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 looking at diversity in different soils with either woodland or grassland habitats.

I have run the scripts

library(vegan)
library(ecodist)
library(MASS)
mydata <- read.table("ash_data.csv", header=TRUE, sep=",", row.names="Site")

envdata_fit <- read.table("ash_env.csv", header=TRUE, sep=",", row.names="Site")

#distance matrix of samples using bray curtis
d= bcdist(mydata, rmzero=FALSE)

And then using the distance matrix from this to use for adoins? Is this correct.

With this I have then run Adonis

results = adonis(d ~ wood, envdata_fit, permutations = 1000)

and get significant values to see if sig diff in diversity between wood and grass habitat.

However I have been reading about combining the variables, but there seems to be different ways for example

results = adonis(d ~ wood+soil, envdata_fit, permutations = 1000)

so get sig values for Wood and soil

or

results = adonis(d ~ wood*soil, envdata_fit, permutations = 1000)

And I get sig values for wood, soil, and wood soil interaction.

This seems to make sense, however for both if I put the variable the other way around (soil+wood or soil*wood) I get very different sig values, even accounting for the fact they vary slightly due to the permutations. So whats is going on and why to the the values change so much?

I was also wondering in Adonis, can you nest treatments, so see effect of soil removing the effect of woodland as you can with anova?

Another general questions as well, if I have more than two groups in a treatment, say for soil, clay, sand, loam and do the stats, and I get a significant value, what does it actually mean, is it that soil generally has an effect, with each group separate, or there are general differences between soils which may be one group is very different to the other two?

Many many thanks to anyone who can help me as I have asked people who use R near me and no-one is sure and uses Adonis..

Ash
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