A Phylogenetic Simulator for Reticulate Evolution

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Documentation for package ‘SiPhyNetwork’ version 1.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

biconnectedComponents	Biconnected Components
deleteTips	Remove tips from a phylogenetic Network
getNetworkLevel	Get the level of a Network
incompleteSampling	Sample Tips on a Phylogenetic Network
isFUstable	Determine whether a phylogeny is FU-stable
isNormal	#' Determine whether a phylogeny is Normal
isTreeBased	Determine whether a network is tree-based
isTreeChild	Determine whether a network is tree-child
ltt.network	Lineages thru time on a network
make.beta.draw	Function that makes a draw from a beta distribution
make.categorical.draw	Function that makes a draw from a categorical distribution
make.exp.decay	Make an exponential decay function
make.linear.decay	Make a linear decay function
make.polynomial.decay	Make a polynomial decay function
make.stepwise	Make a stepwise decay function
make.trait.model	Model for trait evolution across the phylogeny
make.uniform.draw	Function that makes a draw from a uniform distribution
network.gsa	Sample under the Generalized Sampling Approach
plottable.net	Create a more Plotting-Friendly phylogenetic Network
read.net	Read a Network from Parenthetic Format
reconstructedNetwork	Remove Extinct Lineages from a Phylogenetic Network
sim.bdh.age	Simulate a Phylogenetic Network to a Specified Number of Taxa
sim.bdh.taxa.gsa	Simulate a Phylogenetic Network to a Specified Number of Taxa
sim.bdh.taxa.ssa	Simulate a Phylogenetic Network to a Specified Number of Taxa
write.net	Write a Network in Parenthetic Format