vegan

data(dune) data(dune.env) results<-list() for (i in colnames(dune.env)){ results[[i]]<- adonis(dune ~ i, data=dune.env, permutations=99) } When I test each name in colnames(dune.env) , it can work. But it can not work in the loop function above. I think it is due to the i in the loop fuction has " " . How to fix it? Thanks. I know nothing about adonis, but I do know that formulas are language objects which do not take nicely to being treated as though they were ordinary character objects. for (i in colnames(dune.env)){ form <- as.formula(paste("dune", i, sep="~")) results[[i]]<- adonis(form,

I am trying to perform an anosim analysis in Vegan , but it doesn't seem to work... It doesn't give an error after the anosim function, but when I try to see the summary it says: Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 'x' must be atomic My data looks like a simple community matrix with sites and species (identical to the Dune data set). I've tried this: dist.com <- vegdist(data, method = "bray") an = anosim(dist.com, env) summary(an) The class of data is a data.frame , the class of env is factor and the class of dist.com is dist . It is identical to the example

I am trying to do something similar to an old post: plotting - original post For my analysis, I am interested in whether different mammal hosts have different flea communities. The original post I have linked to has 2 different solutions for the ellipses. My problem is when I run both the 1st solution and then the general solution I get vastly different looking plots while I think they should be very similar. Below is my code. My question is: Am I doing something incorrectly or which code produces the correct figure? Or is there a better new code I should be using instead to display

I have data of species at 4 sites over several months. I have successfully created accumulation graphs using package vegan in R but I would like to plot all 4 sites on one graph. At first I had a data sheet with all sites and months but the when I plotted specaccum the result was a curve of accumulation of all data regardless of site. Because of this I split each site into a separate data sheet which I loaded into R. In each data sheet the first row is species names and each additional row below that is a month. For example I loaded the data of one of my sites "FMR". Then I did the following:

I am working on finalizing a NMDS plot that I created in vegan and ggplot2 but cannot figure out how to add envfit species-loading vectors to the plot. When I try to it says "invalid graphics state". The example below is slightly modified from another question ( Plotting ordiellipse function from vegan package onto NMDS plot created in ggplot2 ) but it expressed exactly the example I wanted to include since I used this question to help me get metaMDS into ggplot2 in the first place: library(vegan) library(ggplot2) data(dune) # calculate distance for NMDS NMDS.log<-log(dune+1) sol <- metaMDS