search for: cca

Displaying 20 results from an estimated 159 matches for "cca".

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2013 Mar 27
1
Conditional CCA and Monte Carlo - Help!
...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 conditional CCA. I have been using vegan for the CCA and attempting to use ade4 to run a Monte Carlo. However, these two packages conflict when it comes to CCA. If I use vegan I can run a conditional CCA, and...
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 o...
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 messag...
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 some code or a sample script you could let me kno...
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<...
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 <-read.csv(&q...
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 simi...
2010 Aug 18
2
How to Perform CCA in ??!! Help please
Performing CCA in R I know they say don't say please... or plead...but I'm sorry but I really need some help with this problem. I have tried to perform CCA in R and I can never do this successfully. Can someone please tell me what I'm doing wrong. I can't attach any file...so Please email me and...
2005 May 07
2
The new Linux IGD support
...tumble upon a LinuxIGD bug. Specificaly, the UPnP chain is read as UPn from the upnpd.conf . I double checked it, there some bug in the upnpd, it doesn''t process 4 lettered names correctly. Could you change this chains'' name to something a little longer? -- Costas Cavouracis <cca@freemail.gr> My PGP keys: https://defiant.cca.dynalias.com/~cca/cca@cca.dynalias.com.pgp.key https://defiant.cca.dynalias.com/~cca/cca@freemail.gr.pgp.key
2010 Jul 17
1
data.frame required for cca in ade4
Dear List, I tried to conduct cca using csv data but failed. The message said that data.frame is required. Please kindly share how to convert a csv-imported file to a data.frame. 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)...
2008 Oct 03
2
Mirror Image on Biplot Graphic
He everybody, Well I have a biplot CCA-like origined from plot.cca (vegan package). I need to rotate on y axis the lines and symbols of constrained and sites representation. If I do that on an image editor, I rotate everything, including titles, axes labels and positions. I just need to rotate the inner par and keep the variables names...
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 ma...
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....
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...
2009 Sep 09
2
"predict"-fuction for metaMDS (vegan)
...ing environmental variables. Both, metaMDS and envfit then work without problems. Now I want to bring the releves with missing environmetal variables back to my ordination-plot. Gavin Simpson gave me the advice to use the predict-function for the same missing value problem when I was calculating a cca. This worked without problem. As my species data was recorded in Braun-Blanquet-numbers (ordinal scale) I would prefer to calculate a NMDS. Does anybody know a similar function to the predict function which works with NMDS or does anybody know how to modify the predict function so that it will wor...
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" "Spe...
2009 Nov 23
1
Doubt about CCA and PCA
Dear R community, I'm working with PCA and CCA methods, and I have a theoretical question. Why is it necesary to have more temporal values than variables when the CCA O PCA are going to be used? Could you advise to me some any paper about it? Thanks in advance, [[alternative HTML version deleted]]
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_...
2017 Jul 18
3
Redundancy canonical analysis plot problem in 3D using VEGAN, RGL, SCATTERPLOT3D and SFSMISC
Hello Sir I am getting problem in plotting in CCA . Could you please help me? I wrote the below command but I don't know why it is taking only first 5 env data rather than all 9. > strain.data <- read.xlsx("Dee rhiz.xlsx", sheetName="strain", header = T, row.names = 1) > env.data <- read.xlsx("Dee rhiz.xls...
2004 Jan 14
1
cca in vegan
Hello all, I'm hoping this is a simple problem. I'm trying to do cca of my data. I have my plant data and environmental data as 2 separate files. I have 3 years of data, stacked vertically, within these files. I want to conduct the cca for each year and am trying to create separate year files using the following: cnts94 <- cnts[1:27,] env94 <- env[1:27,]...