained/canonical (cca).

Cheers,

Peter

On Wed, Nov 11, 2020 at 3:27 PM Attila Lengyel  wrote:

> Dear Peter,
>
> as far as I know, vegan::decorana does not do DCCA (detrended canonical
> correspondence analysis) but the unconstrained DCA. If anyone knows the
> answer for Jonathan's question, please, share it with me, I would also be
> interested.
> Best regards,
>
> Attila
>
> Peter Solymos  ezt írta (időpont: 2020. nov. 5., Cs,
> 19:19):
>
>> Jonathan,
>>
>> Have you checked ?vegan::decorana (it is also mentioned in the vignette on
>> p 2:
>> https://cran.r-project.org/web/packages/vegan/vignettes/intro-vegan.pdf
>> )
>>
>> Cheers,
>>
>> Peter
>>
>> On Thu, Nov 5, 2020 at 11:03 AM Jonathan Gordon <
>> jonathangordon...@gmail.com>
>> wrote:
>>
>> > Hello,
>> >
>> > I’m aiming to perform a detrended canonical correspondence analysis on a
>> > pollen sequence, to create beta diversity curves for pollen sequences
>> > through time. An example of this being done is in Felde (2019) <
>> > https://link.springer.com/article/10.1007/s00334-019-00726-5>. As far
>> as
>> > I can tell, DCCA can’t be done in R packages such as vegan, and can
>> only be
>> > completed in Canoco. I’m keen not to use Canoco because it's not open
>> > access and the processes behind the interface are obscured, making for a
>> > non-repeatable methodology. Please could you advise any way for me to
>> > perform a DCCA to obtain my desired results, or of a different method?
>> >
>> > Best wishes,
>> > Jonny
>> > [[alternative HTML version deleted]]
>> >
>> > ___
>> > R-sig-ecology mailing list
>> > R-sig-ecology@r-project.org
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>> >
>>
>>
>> --
>> Péter Sólymos, PhD
>> Senior Statistical Ecologist
>> soly...@ualberta.ca 780-492-8534
>> Alberta Biodiversity Monitoring Institute http://www.abmi.ca
>> Boreal Avian Modelling Project http://www.borealbirds.ca
>>
>> [[alternative HTML version deleted]]
>>
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>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>
>

-- 
Péter Sólymos, PhD
Senior Statistical Ecologist
soly...@ualberta.ca 780-492-8534
Alberta Biodiversity Monitoring Institute http://www.abmi.ca
Boreal Avian Modelling Project http://www.borealbirds.ca

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Re: [R-sig-eco] DCCA in R?

2020-11-11 Thread Attila Lengyel 
Dear Peter,

as far as I know, vegan::decorana does not do DCCA (detrended canonical
correspondence analysis) but the unconstrained DCA. If anyone knows the
answer for Jonathan's question, please, share it with me, I would also be
interested.
Best regards,

Attila

Peter Solymos  ezt írta (időpont: 2020. nov. 5., Cs,
19:19):

> Jonathan,
>
> Have you checked ?vegan::decorana (it is also mentioned in the vignette on
> p 2:
> https://cran.r-project.org/web/packages/vegan/vignettes/intro-vegan.pdf
> )
>
> Cheers,
>
> Peter
>
> On Thu, Nov 5, 2020 at 11:03 AM Jonathan Gordon <
> jonathangordon...@gmail.com>
> wrote:
>
> > Hello,
> >
> > I’m aiming to perform a detrended canonical correspondence analysis on a
> > pollen sequence, to create beta diversity curves for pollen sequences
> > through time. An example of this being done is in Felde (2019) <
> > https://link.springer.com/article/10.1007/s00334-019-00726-5>. As far as
> > I can tell, DCCA can’t be done in R packages such as vegan, and can only
> be
> > completed in Canoco. I’m keen not to use Canoco because it's not open
> > access and the processes behind the interface are obscured, making for a
> > non-repeatable methodology. Please could you advise any way for me to
> > perform a DCCA to obtain my desired results, or of a different method?
> >
> > Best wishes,
> > Jonny
> > [[alternative HTML version deleted]]
> >
> > ___
> > R-sig-ecology mailing list
> > R-sig-ecology@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >
>
>
> --
> Péter Sólymos, PhD
> Senior Statistical Ecologist
> soly...@ualberta.ca 780-492-8534
> Alberta Biodiversity Monitoring Institute http://www.abmi.ca
> Boreal Avian Modelling Project http://www.borealbirds.ca
>
> [[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-eco] DCA Axis1 Scores in SD Units

2020-11-11 Thread Jonathan Gordon 
Hello All,

I am investigating changes in the biodiversity of British vegetation over the 
Holocene and to this end I am implementing DCA to analyse turnover in a 
Holocene pollen sequence.

I have run decorana() in vegan on my pollen dataset and extracted the sample 
scores from DCA1, which give a rough approximation of ecological 
change/turnover over the pollen sequence. I want to, however, have these 
results in standard deviation units, a bit like Felde 
> and 
Correa-Metrio > have done. To achieve 
this, I think I need to calculate the euclidean distance between contiguous 
samples in terms of their ordination on the DCA rescaled ecological space, 
however, I can’t work out how to achieve this, i.e. ending up with SD units, 
myself. Any advice you may be able to provide re. this calculation would be 
greatly received!

Best wishes,
Jonny

—

Jonathan Gordon
Leverhulme Trust Funded PhD Student
Leverhulme Centre for Anthropocene Biodiversity, University of York

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