Displaying 20 results from an estimated 900 matches similar to: "ordination in vegan: what does downweight() do?"
2011 Mar 28
1
ordination in vegan
Hi all,
I have site data with plant species cover and am looking for trends. I'm
kind of new to this, but have done lots of reading and can't find an answer.
I tried decorana (I know it's been replaced by ca.) and see a trend, but I'm
not sure what it means. Is there a way to get the loadings/eigenvectors of
the axes (like in PCA)? Is there a way to do this with rda() too? How
2013 Apr 05
2
transforming data prior to CCA
Hi everyone,
I?m a student and relatively new to R so apologies in advance if this
question seems stupid or obvious to you.
I have collected a dataset with about 60 species of diatoms (count data from
19 different sample sites) and environmental variables for each site
(salinity, pH, etc.). It?s all in the same dataset but distinct in R through
the functions below
diat <- diatom [, 1:60]
2010 Nov 17
1
Total inertia in package Vegan?
Dear all at the R-project help list.
I have run into a problem when it comes to getting values for "total inertia" and "R-squared" for my DCA using "decorana" in the package "vegan". I have tried the "goodness" function, but the reply indicates that it does not work with "decorana" class objects. In Canoco one gets the Total inertia in
2004 Mar 29
1
calculate length of gradient ?
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Dear r-help list,
my question is about ordination technics:
2011 Dec 20
2
any DCCA function in R?
Dear members,
I am performing multivariate analysis on marine benthic populations
using R. At first glance I found ca and VEGANO packages to be the
suitable for the task, but neither has incorporated Detrended Canonical
Correspondence Analysis (DCCA), which is just the method I want to apply
on my data. I've looked for alternative packages containing the method,
but my suspicion is that
2011 Mar 10
1
vegan CCA I am Completely new to ordination analyses
Dear list,
I am trying to predict species volume from bioclimatic data, I have various
sites and I have a data frame with species volume and
the corresponding bioclimatic data for each site.
I read on a discussion forum that you can use ordination to predict species
abundance (in my case volume) from 'new' climate data for sites where you do
not know the abundance.
Unfortunately I
2008 Apr 22
0
Downweighting of cases in GLM
Dear all,
I want to model presence/absence data of tree occurrence using a number of
predictor variables.
Absences of some sample points are probably wrongly specified (they should
be presences) due to land use which can not be incorporated as a predictor
because of some sort of arbitrariness. Some trees were logged while others
were not but to both cases land use as a category would apply.
2001 Feb 16
12
canonical correspondence analysis
Is there an R function that does canonical correspondence analysis. Can
it be done using the VR function corresp()?
If not, how hard it be to write R code to do it? I am a population
biologist with long but patchy programming experience in C, Smalltalk,
Java and other languages.
Thanks,
Patrick Foley
patfoley at csus.edu
2009 Sep 09
2
"predict"-fuction for metaMDS (vegan)
Dear r-Community,
Step1: I would like to calculate a NMDS (package vegan, function metaMDS) with species data.
Step2: Then I want to plot environmental variables over it, using function envfit.
The Problem: One of these environmental variables is cos(EXPOSURE). But 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. Therefore I
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,
2002 Dec 16
1
unknown decorana error returned (vegan package)
Hi
After trying a simple decorana analysis (from the vegan package) on a simple
data frame which contains no NA's the following error was returned:
> tt_decorana(covN)
Error in decorana(covN) : NA/NaN/Inf in foreign function call (arg 1)
Have any vegan users come across this error and know what can be done about it?
Cheers,
J
2010 Aug 14
1
cca biplot (vegan) failed in matplot
Dear List,
I am trying to plot the result of cca using matplot but failed.
Pls kindly help and thanks.
Elaine
The error message was
error in xy.coords(x, y, xlabel, ylabel, log = log) :
(list) object cannot be coerced to type 'double'
code
rm(list=ls())
library(vegan)
library(MASS)
# input richness
birdrich
2005 Jan 04
2
(no subject)
Hi
I'd like to know if the R can do the DCCA? Because I can't find the package about
the DCCA in R. If it can not, please introduce a free software to me, which you
think can easily do the work , thanks!
jeff
2009 Feb 08
0
library vegan - cca - versus CANOCO
Hi R users,
I have two data matrix, one with community data and another with
environmental data. Prior to preform the CCA, I have used PCA to select some
environmental variables and to avoid redundance information. The result is
that I have 4 environmental variables and my community data matrix where,
following bibliography, I have eliminated rare species.
All variables were log-transformed (x+1)
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
2011 Mar 07
1
species projected in a ordiplot
Dear all,
I'm performing a detrended correspondence analysis on vascular plant
community data (296 species), and I have a question on the species scores
projected in the ordination diagram. When I run a ordiplot all species are
projected in the output graph, but I'd like to restrict the number of
species plotted in the final graph. Some species are so rare in the data,
that no relevant
2007 Jul 23
1
cca and cca.predict in vegan-what sort of prediction is possible
Hi All
I am not clear quite how one could use cca from package vegan and the associated
predict.cca to predict species abundance from environmental data (or if this is possible
in a generalised way). In other words, can one derive a cca object based on known
community data and use that to predict e.g. species abundances in a different number
of samples based on environmental data? The help
2007 Apr 27
1
partitioning variation using the Vegan CCA routine?
Hello
I am using Jari Oksanen's CCA routine from the Vegan package on some estuary
data, following a technique applied in (Anderson, M.J. & Gribble, N.A.,
1998, Partitioning the variation among spatial, temporal and environmental
components in a multivariate data set, Australian Journal of Ecology 23,
158-167).
Some steps in the process require that the dependent matrix be constrained
by
2008 Jul 01
2
"Invalid object" error in boxplot
Hi,
I'm trying to make a boxplot with the data at the end of the message, and when I
try to execute the command
>boxplot(Diatoms) (or for any other field instead of "Diatoms")
I get the following error message:
Error in oldClass(stats) <- cl : adding class "factor" to an invalid object
Any advice would be much appreciated.
Thanks a lot,
Miriam
Date
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