Description Usage Arguments Value Author(s) References Examples

View source: R/transformPhylo.sim.R

Simulates continuous trait data under a range of evolutionary models

1 |

`phy` |
An object of class "phylo" (see ape package). |

`n` |
Number of simulations |

`x` |
Vector, matrix or data.frame (with taxon names as names or rownames) of categories for each species. Only applicable if model="mixedRate" |

`model` |
The model of trait evolution (see details). |

`kappa` |
Value of kappa transform. |

`lambda` |
Value of lambda transform. |

`delta` |
Value of delta transform. |

`alpha` |
Value of alpha (OU) transform. |

`psi` |
Value of psi transform. |

`nodeIDs` |
Integer - ancestral nodes of clades. |

`rateType` |
If rate is to be inferred on single branches leading to clades then rateType="branches". If rate is inferred for whole clade, rateType="clade" |

`branchRates` |
Numeric vector specifying relative rates for individual branches. |

`cladeRates` |
Numeric vector specifying relative rates for clades. |

`rate` |
a vector of relative rate parameters. The length of the vector is equal to the number of rates being estimated. |

`group.means` |
a vector of the relative difference in means between rate categories, expressed as a scalar applied to the expected standard deviation (see Ricklefs 2006) |

Returns a matrix of simulated dated with taxon names as rownames (number of columns=n).

Gavin Thomas

Ricklefs RE. 2006. Time, species, and the generation of trait variation in clades. Systematic Biology 55, 151-159.

Thomas GH, Meiri S, & Phillimore AB. 2009. Body size diversification in Anolis: novel environments and island effects. Evolution 63, 2017-2030.

1 2 3 4 5 6 7 8 9 10 | ```
data(anolis.tree)
data(anolis.data)
# Simulate 10 sets of data with kappa=0.1 using the anolis tree
sim.dat1 <- transformPhylo.sim(phy=anolis.tree, n=10, model="kappa", kappa=0.1)
# Simulate 10 sets of data where rates and means differ between to the categories defined by "x"
x <- anolis.data$geo_ecomorph
names(x) <- rownames(anolis.data)
sim.dat2 <- transformPhylo.sim(phy=anolis.tree, n=10, x=x, model="mixedRate", rate=c(1,1,2,4), group.means=c(0,5,0,0))
``` |

ghthomas/motmot documentation built on July 31, 2018, 12:11 a.m.

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