similar to: An ANOVA test that uses a distance matrix like hierarchical cluster analysis?

Dear All, I'm using betadisper {vegan} and I'm interested not only in the dispersion within the group but also the distances between the groups. With betadisper I get distances to group centroids but is it possible to get distances to other groups centroids? It might be possible to do it by hand by the formula given in the description of the betadisper (below) but I'm a bit confused

Hi, forgive me if someone has already posted about this but I have had a look and cannot find the answer, also I am very new to R and been getting the grips with this. I have been trying to use Adonis to find out if there are significant difference between groups on data that I have analyses with NMDS, and have been struggling with getting this to work and understanding what is going on. I am

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, Using Vegan package I was wondering if there's a way to use a distance matrix as an input for adonis (or any of the other similar hypothesis testing functions) instead of the usual species by sample table. Working in the field of microbial ecology, what I'm trying to do is to overcome the problem of having to use discrete units such as species or OTUs, which are problematic in

Hello! After performing an analysis with betadisper, package vegan I would like to plot the results - so far, so good. But I would also like to "tune" a little bit the plotting characters, as '+' and 'x' are a little to similar... My (boiled down) code: [See session info at the bottom of the mail, vegan is vegan_2.0-3] mod <- betadisper(mydata, mygroups,

I am trying to apply a permuation-based MANOVA (Anderson 2001) to a set of morphological data from three ecomorphs of fish reared under two different conditions and measured at two points during ontogeny. I will supply a distance matrix based on Procrustes distances calculated outside of vegan. I have not found an example of a design such as this for adonis. However, I have designed my factors

Hello all, I used google and looked at the documentation to find out why the ADONIS function is called adonis (in the vegan package). I am writing a document and would like to include a abbreviation list (similar to "ANOSIM = Analysis of Similarities"). regards, Steve

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:

Hi, Somebody knows how to make contrasts if i'm using the function adonis? Thanks.

Hi, I'm trying to use adonis on a subset of data from a dataframe. The actual data is in columns 5:118, and the first four columns are various factors. There are 3 levels of the factor Habitat, and I want to examine differences among only two of them. So I started with: > CoastNear = subset(gel_data, Habitat != "I") The resulting data.frame has three levels for Habitat, but

I am trying to apply this technique (M.J Anderson 2001) to a dataset of aquatic insect abundances. There is a sample in the unrestored and restored segement of a stream for every time period. I would like to compare the centroids of the distance matrices for the treatments up (unrestored) and dn (restored) to see if there is a difference in insect communities between the treatments. I will not

Dear all, I am trying to get a PERMANOVA with quite large data set. I am reading a lot about this question, but I do not get the answer about it. Although I know that the R function is adonis () (vegan package), it does not work: adonis(Pha.env~SPha, data=Pha, permutations=10) The error message: Error: cannot allocate vector of size 334.2 Mb In addition: Warning messages: 1: In vegdist(lhs,

Hi! Thanks for providing great help in R-related statistics. Now, however I'm stuck. I'm not a statistics person but I was recommended to use R to perform a nmds plot and PerMANOVA of my dataset. Sample(treatment) in the columns and species (OTU) in the rows. I have 4 treatments (Ambient Temperature, Ambient temperature+Low pH, High temperature, High temperature+low pH), and I have 16

hello list, i'd appreciate help regarding formula expression in adonis(), package vegan. i'm interested in the effect of an impact on species composition and if this effect is the same for different sites. i have an impact survey with plot pairs, one plot with impact the other with similar ecolgical conditions but without impact, which is the control (factor1: impact). two different

Hallo List, I'm trying to implemement a restricted permutation scheme in permutest(). More precisely I have dependence in my data that should be allowed for in the permutation - I simulated the problem in the example of the vegan documentation p.24: library(vegan) data(varespec) ## Bray-Curtis distances between samples dis <- vegdist(varespec) ## First 16 sites grazed, remaining 8 sites

Hey Everyone! I wanted to carry out Hierarchical clustering using distance matrices i have calculated ( instead of euclidean distance etc.) I understand as.dist is the function for this, but the distances in the dendrogram i got by using the following script(1) were not the distances defined in my distance matrices. script: var<-read.table("the distance matrix i calculated",

Dear R-users, Following is part of my data, where slide has 36 levels and block 48 levels. I have done boxplot for each slide on the same graph. There are outliers for each slide and I tried to use indentify functtion to identify outliers in such a way that when I click on an outlier or point, the points will be labelled by either their block or ID or by both but without success. How can I make

We need a two-way non-parametric ANOVA in order to analysis properly some ecological data, do you know any reference in R? or how to do it? Thank you very much All the best diana -- View this message in context: http://www.nabble.com/Two-way-non-parametric-ANOVA--tp15039308p15039308.html Sent from the R help mailing list archive at Nabble.com.

Hi, I have seen a discussion in the R-help asking whether nonparametric manova has been implemented in R yet. This discussion is form March 2006 and there seemed to be no package or function implemented at the time. Has this changed? Is there a package that provides nonparametric manova as in McArdle and Anderson (2001) and Anderson (2001) now? Thanks, Daniel ------------------------- cuncta

Hello guys I am new to this list and for R too. I am wondering if there is a patch for the SPSS reading code on the foreign package, in order to be able to read long variable names. Right now read.spss() just trunc the names to 8 characters. Or if someone could help me on other way: I have to process everyday a lot of SPSS Syntax Files and Dat files that come from one system that can only export