Parsimnet-class: Class `"Parsimnet"` in the Package haplotypes

Description

S4 class to store statistical parsimony networks and additional information.

Arguments

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.

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.