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.