Description Usage Arguments Value Author(s) References See Also Examples

View source: R/transformPhylo.sim.R

Simulates trait data on a tree using a specified model of evolution (see details).

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | ```
transformPhylo.sim(
phy,
n = 1,
x = NULL,
model = NULL,
returnNodes = FALSE,
kappa = NULL,
lambda = NULL,
delta = NULL,
alpha = NULL,
psi = NULL,
acdcRate = NULL,
lambda.sp = NULL,
trend = NULL,
trend.anc.state = 0,
nodeIDs = NULL,
rateType = NULL,
cladeRates = NULL,
branchRates = NULL,
rate = NULL,
group.means = NULL,
splitTime = NULL,
timeRates = NULL,
branchLabels = NULL,
rate.var = NULL,
mode.order = NULL
)
``` |

`phy` |
An object of class |

`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). |

`returnNodes` |
Logical. If TRUE, alongside the tip values all node values are returned corresponding to APE's edge.matrix for the tree. |

`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 |

`trend` |
value of the expectation mean change through time |

`trend.anc.state` |
the expected ancestal state for the trend model (default is 0) |

`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 or logical to indicate scalar is included in the 'modeslice' model (the scalar is included in the mode.param argument with the 'modeslice' model). |

`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. |

`rate.var` |
Allows rate variation in BM modes in the 'modeslice' model |

`mode.order` |
The order of modes for the 'modeslice' model. Any combination of 'BM', 'OU', 'acdc', and 'kappa' |

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

`transformPhylo.ML`

, `transformPhylo.ll`

, `transformPhylo`

, `transformPhylo.MCMC`

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))
``` |

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