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

Description

S4 class to store statistical parsimony networks and additional information.

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

d:: Object of class "list" containing the geodesic distance 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.

as.list: signature(x = "Parsimnet"): assigns slots of an object Parsimnet to list elements.
as.network: signature(x = "Parsimnet"): coerces Parsimnet object to network {network} object
as.networx: signature(x = "Parsimnet"): coerces Parsimnet object to networx {phangorn} object
length: signature(x = "Parsimnet"): returns the length of network(s).
names: signature(x = "Parsimnet"): gets names of networks in Parsimnet object
names<-: signature(x = "Parsimnet"): sets names of networks in Parsimnet object
plot: signature(x = "Parsimnet"): plots statistical parsimony networks.
pieplot: signature(x = "Parsimnet", y = "Haplotype"): plots pie charts on statistical parsimony networks
pielegend: signature(x = "Parsimnet", y = "Haplotype"): add legends to pie charts produced using pieplot.
rownames: signature(x = "Parsimnet"): gets names of vertices in networks.
rownames<-: signature(x = "Parsimnet"): gets names of vertices in networks
show: signature(object = "Parsimnet"): displays the object briefly.