Displaying 20 results from an estimated 9000 matches similar to: "cca with repeated measures"
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 Mar 20
1
CCA - manual selection
Hello,
I am trying to obtain f-values for response (independent) variables from a
CCA performed in vegan package, to see which ones of them have
significative influence in my dependent variables (like the manual selection
in canoco), but I can't find any function (or package) that do such a thing.
The dependents variables are species data, and the independents are
ambiental data.
Than you.
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
2010 Apr 27
1
cca standard error species
Dear all,
I realised a correspondence analysis with function cca() of vegan library.
Just like in Okansen (2010) in the example of R help:
library(vegan)
data(varespec)
data(varechem)
vare.cca<-cca(varespec~ Al + P + K, varechem)
With plot.cca() function I represented the species matrix in the next way:
plot(vare.cca,display="species")
Being similar to:
plot((c(-2,2)),(c(-2,2)),
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,
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
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
2012 Nov 27
1
CCA plot
Hi, I have a couple questions about fitting environmental (land use
factors, plant species presence-absence, and soil variables) constraints to
my CCA biplot. 1. After successfully plotting species and site scores in my
CCA, I have been trying to insert the biplot arrows of the environmental
constraints in my data set using the text() function. When I do that, the
plot changes completely. Is there
2008 Sep 26
1
cca constraining variables table
I performed canonical correspondence analysis (cca) with the example data of
vegan, but I'm not able to obtain a table like scores() for the constraining
variables. I can see them in the summary() mode, but it would be great to
have in a separate table. Any suggestion?, thanx Gianandrea
require(vegan)
data(varespec)
data(varechem)
vare.cca<-cca(varespec,varechem)
scores(vare.cca)
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
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
2023 Dec 08
2
regarding CCA plot
Hii rstudio members
I am learning rstudio, For my manuscript I am trying to plot CCA using
species and environmental data. But I am getting error like
Error in cca.default(sptrans, envtrans) :
all row sums must be >0 in the community data matrix
*My code is like *
library(vegan)
library(ggplot2)
library(dplyr)
rassspec<-read.csv("C:/Users/hp/Desktop/R_data/rassspec.csv",
2011 Oct 11
1
Vegan: Anova.CCA accessing original data using option by="margin"
Hello,
I am attempting to use the ANOVA.CCA function with the by="margin" option.
The process works fine using the by="terms" option and I note in the Vegan
manual that Jari suggests that an error may occur if the anova does not have
access to the data on the original constraints.
This is the error that I get:
Error in dimnames(x) <- dn :
length of 'dimnames'
2009 Sep 07
2
How can I change characteristics of a cca biplot in R
Hi,
I?m doing cca for a community data set in R and I have made a biplot for my data. Otherwise everything seems to be allright but the biplot is so messy I can?t read it well enough or publish it. I would like to get the row numbers out of the plot: I want the species position and the environmental variables in it as vectors but not the station numbers. How do I get them out?
I have a raw
2014 Sep 13
1
vegan moved to GitHub and vegan 2.2-0 is coming (are you ready?)
Dear vegan team,
Vegan development happens now completely in github. R-Forge repository is no more in sync with github. I tried to commit all github changes to R-Forge, but a week ago I got a conflict in file and I haven't had time to resolve that conflict. You can follow vegan development and vegan discussion also without signing to github. The system seems to be completely open and does not
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
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
2010 Jul 17
1
cca in ade4
Dear List,
I used spec and envi for cca in ade4. (both are data.frame)
However, there is a message telling that
error in if (nf > rank) nf <- rank R
missing value in TRUE/FALSE
Please kindly help how to modify the code below.
Thank you.
Elaine
code
rm(list=ls())
spec <-read.csv("c:/migration/M_R_20100718_winterM_spec_vegan.csv",header=T,
row.names=1)
dim(spec)
spec[1,]
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 Aug 14
1
discerning species by color in cca biplot
Dear List,
I am running constrained correspondence analysis for abundance data of 7
birds.
However, I would like to check which bird prefers which environment gradient
by showing the species with different colors of the dots in cca plot
(package vegan).
Please kindly help and thank you
Elaine
[[alternative HTML version deleted]]