similar to: Mirror Image on Biplot Graphic

Hi everybody, I'm trying, without success, to avoid some variables labels to overlap on a capscale (vegan package) object graph. I was able to move the labels with the coding below, but it moves the entire vector... CAPobj<-CAPpotiFT for(i in c(2:8))CAPobj$CCA[[i]][,1]<-CAPpotiFTI$CCA[[i]][,1] CAPpotiFTI$CCA[[i]][,1][2]<-0.85 And here the graphic script

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

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

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]]

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

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)

Dear List, I would like to obtain biplot containing arrows and variable labels. However, after checking the previous message and package CCA and function anacor, my attempt remains an open question. Please kindly advise code or package I might miss to achieve it. Thank you. Elaine [[alternative HTML version deleted]]

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.xlsx", sheetName="env", header = T,

Hi, I'm a beginner with R, but I'm getting excellent results with it. Well I've got an capscale object (vegan package) and I want to made a biplot with symbols representing six groups of areas. With the plot.cca function and some par attributes (like 'labels') I was able to substitute the samples names for keyboard symbols ('x','o','#',ect), but it's

Hi all, thank you for your answers; i've tried both cca from vegan library, and dudi.coa from ade4 library; one last question: my deal is mainly with contingency tables, like the one i'm posting here acciaieria<-c(.41,.02,.44,.04,.09) laminatoio<-c(.34,.28,.26,.01,.11) fonderia<-c(.48,.05,.34,.08,.05) leghe<-c(.45,.19,.25,.03,.08)

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

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

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

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

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)),

Hello Tom, I tried the new UPnP support of shorewall, olny to stumble 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:

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 I'll attach the necessary files. (there's only two) the files will be my CCA R

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,

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",

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) spec[1,] envi