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Jclass

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The jclass calculator returns the traditional Jaccard index describing the dissimilarity between two communities. This calculator can be used in the summary.shared and collect.shared commands.

<math>D_{Jaccard}=\frac{S_{AB}}{S_A+S_B-S_{AB}}</math>

where,

<math> S_{AB}</math> = the number of shared OTUs between communities A and B

<math> S_{A}</math> = the number of OTUs in community A

<math> S_{B}</math> = the number of OTUs in 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()
mothur > read.otu(list=98_lt_phylip_amazon.fn.list, group=amazon.groups, label=0.10)


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

Using these sums to evaluate d we get:


<math>D_{Jaccard}=1-\frac{9}{33+31-9}=0.836</math>


Running...

mothur > summary.shared(calc=jclass)


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

label	comparison		Jclass
0.10	forest	pasture		0.836364

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