Jclass

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.

where,

\(S_{AB}\) = the number of shared OTUs between communities A and B

\(S_{A}\) = the number of OTUs in community A

\(S_{B}\) = 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:

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.