similar to: vegan rda na adaptation

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

I am not familiar with the vegan package, so I am just making a guess here. If 'na.action=na.omit' is part of the call to varpart, try removing it from the function call and moving it above as follows: options(na.action="na.omit") RDA_Ger <- varpart(comm, x1, x2, x3, transfo="hellinger", scale = FALSE) Maybe that will help. Regards, Eric On Sat, Sep 16, 2017 at

I'm trying to perform a RDA analysis in the vegan package using the "varpart" function. I have a matrix of community structure data in different sites (rows), which I want to explain using 3 matrices of environmental data. The 3 matrices are: water quality parameters; local land use variables; total land use variables. In each matrix, the number of the rows is the same (the

This is not a request for coding help so there is no reproducible code, rather I am trying to figure out if anyone had had a similar experience. My question is related to partitioning the variance in rda (vegan) results for multiple groups of variables. I have a high dimensional dataset with 79 explanatory variables and 9 response variables. Within those 79 explanatory variables there are ~8

Dear r-helpers, I just read in an article by Virtanen et al. (2006) where vegetation-environment relationships are studied by fitting smoothed surfaces on an NMDS ordination using GAMs (Wood 2000). The authors describe, that they used R? as goodness-of-fit statistic, which they compare to the R? of fitted vectors. Calculations were carried out using the package vegan (Oksanen). I know that I can

The varpart function does not have na.action argument, and all undefined arguments are regarded as explanatory data sets X (they come after ?). Best wishes, Jari Oksnaen

Hi All, I am trying to perform CCA and RDA several times to compare their performances. To do that I put this two functions of vegan package inside a for loop. Unfortunatly when I am trying to perform the anova(by=axis) to test the individual axes the function don't recognize the species data.frame. The same problem occurs whem I try to run forward selection. The same problem occur when I try

I've tried a few things both with prcomp(), and rda() and its friends in vegan (including biplot.rda and ordiplot), but can't find a solution. I'd like to associate subsets of the points in a resulting biplot ("sites" in the rda object) with different plotting colors/text styles to emphasize certain sets of points. I can't figure out how to keep the arrows (for

Helo you, I try to build a mail server based on Centos 7, postfix and dovecot 2. My backend is a Samba4 ad-dc. I tried a lot and I don't know what else I could try.I'm new to this mailing list so please forgive me if I don't give right information or anything Samba4 ad-dc is up incl. dns. Win10 Client joined domain and authentication works. Postfix is up and checks against ldap

Hi Im using the VEGAN package to do an RDA ordination. In my plot I get my environmental scores as arrows/vectors, but my species scores as points. I would like to get the species scores as arrows as well. I tried the envfit function, and this creates arrows, but the lenght is not proportionate to the strengh of the correlation and the point is still there (so I both have point and arrow). fit

Hello, I am interested in using the capscale function of vegan package of R. I already have a dissimilarity matrix and I am intended to use it as 'distance' argument. But then, I don't know what kind of data must be in 'comm' argument. I don't understand what type of data must be referred as 'species scores' and 'community data frame' since my data refer to

Hi Guys, First, English is not my native language so sorry if the question is too difficult to understand. I can rephrase it if necessary. I have 32-bit Windows Xp SP3, i use R version 2.12.0 (2010-10-15), and the question is about Redundancy canonical analysis? plot problem in 3D using VEGAN, RGL, SCATTERPLOT3D and SFSMISC. I noticed the following? code to explain as clearly as possible the

Dear all, I'm performing RDA on plant presence/absence data, constrained by geographical locations. I'd like to constrain the RDA by the "extended matrix of geographical coordinates" -ie the matrix of geographical coordinates completed by adding all terms of a cubic trend surface regression- . This is the command I use (package vegan): >rda(Helling ~

Hi, I hope someone knows the answer to this or has a real good reference about it (I am using Legendre & Legendre, Numerical Ecology, 1998).... My data is a data.frame with locations as rows and vegetation assemblages / species as columns. I've done a PCA, a correspondance analysis (CA) using ca in ca package and a detrended correspondance analysis (DCA) using decorana from vegan package.

Dear r-helpers! I want to classify my vegetation data with hierachical cluster analysis. My Dataset consist of Abundance-Values (Braun-Blanquet ordinal scale; ranked) for each plant species and relev?. I found a lot of r-packages dealing with cluster analysis, but none of them is able to calculate a distance measure for ranked data. Podani recommends the use of Goodman and Kruskals' Gamma for

Dear R-helpers, Apologies in advance for this (probably) simple question. I've searched the R Archive and can't seem to find a solution to my problem. I have a data frame of vegetation quadrat data with the following format: Q S C 1 A 5 1 B 10 1 C 50 1 D 10 2 A 20 2 E 10 2 C 40 3 D 5 3 F 1 3 G 5 3 B 75 Where Q is the sample (vegetation quadrats), S is the species and C is the

I am getting the following erro rmessage in ordistep. I have a number of similarly structured datasets using ordistep in a loop, and the message only occurs for some of the datasets. I cannot include a reproducible sample - the specific datasets where this is occur ing are fairly large and there are several pcnm's in the rhs of the formula. thanks for any pointers that may allow me to

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

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

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