Description Usage Arguments Details Value Author(s) Examples

Provides a simulation of chromosome number evolution based on tree and one of 3 models. This function uses diversitrees sim.character to perform simulation.

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`tree` |
a phylogenetic tree of the class phylo |

`pars` |
numeric vector of paramters the length of this vector depends on the model specified see details below |

`limits` |
numeric vector of length 2 with upper and lower limit for chromosome number |

`model` |
A text string indicating the model for the simulation. Options are "2010", "ChromTrait", or "PloidEvol" |

The model chosen will determine the correct form of the numeric vector supplied to the pars argument.

If model="2010" the pars vector should be length 5:

chromosome gain

chromosome loss

demipolyploidy

polyploidy

chromosome number at the root of the tree.

If model="ChromPlus" then the numeric vector supplied to pars should be length 12:

chromosome gain in hyperstate 1

chromosome gain in hyperstate 2

chromosome loss in hyperstate 1

chromosome loss in hyperstate 2

demiploidy in hyperstate 1

demiploidy in hyperstate 2

polyploidy in hyperstate 1

polyploidy in hyperstate 2

transition from hyperstate 1 to 2

transition from hyperstate 2 to 1

chromosome number at the root of the tree

hyperstate at the root of the tree (1 or 2)

If model="PloidEvol" then the numeric vector supplied to pars should be length 11:

chromosome gain in diploids

chromosome gain in polyploids

chromosome loss in diploids

chromosome loss in polyploids

demiploidy in diploids

demiploidy in polyploids

polyploidy in diploids

polyploidy in polyploids

rediploidization

chromosome number at the root of the tree.

ploidy level at the root of the tree (0=diploid, 1=polyploid)

a named numeric vector representing chromosome numbers at the tips of the tree is returned for model="2010". For model="chromRate" and model="ploidEvol" a list of length 2 is returned containing the a vector of chromosome numbers for tips of the tree as well as a vector containing the hyperstate or ploidy for each tip.

Heath Blackmon

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coleoguy/chromevolR documentation built on June 10, 2019, 8:07 a.m.

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