Dear list,
This is Elaine, a postgraduate studying bird distributions in East Asia.
I would like to ask how to generate NMDS graphs with the dot number
equal to the site number, using R vegan.
I read the vegan manual and copied the example code metaMDS.
(The code is as below)
However, the resul
Dear List,
This is Elaine, a postgraduate studying in bird distributions in East Asia.
I want to calculate Simpson dissimilarity index,
based on a presence/absence matrix of bird species in islands in East Asia.
(matrix row: 36 islands/matrix column: species ID)
(R package vegan to make NM
and how factors are handled.
>
> Anyway, here is the link to the blog post with working examples:
>
>
> http://www.fromthebottomoftheheap.net/2012/04/11/customising-vegans-ordination-plots/
>
> Anjoy,
>
> G
>
> On 18 August 2013 17:02, Elaine Kuo wrote:
> > Dea
Dear List,
This is Elaine.
I am using metaMDS in package vegan to plot NMDS.
However, I want to draw the points using different colors according to
island sites.
For example:
island site 1: island B, C, D => blue
island site 2: island A, E, F => green
island site 3: island G, H, J => red
www.**fromthebottomoftheheap.net/**2013/01/12/decluttering-**
> ordination-plots-in-vegan-**part-1-ordilabel/<http://www.fromthebottomoftheheap.net/2013/01/12/decluttering-ordination-plots-in-vegan-part-1-ordilabel/>
>
>
> Cheers,
>
> Eduard
>
>
>
> On 08/02/
Hello Kepfer,
An error showed up saying,
Error in plot(mds.object(mds), type = "t", display = c("sites")) :
could not find function "mds.object"
Please kindly help and thanks
ELaine
On Fri, Aug 2, 2013 at 3:07 PM, sebastian kepfer wrote:
> Dear Elaine
>
> Try plot(mds.object("your mds"), ty
Hello,
I am running NMDS using metaMDS, based on a matrix.
The matrix has rows as islands and columns as species ID.
I generated a plot of the result of metaMDS using type="t".
However, the island names are mostly covered by species ID and thus become
unclear.
Please kindly advise any method to
; allows you to define new similarity index, there is a warning about
> the resources used, it is not very efficient:
>
> http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/designdist.html
>
> I hope it helps a bit.
>
> Olmo.
>
> El Sun, 21 Jul 2013 07:46:42 +0800
> El
013, at 03:02 AM, Elaine Kuo wrote:
>
> > Hello
> >
> > I am trying to run MetaMDS but got the following error based on the code.
> > Please kindly indicate the error source and thank you.
> >
> > Elaine
> >
> > Code
> > # Compute the Simpson
Hello
I am trying to run MetaMDS but got the following error based on the code.
Please kindly indicate the error source and thank you.
Elaine
Code
# Compute the Simpson distance matrices for the dataset (3 hr using 4GB)
library(betapart)
dist.sim<-beta.pair(dataR, index.family="sor")
class
Hello
I am trying to perform NMDS using metaMDS (vegan).
However, in the argument of "distance," there is no option for Simpson
Dissimilarity Index.
Please kindly whether it is necessary to set up the distance argument
if the distance matrix is produced based on the Simpson Dissimilarity Index
al
wrote:
> Replied to on the R-sig-ecology list, with a request not to cross-post.
>
> Briefly, the output is a list with named components, so can be
> extracted as usual.
>
> Sarah
>
> On Wed, Jul 17, 2013 at 5:50 AM, Elaine Kuo
> wrote:
> > Dear List,
> >
>
Dear List,
This is Elaine.
I am using beta.part to calculate the beta diversity index.
The function of beta.part can generate three kinds of beta diversity indice
at one time.
However, it is Simpson index that I want.
The calculation result is composed of three rows and N/A columns (dist
class).
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