NMDS using Vegan

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

NMDS using Vegan

Suparna Mitra-2
Hello R experts,
  I am new to Vegan and use trying to follow the tutorial to perform NMDS
for my data. But after performing the metaMDS, when I plotted my results
the default plot shows MDS1 vs MDS2. Thought according to the
tutorial Default ordination plot should display NMDS1vs NMDS2. Why is this
difference? Accourding to tutorial it says: Function metaMDS
is a wrapper to perform NMDS.
Can anybody please help me to understand this?
Thanks,
Mitra

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: NMDS using Vegan

Gavin Simpson
On Wed, 2013-05-15 at 12:06 +0800, Suparna Mitra wrote:

> Hello R experts,
>   I am new to Vegan and use trying to follow the tutorial to perform NMDS
> for my data. But after performing the metaMDS, when I plotted my results
> the default plot shows MDS1 vs MDS2. Thought according to the
> tutorial Default ordination plot should display NMDS1vs NMDS2. Why is this
> difference? Accourding to tutorial it says: Function metaMDS
> is a wrapper to perform NMDS.
> Can anybody please help me to understand this?
> Thanks,
> Mitra

They are just labels and metaMDS **has** performed an NMDS. Not sure why
Jari labelled these as "MDSx". If this bothers you so, add your own
labels:

require("vegan")
data(dune)
sol <- metaMDS(dune)
plot(sol, xlab = "NMDS1", ylab = "NMDS2")

HTH

G

--
Gavin Simpson, PhD                          [t] +1 306 337 8863
Adjunct Professor, Department of Biology    [f] +1 306 337 2410
Institute of Environmental Change & Society [e] [hidden email]
523 Research and Innovation Centre          [tw] @ucfagls
University of Regina
Regina, SK S4S 0A2, Canada

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: NMDS using Vegan

Suparna Mitra-2
In reply to this post by Suparna Mitra-2
Dear Prof. Simpson,
Thanks a lot for your reply. Yes I know that I can change the labels
any time, but I was only worried if I am doing any mistake as default
output didn't match with the output shown in the Vegan tutorial
output.
Thanks,
Mitra


On 15 May 2013 22:43, Gavin Simpson <[hidden email]> wrote:

> On Wed, 2013-05-15 at 12:06 +0800, Suparna Mitra wrote:
>> Hello R experts,
>>   I am new to Vegan and use trying to follow the tutorial to perform NMDS
>> for my data. But after performing the metaMDS, when I plotted my results
>> the default plot shows MDS1 vs MDS2. Thought according to the
>> tutorial Default ordination plot should display NMDS1vs NMDS2. Why is this
>> difference? Accourding to tutorial it says: Function metaMDS
>> is a wrapper to perform NMDS.
>> Can anybody please help me to understand this?
>> Thanks,
>> Mitra
>
> They are just labels and metaMDS **has** performed an NMDS. Not sure why
> Jari labelled these as "MDSx". If this bothers you so, add your own
> labels:
>
> require("vegan")
> data(dune)
> sol <- metaMDS(dune)
> plot(sol, xlab = "NMDS1", ylab = "NMDS2")
>
> HTH
>
> G
>
> --
> Gavin Simpson, PhD                          [t] +1 306 337 8863
> Adjunct Professor, Department of Biology    [f] +1 306 337 2410
> Institute of Environmental Change & Society [e] [hidden email]
> 523 Research and Innovation Centre          [tw] @ucfagls
> University of Regina
> Regina, SK S4S 0A2, Canada
>
>
>

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.