simulate_dd_phylo: Simulate a phylogeny with a diversity-dependent birth-death...
In TheoPannetier/comrad: R implementation of a Competitive Radiation model

simulate_dd_phylo

R Documentation

Simulate a phylogeny with a diversity-dependent birth-death model

Description

Use a Gillespie algorithm to create a phylo object from the DD model specified by dd_model and params. The phylogeny is conditioned on the survival of at least one lineage to the end of the simulation.

Usage

simulate_dd_phylo(params, nb_gens, dd_model, stem_or_crown = "stem")

Arguments

`params`	a named vector containing the values of the parameters of the DD model. Names and length must match those expected by `dd_model$params_check`
`nb_gens`	integer, the number of generations the simulation should run for.
`dd_model`	a list with five named elements that together specify the diversity-dependent model: `name` a two-letter code, the name of the model. First letter specifies the form of the speciation function, second letter the form of the extinction function: "l" for "linear", "x" for exponential, "c" for constant. `speciation_func`, a function specifying the diversity-dependent speciation rate. Must take arguments `params` and `N`. `extinction_func`, a function specifying the diversity-dependent extinction rate. Must take arguments `params` and `N`. `constraints` a list of conditions that parameter values must satisfy. Each element is a function that takes arguments `params` and `...`, and returns `TRUE` if the constraint is satisfied, `FALSE` if it isn't. `params_check` a function that controls the format of `params`. Returns an error if the elements of `params` are named differently from what is expected or if the length differs from the expectation. `comrad` contains several `dd_model` functions, see for example `dd_model_lc()`.
`stem_or_crown`	character, either "stem" or "crown", should the simulation start from 1 species (stem lineage) or 2 species (crown lineages)?