Bergerparker
The bergerparker calculator returns the Berger-Parker dominance index for an OTU definition. This calculator can be used in the summary.single, collect.single, and rarefaction.single commands.
\[d=\frac{n_{max}}{N}\]where,
\(n_{max}\) = the abundance of the dominant OTU
\(N\) = the total number of individuals in the sample
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.sabund file is also outputted to the terminal window when the cluster() command is executed:
unique 2 94 2
0.00 2 92 3
0.01 2 88 5
0.02 4 84 2 2 1
0.03 4 75 6 1 2
0.04 4 69 9 1 2
0.05 4 55 13 3 2
0.06 4 48 14 2 4
0.07 4 44 16 2 4
0.08 7 35 17 3 2 1 0 1
0.09 7 35 14 3 3 0 0 2
0.10 7 34 13 3 2 0 0 3
The first column is the label for the OTU definition and the second column is an integer indicating the number of sequences in the dominant OTU. The Berger-Parker index is then calculated using the values found in the subsequent columns. For demonstration we will calculate the Berger-Parker index for an OTU definition of 0.03:
\[d=\frac{4}{98} = 0.0408\]Running...
mothur > summary.single(calc=bergerparker)
...and opening 98_lt_phylip_amazon.fn.summary gives:
label bergerparker
unique 0.020408
0.00 0.020408
0.01 0.020408
0.02 0.040816
0.03 0.040816 <---
0.04 0.040816
0.05 0.040816
0.06 0.040816
0.07 0.040816
0.08 0.071429
0.09 0.071429
0.10 0.071429
These are the same values that we found above for a cutoff of 0.03.