Other packages > Find by keyword >

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
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)
Other packages that cited TreeSimGM R package
View TreeSimGM citation profile
Other R packages that TreeSimGM depends, imports, suggests or enhances
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
Downloads during the last 30 days
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
ftaproxim  
Fault Tree Analysis Based on Proxel Simulation
Calculation and plotting of instantaneous unavailabilities of basic events along with the top event ...
Download / Learn more Package Citations See dependency  
rdbnomics  
Download DBnomics Data
R access to hundreds of millions data series from DBnomics API (). ...
Download / Learn more Package Citations See dependency  
critpath  
Setting the Critical Path in Project Management
Solving the problem of project management using CPM (Critical Path Method), PERT (Program Evaluation ...
Download / Learn more Package Citations See dependency  
mistral  
Methods in Structural Reliability
Various reliability analysis methods for rare event inference (computing failure probability and qua ...
Download / Learn more Package Citations See dependency  
steepness  
Testing Steepness of Dominance Hierarchies
The steepness package computes steepness as a property of dominance hierarchies. Steepness is define ...
Download / Learn more Package Citations See dependency  

22,114

R Packages

188,080

Dependencies

55,244

Author Associations

22,115

Publication Badges

© Copyright 2022 - present. All right reserved, rpkg.net. Contact Us / Suggestions / Concerns