<s>
Analysis	B-General_Concept
of	I-General_Concept
similarities	I-General_Concept
(	O
ANOSIM	B-General_Concept
)	O
is	O
a	O
non-parametric	B-General_Concept
statistical	I-General_Concept
test	I-General_Concept
widely	O
used	O
in	O
the	O
field	O
of	O
ecology	O
.	O
</s>
<s>
The	O
test	O
was	O
first	O
suggested	O
by	O
K	O
.	O
R	O
.	O
Clarke	O
as	O
an	O
ANOVA-like	O
test	O
,	O
where	O
instead	O
of	O
operating	O
on	O
raw	O
data	O
,	O
operates	O
on	O
a	O
ranked	O
dissimilarity	O
.	O
</s>
<s>
Given	O
a	O
matrix	O
of	O
rank	O
dissimilarities	O
between	O
a	O
set	O
of	O
samples	O
,	O
each	O
solely	O
belong	O
to	O
one	O
treatment	O
group	O
,	O
the	O
ANOSIM	B-General_Concept
tests	O
whether	O
we	O
can	O
reject	O
the	O
null	B-General_Concept
hypothesis	I-General_Concept
that	O
the	O
similarity	O
between	O
groups	O
is	O
greater	O
than	O
or	O
equal	O
to	O
the	O
similarity	O
within	O
the	O
groups	O
.	O
</s>
<s>
For	O
the	O
purpose	O
of	O
hypothesis	O
testing	O
,	O
where	O
the	O
null	B-General_Concept
hypothesis	I-General_Concept
is	O
that	O
the	O
similarities	O
within	O
sites	O
are	O
smaller	O
or	O
equal	O
to	O
the	O
similarities	O
between	O
sites	O
,	O
the	O
R	O
statistic	O
is	O
usually	O
compared	O
to	O
a	O
set	O
of	O
R′	O
values	O
that	O
are	O
achieved	O
by	O
means	O
of	O
randomly	O
shuffling	O
site	O
labels	O
between	O
the	O
samples	O
and	O
calculating	O
the	O
resulting	O
R′	O
,	O
repeated	O
many	O
times	O
.	O
</s>
<s>
The	O
percent	O
of	O
times	O
that	O
the	O
actual	O
R	O
surpassed	O
the	O
permutations	B-Algorithm
derived	O
R′	O
values	O
is	O
the	O
p-value	O
for	O
the	O
actual	O
R	O
statistic	O
.	O
</s>
<s>
Ranking	O
of	O
dissimilarity	O
in	O
ANOSIM	B-General_Concept
and	O
NMDS	O
(	O
non-metric	O
multidimensional	O
scaling	O
)	O
go	O
hand	O
in	O
hand	O
.	O
</s>
<s>
Combining	O
both	O
methods	O
complement	O
visualisation	O
of	O
group	O
differences	O
along	O
with	O
significance	B-General_Concept
testing	I-General_Concept
.	O
</s>
<s>
ANOSIM	B-General_Concept
is	O
implemented	O
in	O
several	O
statistical	O
software	O
including	O
PRIMER	O
,	O
R	O
Vegan	O
package	O
and	O
PAST	O
.	O
</s>
