Braycurtis

The braycurtis calculator returns the Bray-Curtis index describing the dissimilarity between the structure of two communities. This calculator can be used in the summary.shared and collect.shared commands.

$D_{Bray-Curtis}=1-2\frac{\sum min\left(S_{A,i}\mbox{, } S_{B,i}\right)}{\sum S_{A,i}+\sum S_{B,i}}$

where,

$S_{A,i}$ = the number of individuals in the ith OTU of community A

$S_{B,i}$ = the number of individuals in the ith OTU of community B

Open the file 98_lt_phylip_amazon.fn.sabund generated using the Amazonian dataset with the following commands:

mothur > read.dist(phylip=98_lt_phylip_amazon.dist, cutoff=0.10)
mothur > cluster()


The 98_lt_phylip_amazon.fn.shared file will contain the following two lines:

0.10	forest	55	1	1	1	1	1	1	3	3	2	2	1	1	3	2	1	1	1	1	2	1	1	2	5	1	1	1	1	2	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
0.10	pasture	55	0	0	0	1	1	0	1	0	0	5	0	0	0	0	0	2	0	0	0	3	0	0	2	1	0	1	0	0	0	0	0	0	1	2	1	1	1	1	1	7	1	1	2	1	1	1	1	1	1	1	1	1	2	1	1


This indicates that the label for the OTU definition was 0.10. The first line is from the forest sample and the second is from the pasture sample. There are a total of 55 OTUs between the two communities. Writing the data in a more presentable manner we see:

index forest pasture min(A, B)
1 1 0 0
2 1 0 0
3 1 0 0
4 1 1 1
5 1 0 0
6 1 0 0
7 3 1 1
8 3 0 0
9 2 0 0
10 2 5 2
11 1 0 0
12 1 0 0
13 3 0 0
14 2 0 0
15 1 0 0
16 1 3 1
17 1 0 0
18 1 0 0
19 2 0 0
20 1 3 1
21 1 0 0
22 2 0 0
23 5 2 2
24 1 1 1
25 1 0 0
26 1 1 1
27 1 0 0
28 2 0 0
29 1 0 0
30 1 0 0
31 1 0 0
32 1 0 0
33 1 1 1
34 0 2 0
35 0 1 0
36 0 1 0
37 0 1 0
38 0 1 0
39 0 1 0
40 0 7 0
41 0 1 0
42 0 1 0
43 0 2 0
44 0 1 0
45 0 1 0
46 0 1 0
47 0 1 0
48 0 1 0
49 0 1 0
50 0 1 0
51 0 1 0
52 0 1 0
53 0 2 0
54 0 1 0
55 0 1 0
Total 49 49 11

Using these sums to evaluate D we get:

$D_{Bray-Curtis}=1-2\frac{11}{49+49}=0.7755$

Running...

mothur > summary.shared(calc=braycurtis)


...and opening 98_lt_phylip_amazon.fn.shared.summary gives:

label	comparison		BrayCurtis
0.10	forest	pasture		0.77551


These are the same values that we found above for a cutoff of 0.10.