transformPhylo: Phylogenetic tree transformations

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

Description

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

Usage

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transformPhylo(
  phy,
  model = NULL,
  y = NULL,
  meserr = NULL,
  kappa = NULL,
  lambda = NULL,
  delta = NULL,
  alpha = NULL,
  psi = NULL,
  lambda.sp = NULL,
  nodeIDs = NULL,
  rateType = NULL,
  branchRates = NULL,
  cladeRates = NULL,
  splitTime = NULL,
  timeRates = NULL,
  acdcRate = NULL,
  branchLabels = NULL,
  cophenetic.dist = NULL,
  vcv.matrix = NULL,
  mode.order = NULL,
  mode.param = NULL,
  rate.var = NULL
)

Arguments

phy

An object of class phylo (see ape).

model

The model of trait evolution (see details).

y

A matrix of trait values.

meserr

A vector (or matrix) of measurement error for each tip. This is only applicable to univariate analyses. Largely untested - please use cautiously

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.

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").

branchRates

Numeric vector specifying relative rates for individual branches

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).

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

acdcRate

Value of ACDC transform.

branchLabels

A vector of length equal to the number of internal branches, signifying the which "multiPsi" class it belongs to

cophenetic.dist

a cophenetic distance matrix showing the absolute distance between taxa - only applicable for OU models run on non-ultrmetric trees. If null will be calculated internally, but supplying the data can speed up run time

vcv.matrix

a variance-covariance matrix - only applicable for OU models run on non-ultrmetric trees. If null will be calculated internally, but supplying the data can speed up run time

mode.order

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

mode.param

Parameters for the modes of evoluton in the 'modeslice' model

rate.var

Allows rate variation in BM modes in the 'modeslice' model

Details

Transforms the branch lengths of a phylo object according to one of the following models:

Value

phy A phylo object with branch lengths scaled according to the given model and parameters

Author(s)

Gavin Thomas, Mark Puttick

References

Ingram T. 2011. Speciation along a depth gradient in a marine adaptive radiation. Proc. Roy. Soc. B. 278, 613-618.

Ingram T, Harrison AD, Mahler L, Castaneda MdR, Glor RE, Herrel A, Stuart YE, and Losos JB. Comparative tests of the role of dewlap size in Anolis lizard speciation. Proc. Roy. Soc. B. 283, 20162199.

Mooers AO, Vamosi S, & Schluter D. 1999. Using phylogenies to test macroevolutionary models of trait evolution: sexual selection and speciation in Cranes (Gruinae). American Naturalist 154, 249-259.

O'Meara BC, Ane C, Sanderson MJ & Wainwright PC. 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution 60, 922-933

Pagel M. 1997. Inferring evolutionary processes from phylogenies. Zoologica Scripta 26, 331-348.

Pagel M. 1999 Inferring the historical patterns of biological evolution. Nature 401, 877-884.

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

See Also

transformPhylo.ML, transformPhylo.ll, transformPhylo.MCMC

Examples

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data(anolis.tree)
anolis.treeDelta <- transformPhylo(phy=anolis.tree, model="delta", delta=0.5)

PuttickMacroevolution/motmot documentation built on June 5, 2020, 7 p.m.