Npshannon
The npshannon calculator returns a non-parametric estimate of the classical shannon diversity index for an OTU definition. This calculator can be used in the summary.single, collect.single, and rarefaction.single commands. The calculations for the non-parametric Shannon index are implemented as described by Chao and Shen.
\[\hat{H}_{shannon}=\sum_{i=1}^{S_t}\frac{\hat{C}\pi_i \ln\left( \hat{C}\pi_i\right)}{1-\left(1-\hat{C}\pi_i\right)^N}\] \[var \left(\hat{H}_{shannon} \right ) {\approx} \sum_{j=1}^{n} \sum_{i=1}^{n} \frac{ {\partial}\hat{H}}{ {\partial}n_i} \frac{ {\partial}\hat{H}}{ {\partial}n_j}\] \[cov \left( f_i, f_j \right) = f_i \left(1-f_i / S_{ACE} \right ), i = j\] \[cov\left ( f_i, f_j \right) = -f_i f_j / {S_{ACE}}, i\ne j\]where,
\[\hat{C} = 1-\frac{n_1}{N}\] \[\pi_i = \frac{n_i}{N}\]n_i = the number of individuals in the ith OTU
\[N \mbox{ = the number of individuals in the sample}\] \[S_t \mbox{ = the total number of OTUs}\]\(S_{ACE}\) = the richness estimated using the ace calculator
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)
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 third column indicates the number of OTUs with only one indivdiual, the fourth the number of OTUs with two individuals, etc. The non-parametric Shannon index is then calculated using the values found in the subsequent columns. For demonstration we will calculate the non-parametric Shannon index for an OTU definition of 0.03:
\[\hat{C} = 1-\frac{75}{98} = 0.2347\] \[\hat{H}_{shannon}= 75\frac{\ 0.2347 \left(\frac{1}{98}\right) \ln\left( 0.2347\left(\frac{1}{98}\right)\right)}{1-\left(1-0.2347\left(\frac{1}{98}\right)\right)^{98}} +6\frac{\ 0.2347 \left(\frac{2}{98}\right) \ln\left( 0.2347\left(\frac{2}{98}\right)\right)}{1-\left(1-0.2347\left(\frac{2}{98}\right)\right)^{98}} +1\frac{\ 0.2347 \left(\frac{3}{98}\right) \ln\left( 0.2347\left(\frac{3}{98}\right)\right)}{1-\left(1-0.2347\left(\frac{3}{98}\right)\right)^{98}} +2\frac{\ 0.2347 \left(\frac{4}{98}\right) \ln\left( 0.2347\left(\frac{4}{98}\right)\right)}{1-\left(1-0.2347\left(\frac{4}{98}\right)\right)^{98}}\] \[\hat{H}_{shannon}=5.801\]Running...
mothur > summary.single(calc=npshannon)
...and opening 98_lt_phylip_amazon.fn.summary gives:
label NPShannon
unique 7.768419
0.00 7.355786
0.01 6.831284
0.02 6.344819
0.03 5.800593<---
0.04 5.559488
0.05 5.090494
0.06 4.853388
0.07 4.776910
0.08 4.495760
0.09 4.390298
0.10 4.297894
These are the same values that we found above for a cutoff of 0.03. At this point we have not implemented the 95% confidence interval calculations. As a point of reference it is worth noting that the classical shannon index gave a value of 4.353.