chaoHaplo: Chao estimator of haplotype number
In spider: Species Identity and Evolution in R

Description Usage Arguments Details Value Author(s) References See Also Examples

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.

1	chaoHaplo(DNAbin)

DNAbin

An object of class ‘DNAbin’.

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.

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

Samuel Brown <s_d_j_brown@hotmail.com>

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.

haploAccum

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)