spider (version 1.2-0)

haploAccum: Haplotype accumulation curves

Description

haploAccum identifies the different haplotypes represented in a set of DNA sequences and performs the calculations for plotting haplotype accumulations curves (see plot.haploAccum).

Usage

haploAccum(DNAbin, method = "random", permutations = 100, ...)

Arguments

DNAbin

A set of DNA sequences in an object of class `DNAbin'.

method

Method for haplotype accumulation. Method "collector" enters the sequences in the order that they appear in the sequence alignment and "random" adds the sequences in a random order.

permutations

Number of permutations for method "random".

...

Other parameters to functions.

Value

• An object of class `haploAccum' with items:
• call
  Function call.
• method
  Method for accumulation.
• sequences
  Number of analysed sequences.
• n.haplotypes
  Accumulated number of haplotypes corresponding to each number of sequences.
• sd
  The standard deviation of the haplotype accumulation curve. Estimated through permutations for method = "random" and NULL for method = "collector".
• perm
  Results of the permutations for method = "random".

Details

Haplotype accumulation curves can be used to assess haplotype diversity in an area or compare different populations, or to evaluate sampling effort. ``random'' calculates the mean accumulated number of haplotypes and its standard deviation through random permutations (subsampling of sequences), similar to the method to produce rarefaction curves (Gotelli and Colwell 2001).

References

Gotellli, N.J. & Colwell, R.K. (2001). Quantifying biodiversity: procedures and pitfalls in measurement and comparison of species richness. _Ecology Letters_ *4*, 379--391.

Examples

data(dolomedes)
#Generate multiple haplotypes
doloHaplo <- dolomedes[sample(37, size = 200, replace = TRUE), ] 
dolocurv <- haploAccum(doloHaplo, method = "random", permutations = 100)
dolocurv
plot(dolocurv)