# 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.