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()
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 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.