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SiPhyNetwork
View on CRAN: Click
here
Download and install SiPhyNetwork package within the R console
Install from CRAN:
install.packages("SiPhyNetwork")
Install from Github:
library("remotes")
install_github("cran/SiPhyNetwork")
Install by package version:
library("remotes")
install_version("SiPhyNetwork", "1.1.0")
Attach the package and use:
library("SiPhyNetwork")
Maintained by
Joshua Justison
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-09-20
Latest Update: 2023-04-14
Description:
A simulator for reticulate evolution under a birth-death-hybridization process. Here the birth-death process is extended to consider reticulate Evolution by allowing hybridization events to occur. The general purpose simulator allows the modeling of three different reticulate patterns: lineage generative hybridization, lineage neutral hybridization, and lineage degenerative hybridization. Users can also specify hybridization events to be dependent on a trait value or genetic distance. We also extend some phylogenetic tree utility and plotting functions for networks. We allow two different stopping conditions: simulated to a fixed time or number of taxa. When simulating to a fixed number of taxa, the user can simulate under the Generalized Sampling Approach that properly simulates phylogenies when assuming a uniform prior on the root age.
How to cite:
Joshua Justison (2022). SiPhyNetwork: A Phylogenetic Simulator for Reticulate Evolution. R package version 1.1.0, https://cran.r-project.org/web/packages/SiPhyNetwork. Accessed 21 Nov. 2024.
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Complete documentation for SiPhyNetwork
Functions, R codes and Examples using
the SiPhyNetwork R package
Some associated functions: biconnectedComponents . deleteTips . getNetworkLevel . incompleteSampling . isFUstable . isNormal . isTreeBased . isTreeChild . ltt.network . make.beta.draw . make.categorical.draw . make.exp.decay . make.linear.decay . make.polynomial.decay . make.stepwise . make.trait.model . make.uniform.draw . network.gsa . plottable.net . read.net . reconstructedNetwork . sim.bdh.age . sim.bdh.taxa.gsa . sim.bdh.taxa.ssa . write.net .
Some associated R codes: NetworkSim.R . RcppExports.R . SiPhyNetwork-package.R . make.functions.R . network.gsa.R . read.net.R . sim.bdh.age.R . sim.bdh.age.help.R . sim.bdh.taxa.R . sim.bdh.taxa.help.R . utils.R . write.net.R . Full SiPhyNetwork package functions and examples
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