sim.taxa
(Package: TreeSimGM) :
Simulating General Model Trees on a fixed number of extant Taxa
sim.taxa simulates trees on n species under a general model (i.e. any given distribution for speciation and extinction). The method allows to stop the simulation right after reaching a given number of tips/taxa or to simulate a bigger tree (m-tips) and then uniformly sample one of the n-tips trees that existed in the past until m tips. For this the gsa code from the R package TreeSim is used. The method allows for symmetric and asymmetric binary split speciation mode. To keep all extinct tips use complete=TRUE, if complere=FALSE the tree is pruned, resulting on a so called reconstructed tree.
● Data Source:
CranContrib
● Keywords: general model, macroevolution, phylogenetic trees, phylogenies, simulation
● Alias: sim.taxa
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TreeSimGM-package
(Package: TreeSimGM) :
Simulating Phylogenies under a General Model (symmetric & asymmetric)
TreeSimGM is a flexible simulation tool for phylogenetic trees that uses a general model. This model can assume any probability distribution for the waiting time until speciation, as well as any distribution for the waiting time until extinction. In clear English this means that 'TreeSimGM, allows you to simulate stochastic phylogenetic trees using any probability distribution and parameters for speciation and extinction. Moreover, a general model can be distinguished in the way that speciation and extinction processes happen. In this package, we provide two general binary splitting models: (i) symmetric, in which for every speciation event new waiting times until speciation and extinction are drawn for both daughter lineages; and (ii) asymmetric, in which a speciation event results in one species with new waiting times, and another that carries the extinction time and age of its ancestor. Those models were inspired by allopatric and peripatric speciation modes respectively. Both models (symmetric and asymmetric) were created and implemented so that different processes (distributions) for speciation and extinction could be independently and explicitly specified. It is also possible to have an implicit extinction process by setting the extinction rate to zero and simulating only based on speciation processes.
sim.age
(Package: TreeSimGM) :
Simulating General Model Trees on Age
sim.age simulates stochastic trees conditioned on the time since origin of the extant tips under a general model (i.e. any given distribution for speciation and extinction). The method allows for symmetric and asymmetric binary split speciation mode. To keep all extinct trees use complete=TRUE, if complete=FALSE the tree is pruned, resulting on a so called reconstructed tree.
● Data Source:
CranContrib
● Keywords: general model, macroevolution, phylogenetic trees, phylogenies, simulation
● Alias: sim.age
●
0 images
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