Class "Parsimnet" in the Package haplotypes

Description

S4 class to store statistical parsimony networks and additional information.

Objects from the Class

Objects can be created by calls of the form new("Parsimnet", d, tempProbs, conlimit, prob, nhap, rowindex), however use function parsimnet instead.

Slots

d:

Object of class "list" containing the absolute pairwise character difference matrix of haplotypes and intermediates for each network.

tempProbs:

Object of class "numeric" giving the probabilities of parsimony for mutational steps beyond the connection limit.

conlimit:

Object of class "numeric" giving the number of maximum connection steps at connection limit.

prob:

Object of class "numeric" giving the user defined connection limit.

nhap:

Object of class "numeric" giving the number of haplotypes in each network.

rowindex:

Object of class "list" containing vectors giving the index of haplotypes in each network.

Methods

as.list

signature(x = "Parsimnet"): assigns slots of an object Parsimnet to list elements.

length

signature(x = "Parsimnet"): returns the length of network(s).

plot

signature(x = "Parsimnet", y = "ANY"): plots statistical parsimony networks.

show

signature(object = "Parsimnet"): displays the object briefly.

Author(s)

Caner Aktas, caktas.aca@gmail.com

References

Templeton, A. R., Crandall, K. A. and Sing, C. F. (1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics, 132, 619-635.

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