search for: vegan

Displaying 20 results from an estimated 365 matches for "vegan".

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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 disc...
2002 Jan 17
2
Problem building packages from source (WIN32)
...some packages from CRAN. I downloaded the tar files from CRAN and unpacked them into R-HOME\rw1040\src\gnuwin32. I then ran Rcmd INSTALL on the directory containing the package. This is where I started to have problems: The following is the output from Rcmd INSTALL when trying to install package vegan: C:\R\rw1040\src\gnuwin32>Rcmd INSTALL C:\R\rw1040\src\gnuwin32\vegan make: Entering directory `/cygdrive/c/R/rw1040/src/gnuwin32' make DLLNM= \ -C C:/R/rw1040/src/gnuwin32/vegan PKG=vegan RHOME=C:/R/rw1040 RLIB=C:/R/rw1040 /library \ -f C:/R/rw1040/src/gnuwin32/MakePkg make[1]: Enteri...
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") : cann...
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 \file16...
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...
2013 Apr 11
1
Cannot find ldfortran (R on Cygwin)
...fortran. *Under Cygwin, how do I check and configure the path to the various libraries?* I am trying below command and it says, cannot find "lgfortran" But I have installed gfortran from "All" and "Libs" during setup I access R as below 1) R 2) install.pacakges('vegan') 3) After choosing mirror, here is the output I get * installing *source* package ‘vegan’ ... ** package ‘vegan’ successfully unpacked and MD5 sums checked ** libs gfortran -g -O2 -pipe -c cepin.f -o cepin.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c data2hill....
2010 Jun 30
3
Factor Loadings in Vegan's PCA
Hi all, I am using the vegan package to run a prcincipal components analysis on forest structural variables (tree density, basal area, average height, regeneration density) in R. However, I could not find out how to extract factor loadings (correlations of each variable with each pca axis), as is straightforwar in princom...
2013 Mar 27
1
Conditional CCA and Monte Carlo - Help!
...nships 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 if I use ade4 I can do a Monte Carlo - but I can't figure out how to do a conditional CCA with ade4 OR a Monte Carlo with vega...
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 accept a "la...
2010 Jul 17
2
cca in vegan (formula instead of community matrix data)
...ar 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 rm(list=ls()) library(vegan) datam <-read.csv("c:/migration/M_R_20100707_winterM.csv",header=T, row.names=1) dim(datam) datam[1,] m.cca <- cca(datam$WinterM_ratio~datam$topo_mean+datam$coast+datam$...
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 -- View this message in context: http://n4.nabble.com/hvcluster-with-di...
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 -- View this message in context: http://r.789695.n4.nabble.com/PERMANOVA-and-adonis-in-vegan-package...
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"...
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 ig...
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 make it clear. Best Wis...
2009 Nov 15
1
Problem building package for R 2.10.0 on Mac OS X
Hi I have submitted a package (rioja) to CRAN. It checks OK for all R versions and OS's except r-release-macosx-ix86 where it fails when checking the examples. Specifically, it fails because R can't find the package vegan which is needed in a function. Here is the snippet from the check results: ### Begin snippet checking examples ... ERROR Running examples in 'rioja-Ex.R' failed. The error most likely occurred in: > ### * chclust > > flush(stderr()); flush(stdout()) > > ### Name: chclust &...
2001 Nov 13
0
VEGAN: R functions for vegetation ecologists
A colleague has just passed me this interesting address: http://cc.oulu.fi/~jarioksa/softhelp/vegan.html "Vegan: R functions for vegetation ecologists" "Vegan package is intended to help vegetation ecologists and other community ecologists to use R. It is not a completely self-contained package, but it complements other R functions. .../... At this first stage, vegan implements...
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 Pr(>r) precip 0.41539 -0.90964...
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: plo...
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 index, the dissimilarity index is generated by grid data in continents. The calculation of this index is done by comparing species presence/absence between a pair of grids adjacent to each o...