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
chaoHaplo(DNAbin)
Arguments
DNAbin
An object of class `DNAbin'.
Value
An vector of length three, giving the estimated total number of
haplotypes in the population, and lower and upper 95% confidence limits.
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.
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.