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Bootstrap

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Validate output by making calculations by hand

Example Calculations

*boot*

These files give the bootstrap estimate as described by Smith and Van Belle (5) but implemented for a single "quadrant".


<math>S_{Bootstrap} = S_{obs} + \sum_{i=1}^{S_{obs}} \left ( 1 - \frac {S_i}{N}\right )^N </math>

where,

N = The number of individuals sampled

<math>S_{i}</math> = The number of sequences in the ith OTU

<math>S_{obs}</math> = Observed number of species


For the Amazonian dataset at distance 0.03, <math>S_{Bootstrap}</math> =112.33 and there is not a simple expression for the 95% confidence interval.


File Samples on the Amazonian Dataset

  • .sabund

This file contains data for constructing a rank-abundance plot of the OTU data for each distance level. The first column contains the distance and the second is the number of OTUs observed at that distance. The successive values in the row are the number of OTUs that were found once, twice, etc.

unique	   2	94	2	
0	   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	36	15	4	2	1	0	1	
0.09	   7	36	12	4	3	0	0	2	
0.1	   7	35	12	2	3	0	0	3	


  • .bootstrap
numsequences	unique	0.01	0.02	0.03	0.04	0.05	0.06	0.07	0.08	0.09	0.1
1	        1.00	1.00	1.00	1.00	1.00	1.00	1.00	1.00	1.00	1.00	1.00
10	        13.49	13.49	13.49	13.49	13.49	13.49	11.90	11.90	11.90	10.31	13.49
20	        27.17	27.17	27.17	27.17	27.17	22.38	25.57	24.13	23.98	20.94	22.54
30	        40.85	40.85	40.85	40.85	39.25	34.46	32.86	36.21	32.86	33.02	26.99
40	        54.53	54.53	51.33	52.93	51.33	46.69	44.94	43.49	37.10	40.45	33.24
50	        68.21	66.61	65.01	65.01	58.62	57.17	54.12	52.52	47.93	48.08	42.12
60	        80.29	80.29	74.04	78.69	66.25	64.45	61.40	63.00	55.66	56.96	49.76
70	        92.37	92.37	84.87	86.12	75.13	71.88	65.98	71.88	65.10	61.84	57.27
80	        106.05	104.45	95.50	98.40	85.91	79.36	75.36	82.36	69.93	63.62	60.83
90	        119.73	116.53	109.18	107.43	96.59	86.94	81.24	82.84	71.16	68.40	65.71
98	        130.67	125.87	120.12	112.33	107.53	95.03	87.59	84.39	74.39	72.01	69.55