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. Accessed 16 Jul. 2026.
Previous versions and publish date:
(2026-07-09 08:28), 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
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
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
tibble  
Simple Data Frames
Provides a 'tbl_df' class (the 'tibble') with stricter checking and better formatting than the tradi ...
Download / Learn more Package Citations See dependency  
tarchetypes  
Archetypes for Targets
Function-oriented Make-like declarative pipelines for Statistics and data science are supported in t ...
Download / Learn more Package Citations See dependency  
schoolmath  
Functions and Datasets for Math Used in School
Contains functions and datasets for math taught in school. A main focus is set to prime-calculation. ...
Download / Learn more Package Citations See dependency  
Rnmr1D  
Perform the Complete Processing of a Set of Proton Nuclear Magnetic Resonance Spectra
Perform the complete processing of a set of proton nuclear magnetic resonance spectra from the free ...
Download / Learn more Package Citations See dependency  
wordnet  
WordNet Interface
An interface to WordNet using the Jawbone Java API to WordNet. WordNet (< ...
Download / Learn more Package Citations See dependency  

27,806

R Packages

239,283

Dependencies

73,837

Author Associations

27,807

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA