Man pages for jjustison/SiPhyNetwork
A Phylogenetic Simulator for Reticulate Evolution
| 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 |
