Ace

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The ace calculator returns the ACE richness estimate for an OTU definition. This calculator can be used in the summary.single, collect.single, and rarefaction.single commands. The calculations for the ACE richness estimator are implemented as described by Chao in the user manual for her program SPADE and modified by Colwell in his program EstimateS. Note that this implementation uses a bias-corrected version of γ when the coefficient of variation is too large.

$S_{ACE} = \begin{cases}  S_{abund} + \frac {S_{rare}}{C_{ACE}} + \frac{n_1}{C_{ACE}}{{\hat{\gamma}}_{ACE}^2}\mbox{, for }\hat{\gamma}_{ACE}<\mbox{0.80} \\ S_{abund} + \frac {S_{rare}}{C_{ACE}} + \frac{n_1}{C_{ACE}}{{\tilde{\gamma}}_{ACE}^2}\mbox{, for }\hat{\gamma}_{ACE}\geqslant\mbox{0.80}  \end{cases}$

where,

$N_{rare} = \sum_{i=1}^{abund}{in_i}$

$C_{ACE} = 1 - \frac {n_1}{N_{rare}}$

${{\hat{\gamma}}_{ACE}^2} = max \left[ \frac {S_{rare}}{C_{ACE}} \frac{\sum_{i=1}^{abund} i \left ( i-1 \right ) n_i }{N_{rare} \left( N_{rare} - 1 \right )} - 1,0 \right ]$

$\tilde{\gamma}_{ACE}^2 = max \left[\hat{\gamma}_{ACE}^2 \left\{1+\frac{N_{rare}\left(1-C_{ACE}\right)\sum_{i=1}^{abund} i \left ( i-1 \right ) n_i }{N_{rare}\left(N_{rare}-C_{ACE}\right)}\right\}\mbox{, 0}\right]$

$var \left( S_{ACE} \right ) {\approx} \sum_{j=1}^{n} \sum_{i=1}^{n} \frac{{\partial}S_{ACE}}{{\partial}n_i} \frac{{\partial}S_{ACE}}{{\partial}n_j}$

$cov \left( f_i, f_j \right) = f_i \left(1-f_i / S_{ACE} \right ), i = j$

$cov\left ( f_i, f_j \right) = -f_i f_j / {S_{ACE}}, i\ne j$

$n_{i}$ = The number of OTUs with i individuals

$S_{rare}$ = The number of OTUs with 'abund' or fewer individuals

$S_{abund}$ = The number of OTUs with more than 'abund' individuals

$abund$ = the threshold to be considered an 'abundant' OTU; this is set to 10 by default and can be changed with the 'abund' parameter in summary.single, collect.single, and rarefaction.single.

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 ACE estimator is then calculated using the values found in the subsequent columns. By default ACE is calculated using an abundance threshold of 10. This value was empirically selected in the original publications, but can be altered. You may wish to increase or decrease this value. For demonstration we will calculate the ACE estimator with an abundance threshold of 5 and an OTU definition of 0.10:

$S_{rare} = 34 + 13+3+2+0 =52$

$S_{abund} = 3$

$N_{rare} = \sum_{i=1}^{5}{in_i} = 1\left(34\right)+2\left(13\right)+3\left(3\right)+4\left(2\right)+5\left(0\right) = 77$

$C_{ACE} = 1 - \frac {34}{77} = 0.558442$

${{\gamma}_{ACE}^2} = max \left[ \frac {52}{0.558442} \frac{ 1 \left ( 1-1 \right ) 34 + 2 \left ( 2-1 \right ) 13 + 3 \left ( 3-1 \right ) 3+ 4 \left ( 4-1 \right ) 2+ 5 \left ( 5-1 \right ) 0 }{77 \left( 77 - 1 \right )} - 1,0 \right ] = 0.0820$

$S_{ACE} = 3 + \frac {52}{0.558442} + \frac{34}{0.558442}0.0820 = 101.1$

The code to calculate the confidence intervals was provided by Anne Chao and is left for masochists to work out on their own.

Running...

mothur > summary.single(calc=ace, abund=5)


...and opening 98_lt_phylip_amazon.fn.summary gives:

label	ace		ace_lci		ace_hci
unique	2352.000000	165.123709	73725.382535
0.00	1551.666667	166.520625	29763.054270
0.01	911.400000	171.653666	8608.541528
0.02	1964.419917	1196.763495	3264.045830
0.03	543.693450	296.302894	1079.361221
0.04	362.831975	217.072510	664.727469
0.05	190.203699	131.260760	308.779744
0.06	155.277262	111.141296	244.566797
0.07	132.491876	98.445244	202.265564
0.08	101.208333	78.400541	150.829575
0.09	102.821244	77.832409	157.784620
0.10	101.109191	75.477067	158.826271 <---


These are the same values that we found above for a cutoff of 0.10.