Description Objects from the Class Slots Methods Author(s) References

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 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.

- 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.

Caner Aktas, [email protected]

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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