Chao estimator of haplotype number

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Description

Calculates the Chao1 estimate of the number of haplotypes in a population based on the total number of haplotypes present, and the number of singletons and doubletons in the dataset.

Usage

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chaoHaplo(DNAbin)

Arguments

DNAbin

An object of class ‘DNAbin’.

Details

The function assumes a large number of specimens have been sampled and that duplicate haplotypes have not been removed. Interpretation becomes difficult when more than one species is included in the dataset.

Value

An vector of length three, giving the estimated total number of haplotypes in the population, and lower and upper 95% confidence limits.

Author(s)

Samuel Brown <s_d_j_brown@hotmail.com>

References

Vink, C. J., McNeill, M. R., Winder, L. M., Kean, J. M., and Phillips, C. B. (2011). PCR analyses of gut contents of pasture arthropods. In: Paddock to PCR: Demystifying Molecular Technologies for Practical Plant Protection (eds. Ridgway, H. J., Glare, T. R., Wakelin, S. A., O'Callaghan, M.), pp. 125-134. New Zealand Plant Protection Society, Lincoln.

Chao, A. (1989). Estimating population size for sparse data in capture-recapture experimnets. _Biometrics_ *45* 427-438.

See Also

haploAccum

Examples

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data(dolomedes)
#Create dataset with multiple copies of Dolomedes haplotypes
doloSamp <- dolomedes[sample(16, 100, replace=TRUE, prob=c(0.85, rep(0.01, 15))), ]

chaoHaplo(doloSamp)

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