[R] Adonis and nmds help and questions for a novice.

[Gavin Simpson]

On Tue, 2011-10-04 at 08:45 +0000, Ashley Houlden wrote:
> Hi,
<snip />
> #distance matrix of samples using bray curtis
> d= bcdist(mydata, rmzero=FALSE)

In addition, you don't necessarily need ecodist for the bray curtis
distance. vegdist() in vegan will compute this for you.

Not that there is anything wrong with ecodist I hasten to add - just
that you can do this all in vegan if you wanted.

G

> 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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