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
DCCA in R?
4 messages · Jonathan Gordon, Attila Lengyel, Peter Solymos
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 <jonathangordon107 at 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 at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
P?ter S?lymos, PhD Senior Statistical Ecologist solymos at 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]]
6 days later
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 <solymos at ualberta.ca> ezt ?rta (id?pont: 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 < jonathangordon107 at 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 at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
-- P?ter S?lymos, PhD Senior Statistical Ecologist solymos at 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 at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
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 <lengyel.at at gmail.com> 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 <solymos at ualberta.ca> ezt ?rta (id?pont: 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 < jonathangordon107 at 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 at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
-- P?ter S?lymos, PhD Senior Statistical Ecologist solymos at 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 at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
P?ter S?lymos, PhD Senior Statistical Ecologist solymos at 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]]