Description Usage Arguments Value Author(s) References Examples

View source: R/transformPhylo.sim.R

Transforms the branch lengths of a phylo object according to a model of trait evolution (see details).

1 2 3 4 5 6 | ```
transformPhylo.sim(phy, n = 1, x = NULL, model = NULL, kappa = NULL,
lambda = NULL, delta = NULL, alpha = NULL, psi = NULL,
acdcRate = NULL, lambda.sp = NULL, nodeIDs = NULL, rateType = NULL,
cladeRates = NULL, branchRates = NULL, rate = NULL,
group.means = NULL, splitTime = NULL, timeRates = NULL,
branchLabels = NULL)
``` |

`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. Note that 'original nodes' from the full phylogeny can be included as an element on the phylogeny (e.g., phy$orig.node) as well as estimates of 'hidden' speciation (e.g., phy$hidden.speciation) if estimates of extinction (mu) are > 0. |

`acdcRate` |
Value of ACDC transform. |

`lambda.sp` |
Estimate of speciation (lambda) for the psi models |

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

`rateType` |
If model="clade", a vector specifying if rate shift occurs in a clade ("clade") or on the single branch leading to a clade ("branch"). |

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

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

`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) |

`splitTime` |
A split time (measured from the present, or most recent species) at which a shift in the rate occurs for the "timeSlice" model |

`timeRates` |
The rates (from ancient to recent) for the timeSlice model |

`branchLabels` |
Branches on which different psi parameters are estimated in the "multipsi" model. |

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

Gavin Thomas, Mark Puttick

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

Ricklefs RE. 2006. 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 11 | ```
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))
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.