R: A Phylogenetic Simulator for Reticulate Evolution

# A Phylogenetic Simulator for Reticulate Evolution

## Documentation for package ‘SiPhyNetwork’ version 1.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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