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TreeSimGM  

Simulating Phylogenetic Trees under General Bellman Harris and Lineage Shift Model
View on CRAN: Click here


Download and install TreeSimGM package within the R console
Install from CRAN:
install.packages("TreeSimGM")

Install from Github:
library("remotes")
install_github("cran/TreeSimGM")

Install by package version:
library("remotes")
install_version("TreeSimGM", "2.5")



Attach the package and use:
library("TreeSimGM")
Maintained by
Oskar Hagen
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2013-02-14
Latest Update: 2020-03-05
Description:
Provides a flexible simulation tool for phylogenetic trees under a general model for speciation and extinction. Trees with a user-specified number of extant tips, or a user-specified stem age are simulated. It is possible to assume any probability distribution for the waiting time until speciation and extinction. Furthermore, the waiting times to speciation / extinction may be scaled in different parts of the tree, meaning we can simulate trees with clade-dependent diversification processes. At a speciation event, one species splits into two. We allow for two different modes at these splits: (i) symmetric, where for every speciation event new waiting times until speciation and extinction are drawn for both daughter lineages; and (ii) asymmetric, where a speciation event results in one species with new waiting times, and another that carries the extinction time and age of its ancestor. The symmetric mode can be seen as an vicariant or allopatric process where divided populations suffer equal evolutionary forces while the asymmetric mode could be seen as a peripatric speciation where a mother lineage continues to exist.Reference: O. Hagen and T. Stadler (2017). TreeSimGM: Simulating phylogenetic trees under general Bellman Harris models with lineage-specific shifts of speciation and extinction in R. Methods in Ecology and Evolution. <doi:10.1111/2041-210X.12917>.
How to cite:
Oskar Hagen (2013). TreeSimGM: Simulating Phylogenetic Trees under General Bellman Harris and Lineage Shift Model. R package version 2.5, https://cran.r-project.org/web/packages/TreeSimGM. Accessed 22 Dec. 2024.
Previous versions and publish date:
1.0 (2013-02-14 10:39), 1.1 (2013-02-21 07:52), 1.2 (2014-07-25 07:39), 2.1 (2017-05-05 19:38), 2.2 (2017-08-10 19:20), 2.3 (2017-09-25 20:40)
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Other R packages that TreeSimGM depends, imports, suggests or enhances
Complete documentation for TreeSimGM
Functions, R codes and Examples using the TreeSimGM R package
Some associated functions: TreeSimGM-package . sim.age . sim.taxa . track.shift . 
Some associated R codes: mytree.asymmetric.age.R . mytree.asymmetric.taxa.R . mytree.symmetric.age.R . mytree.symmetric.taxa.R . sim.age.R . sim.taxa.R . track.shift.R .  Full TreeSimGM package functions and examples
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