Description Usage Arguments Details Value Note Author(s) References Examples
haploAccum
identifies the different haplotypes represented in a set
of DNA sequences and performs the calculations for plotting haplotype
accumulations curves (see plot.haploAccum
).
1  haploAccum(DNAbin, method = "random", permutations = 100, ...)

DNAbin 
A set of DNA sequences in an object of class ‘DNAbin’. 
method 
Method for haplotype accumulation. Method 
permutations 
Number of permutations for method 
... 
Other parameters to functions. 
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).
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

perm 
Results of the permutations for 
This function is based on the functions haplotype
(E. Paradis)
from the package 'pegas' and specaccum
(R. Kindt) from the
package'vegan'. Missing or ambiguous data will be detected and indicated by
a warning, as they may cause an overestimation of the number of haplotypes.
Jagoba MalumbresOlarte <[email protected]>.
Gotellli, N.J. & Colwell, R.K. (2001). Quantifying biodiversity: procedures and pitfalls in measurement and comparison of species richness. _Ecology Letters_ *4*, 379–391.
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