I used adonis to test tested for differences in the relative species (OTU)
abundances from incubation experiments with a common starting water source
and duplicates for each of three treatments (a one way test with three
levels in the independent variable).  For full disclosure (but  it may not
be relevant) I came up with a metric to reflect change in rel species
abundance from t0 to t9 days, weighted to not overly inflate significance
of rare species. The Bray Curtis similarity table looked compelling (where
A and B represent replicates).  I was surprised to see p ~0.06.  So, I made
a dummy file with a blatant differences (dummy file below) and only
obtained a p value of 0.05. I’m clearly missing something here.  BTW I also
noticed if you purposefully mismatch your env file you can still get a
“result”.  I'm so grateful for your help!!!





B-C output from real data (three treatments each replicated twice)



St24FeA

St24FeB

St24NoFeA

St24NoFeB

St24EntA

St24FeB

0.081774

St24NoFeA

0.322509

0.282081

St24NoFeB

0.343357

0.301258

0.064281

St24EntA

0.268338

0.221075

0.098628

0.161846

St24EntB

0.203852

0.194518

0.166727

0.221682

0.096111



Dummy file used as

OTU1

OTU2

OTU3

OTU5

St24FeA

100

20

100

20

St24FeB

100

25

100

25

St24NoFeA

5

80

5

80

St24NoFeB

5

80

5

80

St24EntA

7

100

7

100

St24EntB

7

100

7

100



BC of dummy file (BCdum) is even more compelling than the real data (no
transforms done for this).



Output from adonis using BCdum as input.



Call:

adonis(formula = Bcdum ~ treatment data=st24.env, permutation=2000)

Terms

added

sequentially

(first

to

last)

Df

SumsOfSqs

MeanSqs

F.Model

R2

Pr(>F)

treatment

2

0.73764

0.36882

5313.2

0.99972

0.05147

Residuals

3

0.00021

0.00007

0.00028

Total

5

0.73785

1


The entire script is here.  Note the “abundance” data is not transformed in
R.  Rather, I calculate a metric of change in percent abundance



t= 9 d(counts(i)/counts(total) /

t = 0 d(counts(i)/counts(total)



which is then normalized so small abs changes in rare species don’t have an
undue influence.





St24Y<-read.table("st24relchangeforR.txt")

BC24<-vegdist(St24Y,method=”bray”,binary=FALSE, diag=FALSE,
upper=FALSE,na.rm = FALSE)

st24.env<-read.table("st24envfileforR.txt")

adonis(BC24~ treatment,st24.env,perm=2000)

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