spider (version 1.2-0)

chaoHaplo: Chao estimator of haplotype number

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

chaoHaplo(DNAbin)

Arguments

DNAbin

An object of class `DNAbin'.

Value

• An integer giving the estimated total number of haplotypes in the population.

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.

See Also

haploAccum

Examples

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)