Displaying 20 results from an estimated 2000 matches similar to: "vegan moved to GitHub and vegan 2.2-0 is coming (are you ready?)"
2010 Jan 19
1
restricted permutations in permtest()?
Hallo List,
I'm trying to implemement a restricted permutation scheme in permutest(). More
precisely I have dependence in my data that should be allowed for in the
permutation - I simulated the problem in the example of the vegan documentation
p.24:
library(vegan)
data(varespec)
## Bray-Curtis distances between samples
dis <- vegdist(varespec)
## First 16 sites grazed, remaining 8 sites
2013 Mar 27
1
Conditional CCA and Monte Carlo - Help!
Hi All,
I am using canonical correspondence analysis to compare a community
composition matrix to a matrix of sample spatial relationships and
environmental variables. In order to parse out how much variance is
explained purely by space (S/E) or the environment (E/S) I am using a
conditional (partial) CCA. I want to test significance via Monte Carlo but
I can not find a way to do this with a
2009 Nov 03
1
why is adnonis function called adonis {package vegan}
Hello all,
I used google and looked at the documentation to find out why the
ADONIS function
is called adonis (in the vegan package).
I am writing a document and would like to include a
abbreviation list (similar to "ANOSIM = Analysis of Similarities").
regards,
Steve
2012 May 09
2
plot betadisper, change of pch
Hello!
After performing an analysis with betadisper, package vegan I would like
to plot the results - so far, so good. But I would also like to "tune" a
little bit the plotting characters, as '+' and 'x' are a little to
similar...
My (boiled down) code:
[See session info at the bottom of the mail, vegan is vegan_2.0-3]
mod <- betadisper(mydata, mygroups,
2013 Apr 17
1
failed to download vegan
Hello,
This is Elaine.
I am using R 3.0 to download package vegan but failed.
The warning message is
package ‘vegan’ successfully unpacked and MD5 sums checked
Warning: unable to move temporary installation
‘C:\Users\elaine\Documents\R\win-library\3.0\file16c82da53b1b\vegan’ to
‘C:\Users\elaine\Documents\R\win-library\3.0\vegan’
I cannot find the folder \file16c82da53b1b\ below
2011 Mar 09
2
Problem with vegan package instalation on linux
Hi,
I try to install vegan package on debian linux and I give this error:
=================================================
* installing *source* package 'vegan' ...
** libs
make: *** No rule to make target `cepin.o', needed by `vegan.so'. Stop.
*** arch - Rgnome
Warning in file(con, "r") :
cannot open file '/usr/lib/R/etc/Rgnome/Makeconf': No such file or
2013 Apr 24
1
RDA permutest envfit
Dear all,
I did a RDA and when I looked to the signification of the test with permutest, the output was non-significant. But when I used the envfit function, some of the vectors are significant. All the test's conditions are respected. What it means? Is it an error in the script?
Commands and output:
> permutest(rda.ind, perm=999, first=TRUE)
Permutation test for rda
Call:
2006 Nov 10
2
Problems with metaMDS from vegan
Hello all,
I recently used the Vegan library quite extensively (in the context of
text similarity assessment) on an Ubuntu 6.06 LTS system with R version
2.2.1 (2005-12-20 r36812). The Vegan lib is version 1.6-10.
I hit on a problem yesterday, though, when trying to install R and Vegan
on two further computers - one Windows XP and one further Ubuntu 6.06
machine, taking either R version 2.4.0
2011 Nov 24
1
Vegan: how to plot sites labes in diversity plot
Dear List,
I can'f figure how to add point labels in the next plot (example from
?taxondive help page, from vegan package):
library(vegan)
data(dune)
data(dune.taxon)
taxdis <- taxa2dist(dune.taxon, varstep=TRUE)
mod <- taxondive(dune, taxdis)
plot(mod)
The points in this plot are diversity values of single sites, and I'd
like to add a label to each one. The plot command don't
2010 Jul 17
2
cca in vegan (formula instead of community matrix data)
Dear List,
I tried to do cca based on species data and environmental variables (formula
instead of community data).
