search for: betadisper

Displaying 7 results from an estimated 7 matches for "betadisper".

2012 May 09
2
plot betadisper, change of pch
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]...
2013 Jan 30
0
betadisper plot
Hello, I tried to make a betadisper plot; however, it is quite messy at the moment with lines and symbols. I made two plots, one focusing on sites and the other on treatments. This is the code that I used: plot(betadisper(vegdist(y.nth,method="euclidean"),site)) plot(betadisper(vegdist(y.nth,method="euclidean"),...
2013 Nov 28
1
Multivariate dispersion & distances
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...
2008 Apr 27
1
An ANOVA test that uses a distance matrix like hierarchical cluster analysis?
Hi All, I have a question which does not pertain directly to the use of R but comes from my use of R! I have data which can be described as 3-dimensional e.g. (x,y,z), with no negative component. The suggested way to analyze this data is via multivariate techniques or by calculating what amounts to a levene's test on the data and then an ANOVA on the three components if the first test is
2010 Jan 19
1
restricted permutations in permtest()?
...library(vegan) data(varespec) ## Bray-Curtis distances between samples dis <- vegdist(varespec) ## First 16 sites grazed, remaining 8 sites ungrazed groups <- factor(c(rep(1,16), rep(2,8)), labels = c("grazed","ungrazed")) ## Calculate multivariate dispersions mod <- betadisper(dis, groups) ## Perform test anova(mod) ##simulation of dependence; blocks blocks<-factor(c(rep(1,4),rep(2,4),rep(3,4),rep(4,4))) ##the unrestricted Permutation test for F is permutest(mod, pairwise = TRUE) ..I wasn't able to find out the right syntax for implementation of blocks, I tri...
2014 Sep 13
1
vegan moved to GitHub and vegan 2.2-0 is coming (are you ready?)
...mple permutation and this can be expressed by giving just the number of permutations on the command line. The functions using the new permutation scheme are adonis, anosim, anova.cca for CCA/RDA/dbRDA and hence also for ordistep etc., CCorA, envfit, mantel & mantel.partial, mrpp, mso, permutest.betadisper, permutest.cca, protest and simper. The change for functions is now complete, but same clean up and updating of documentation is still to be done. This is discussed in https://github.com/vegandevs/vegan/issues/31 - vegan 2.2-0 will also use parallel processing in several functions. This was alread...
2011 Oct 04
2
Adonis and nmds help and questions for a novice.
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