Geometric
The geometric calculator returns the Kolmogorov-Smirnov test statistic for the comparison of observed rank-abundance data to a fitted geometric series distribution and the critical values for α equal to 0.01 or 0.05. This calculator can be used in the summary.single, collect.single, and rarefaction.single commands.
\[S_i=NC_K K\left(1-K\right)^\left(i-1\right)\]where,
\[C_K=\left(1-\left(1-K \right)^{S_{obs}} \right)^{-1}\]\(S_i\) = number of individuals in the ith OTU
\(N\) = the total number of individuals
To calculate K, the following equation is solved for K
\[\frac{N_{min}}{N}=\left(\frac{k}{1-k}\right)\frac{\left(1-k\right)^{S_{obs}}}{1-\left(1-k\right)^{S_{obs}}}\]where,
\(N_{min}\) = the number of individuals in the most rare OTU
\(S_{obs}\) = total number of observed OTUs
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 numbers in the subsequent columns indicate the number of singletons, doubletons, etc. Here we will calculate the expected number of individuals in each OTU based on the geometric series distribution:
\(\frac{1}{98}=\left(\frac{K}{1-K}\right)\frac{\left(1-K\right)^{55}}{1-\left(1-K\right)^{55}}\), \(K = 0.019424\), by Excel
\[C_K=\left(1-\left(1-0.019424 \right)^{55} \right)^{-1} = 1.5151\] \[S_i=\left(98\right)\left(1.5151\right) \left(0.019424\right) \left(1-0.019424\right)^\left(i-1\right) = 2.8841\left(0.9806\right)^\left(i-1\right)\]OTU Rank Indiv. Obs. Expected Cum. Obs. Cum. Exp. Difference ———- ————- ———- ———– ———– ———— 1 7 2.884 7 2.88 4.12 2 7 2.828 14 5.71 8.29 3 7 2.773 21 8.49 12.51 4 4 2.719 25 11.21 13.79 5 4 2.667 29 13.87 15.13 6 3 2.615 32 16.49 15.51 7 3 2.564 35 19.05 15.95 8 3 2.515 38 21.57 16.43 9 2 2.466 40 24.03 15.97 10 2 2.418 42 26.45 15.55 11 2 2.371 44 28.82 15.18 12 2 2.325 46 31.15 14.85 13 2 2.280 48 33.42 14.58 14 2 2.236 50 35.66 14.34 15 2 2.192 52 37.85 14.15 16 2 2.150 54 40.00 14.00 17 2 2.108 56 42.11 13.89 18 2 2.067 58 44.18 13.82 19 2 2.027 60 46.20 13.80 20 2 1.988 62 48.19 13.81 21 2 1.949 64 50.14 13.86 22 1 1.911 65 52.05 12.95 23 1 1.874 66 53.93 12.07 24 1 1.838 67 55.77 11.23 25 1 1.802 68 57.57 10.43 26 1 1.767 69 59.33 9.67 27 1 1.733 70 61.07 8.93 28 1 1.699 71 62.77 8.23 29 1 1.666 72 64.43 7.57 30 1 1.634 73 66.07 6.93 31 1 1.602 74 67.67 6.33 32 1 1.571 75 69.24 5.76 33 1 1.541 76 70.78 5.22 34 1 1.511 77 72.29 4.71 35 1 1.482 78 73.77 4.23 36 1 1.453 79 75.23 3.77 37 1 1.425 80 76.65 3.35 38 1 1.397 81 78.05 2.95 39 1 1.370 82 79.42 2.58 40 1 1.343 83 80.76 2.24 41 1 1.317 84 82.08 1.92 42 1 1.292 85 83.37 1.63 43 1 1.267 86 84.64 1.36 44 1 1.242 87 85.88 1.12 45 1 1.218 88 87.10 0.90 46 1 1.194 89 88.29 0.71 47 1 1.171 90 89.46 0.54 48 1 1.148 91 90.61 0.39 49 1 1.126 92 91.74 0.26 50 1 1.104 93 92.84 0.16 51 1 1.083 94 93.93 0.07 52 1 1.062 95 94.99 0.01 53 1 1.041 96 96.03 0.03 54 1 1.021 97 97.05 0.05 55 1 1.001 98 98.05 0.05
To determine whether the geometric model describes the distribution of individuals among OTUs as we observed, we will use the Kolmogorov-Smirnov test statistic (\(D_{max}\)). The statistic is the maximum difference between the cumulative observed and expected values (i.e. 16.43) divided by the total number of individuals sampled (i.e. 98). So for this case the value was 0.1677. To test this statistic we can calculate the critical value for α=0.05 as
0.886{ {math|{ {radical|Sobs}}}}{=mediawiki} or 0.1195 and α=0.01 as
1.031{ {math|{ {radical|Sobs}}}}{=mediawiki} or 0.1390. Because our
calculated value is greater than both critical values we are confident
(P<0.01) that the observed and expected values are significantly
different and we can reject the hypothesis that the observed data
follows the geometric distribution.
Running...
mothur > summary.single(calc=geometric)
...and opening 98_lt_phylip_amazon.fn.summary gives:
label geometric geometric_lci geometric_hci
unique 0.019556 0.105226 0.090427
0.00 0.028679 0.105778 0.090902
0.01 0.045567 0.106910 0.091874
0.02 0.081446 0.109286 0.093916
0.03 0.112433 0.112491 0.096671
0.04 0.123174 0.114556 0.098444
0.05 0.136999 0.120669 0.103698
0.06 0.140532 0.125027 0.107443
0.07 0.131241 0.126907 0.109059
0.08 0.121753 0.134225 0.115347
0.09 0.148807 0.136559 0.117354
0.10 0.167704 0.139020 0.119468 <---
In this table the data in the column “geometric” are the calculated statistic value, those in column “geometric_lci” are the critical values for α=0.01, and those in column “geometric_hci” are the critical values for α=0.05. These are the same values that we found above for a cutoff of 0.10.