However, there was an error saying row sums must be >0.
I searched the previous related messages but found few solutions.
Please kindly help and thank you in advance.
code
This is vegan 1.17-3
Warning message:
package 'vegan' was built under R version 2.10.1
2012 Nov 09
1
CCA with Vegan - Plot problem
Hi,
I've just started using R and am having some problems with CCA using vegan.
I'm looking at abundance p/m2 (hence decimals) vs environmental variables
and have been using
http://ecology.msu.montana.edu/labdsv/R/labs/lab12/lab12.html to guide me
through.
My organism data looks like this:
Sample "Species_1" "Species_2" "Species_3" etc
Sample_1
2010 Feb 02
2
hvcluster() with distance method from vegdist(), package = vegan
hello,
i'd be happy if someone could provide help with the following problem:
i have a dist.matrix that comes from vegdist() function of the vegan
package. the used method = "horn" is not accepted as argument in
hvcluster(...,dist.method="...").
is there a way to incorporate the method "horn" in hvcluster()?
thanks in advance!
yours,
kay
--
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2011 Jul 09
1
PERMANOVA+ and adonis in vegan package
Hi,
I was wondering if someone can tell me what is the difference between
"strata" argument (function "adonis" in "vegan" package) and
using random effects in PERMANOVA+ add-on package to PRIMER6 when doing
permutational MANOVA-s? Is the way permutations are done the same?
Thank you very much in advance,
Vesna
--
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2009 Sep 04
1
NA in cca (vegan)
Dear all,
I would like to calculate a cca (package vegan) with species and environmental data. One of these environmental variables is cos(EXPOSURE).
The problem: for flat releves there is no exposure. The value is missing and I can't call it 0 as 0 stands for east and west.
The cca does not run with missing values. What can I do to make vegan cca ignoring these missing values?
Thanks a lot,
2010 Sep 21
1
partial dbRDA or CCA with two distance objects in Vegan.
I am trying to use the cca/rda/capscale functions in vegan to analyse
genetic distance data ( provided as a dist object calculated using
dist.genpop in package adegenet) with geographic distance partialled out
( provided as a distance object using dist function in veganthis method
is attempting to follow the method used by Geffen et al 2004 as
suggested by Legendre and . FORTIN (2010).
I
2013 Sep 06
1
Fwd: calculating dissimilarity index of islands (vegan and betapart)
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 NMDS and R package betapart)
In most papers using vegan for NMDS and betapart for dissimilarity
2012 May 10
1
envfit output (vegan package) - not sure what it means
I'm pretty new to R and would appreciate some help interpreting the output of
a function that was recommended to me.
I've used the *envfit *function in the vegan package to plot vectors of four
climate variables onto a species matrix ordination. The output indicates
that only a single variable (mean_temp) is significant:
***VECTORS
NMDS1 NMDS2 r2
2004 Jul 19
1
Dendrogram plotting options?
Hi, I was wondering if there is more flexibility in the output of
dendrograms when plotting a hclust object. I can't seem to find
information on how to change the default output of a "hanging" style
tree with the axis on the right to a left-to-right plot with and axis
on the bottom. Example code follows:
library(vegan) #loads the "vegan" module that compuptes ANOSIM
2008 Apr 14
1
Vegan R^2 and tau values for metaMDS
I am using the function metaMDS with jaccard distances to ordinate a
set of constituent by site matrix. I can post this data if it would
be helpful, but it is large to include in an email. I can also
provide reproducable code if necessary. I would like to get an R^2
value for the axes of the ordination configuration that I get with
metaMDS in the vegan package is there a way to do this- is it
2013 May 06
2
BIOENV
Dear all,
Does anyone knows why the results of a BIOENV (PRIMER v. 6.1.15) are
diferent of the bioenv() + mantel() in vegan? Not the spearman correlation,
indeed the pseudo-p value.
I know that the approach bioenv() + mantel() is biased. So, how the BIOENV
(PRIMER) ends with larger p values (permutated).
Acctualy how the permutation test in BIOENV (PRIMER) is conducted. The user
guide does not