Sorclass

The sorclass calculator returns the traditional Sorenson index describing the dissimilarity between two communities. This is also known as the Dice coefficient. 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 > cluster(phylip=98_lt_phylip_amazon.dist, cutoff=0.10)
mothur > make.shared(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:

\(D_{Sorenson}=1- \frac{2 \left(9\right)}{33 + 31}= 0.71875\),

Running...

mothur > summary.shared(shared=98_lt_phylip_amazon.fn.shared, calc=sorclass)

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

label  comparison      SorClass
0.10   forest  pasture     0.71875

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