Mia Bengtsson gmail.com> writes:
>
> Dear R and vegan package users,
>
> I have been experiencing problems with the metaMDS function when working
on a dataset (euk) consisting of 9
> "sites" (RNA extracts of 9 biofilms samples) and 340 "species" (microbial
taxa based on rRNA sequences).
> The p
Dear R and vegan package users,
I have been experiencing problems with the metaMDS function when working on a
dataset (euk) consisting of 9 "sites" (RNA extracts of 9 biofilms samples) and
340 "species" (microbial taxa based on rRNA sequences). The problem is that I
get nMDS ordinations with ov
H
ello R-experts,
I want to do ordination plots using vegan metaMDS.
I have a where many cells have zero values.
Data structure:
X[1:10,1:14]
Height.1 Height.2 Height.3 Height.4 Height.5 Height.6 Height.7
Height.8 Height.9 Height.10 Height.11 Height.12 Height.13
D30I1A 460
Raeanne Miller sams.ac.uk> writes:
>
> Greetings everyone,
>
> I am running MDS on a very large dataset (12 x 25071 - 12 model runs with
25071 output values each), and also on a
> very much reduced version of the dataset (randomly select 1000 of the
25071 output values). I would like to
> look
Greetings everyone,
I am running MDS on a very large dataset (12 x 25071 - 12 model runs with 25071
output values each), and also on a very much reduced version of the dataset
(randomly select 1000 of the 25071 output values). I would like to look at
similarities/dissimilarities between the 12
On Fri, 2011-09-23 at 12:43 -0500, Jean V Adams wrote:
> Lineth Contreras wrote on 09/23/2011 11:35:10 AM:
> >
> > Hello R-user community,
> >
> > I am applying the function metaMDS. However, I would like to know if
> there
> > is any option to export the data I got from the axis as a data frame
Lineth Contreras wrote on 09/23/2011 11:35:10 AM:
>
> Hello R-user community,
>
> I am applying the function metaMDS. However, I would like to know if
there
> is any option to export the data I got from the axis as a data frame.
>
> I have tried as.data.frame.list but is not working. Any sugge
Hello R-user community,
I am applying the function metaMDS. However, I would like to know if there
is any option to export the data I got from the axis as a data frame.
I have tried as.data.frame.list but is not working. Any suggestion?
Thank you in advance for your help,
Lineth
[[alt
Hi Katie,
This is probably a bit late given the date of your post, but I was having
similar problems with my own work and thought I'd respond anyway. I'm not
sure that the script you've written here will fit 3D vectors for your 3D
nmds. I tried it and it doesn't seem to work for me - it only gives
On Wed, 2011-05-11 at 07:07 -0400, Michael Denslow wrote:
> Hi Katie,
>
> On Tue, May 10, 2011 at 4:51 PM, Songer, Katherine B - DNR
> wrote:
> > Hello R experts,
> >
> > I've used metaMDS to run NMDS on some fish abundance data, and am also
> > working on correlating environmental data to the N
Thank you Michael; this was helpful!
Katie
-Original Message-
From: Michael Denslow [mailto:michael.dens...@gmail.com]
Sent: Wednesday, May 11, 2011 06:07 AM
To: Songer, Katherine B - DNR
Cc: r-help@r-project.org
Subject: Re: [R] metaMDS and envfit: Help reading output
Hi Katie,
On
Chamberlain [mailto:scttchamberla...@gmail.com]
Sent: Tuesday, May 10, 2011 05:56 PM
To: Songer, Katherine B - DNR
Cc: r-help@r-project.org
Subject: Re: [R] metaMDS and envfit: Help reading output
Here is a thread I found on this
issue:http://www.mail-archive.com/r-sig-ecology@r-project.org/msg00755.html
Hi Katie,
On Tue, May 10, 2011 at 4:51 PM, Songer, Katherine B - DNR
wrote:
> Hello R experts,
>
> I've used metaMDS to run NMDS on some fish abundance data, and am also
> working on correlating environmental data to the NMDS coordinates. I'm fairly
> new to metaMDS and NMDS in general, so I ha
Here is a thread I found on this
issue:http://www.mail-archive.com/r-sig-ecology@r-project.org/msg00755.html
It's not a simple correlation apparently, but I can't figure out how they get
the output from envfit using lm(Y ~ scores1 + scores2).
You can plot the data like:
library(MASS); require(
Hello R experts,
I've used metaMDS to run NMDS on some fish abundance data, and am also working
on correlating environmental data to the NMDS coordinates. I'm fairly new to
metaMDS and NMDS in general, so I have what are probably some very basic
questions. My fish abundance data consists of 66
Kim Vanselow gmx.de> writes:
>
> Dear r-helpers!
> How can I integrate other distances (in the form of a dist object) into
function metaMDS? The problem:
> metaMDS needs the original data.frame for the calculation and only the default
distances of function
> vegdist are allowed.
> Any suggestion
On Wed, 2009-10-14 at 16:57 +0200, Kim Vanselow wrote:
> Dear r-helpers!
> How can I integrate other distances (in the form of a dist object)
> into function metaMDS? The problem: metaMDS needs the original
> data.frame for the calculation and only the default distances of
> function vegdist are al
Dear r-helpers!
How can I integrate other distances (in the form of a dist object) into
function metaMDS? The problem: metaMDS needs the original data.frame for the
calculation and only the default distances of function vegdist are allowed.
Any suggestions are greatly appreciated!
Thank you,
Kim
Sorry for not translating, misspackaging (MASS) and not reading
properly (zerodist).
I would like to implement the weighting in distance()
foo <- function(x, method, ...)
as.dist(distance(x = x, method = method,
weights=vectorname))
This seems to work but it would b
On Thu, 2008-05-15 at 13:13 +0200, Birgit Lemcke wrote:
> Hello R-user community!
>
> I am running R 2.7.0 on a Power Book (Tiger). (I am still R and
> statistics beginner)
>
> Presently I try to run the function metaMDS (vegan) using an existing
> dissimilarity-matrix.
The help for metaMDS
Hello R-user community!
I am running R 2.7.0 on a Power Book (Tiger). (I am still R and
statistics beginner)
Presently I try to run the function metaMDS (vegan) using an existing
dissimilarity-matrix.
As I would like to start with this matrix I thought I could just give
the matrix using
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