startingpt.mecca: starting values for MECCA

In geiger: Analysis of Evolutionary Diversification

starting values for MECCA

Description

This function takes the output of calibrateMecca along with observed data and partial least squares loadings and outputs starting values and tuning parameters for the ABC-MCMC (Wegmann et al. 2009).

Usage

startingpt.mecca(calibrationOutput, phy, cladeMean, cladeVariance,
                 tolerance = 0.01, plsComponents, BoxCox = TRUE)

Arguments

calibrationOutput	The output from calibrateMecca
phy	A time calibrated phylogeny in "phylo" format
cladeMean	A named vector of trait means. All tips in the tree must be represented
cladeVariance	A names vector of trait variances. All tips in the tree must be represented. If only one taxon is present, use 0 for the variance
tolerance	The proportion of calibrations simulations that fall closest to the oberved data that will be retained to compute MECCA tuning parameters
plsComponents	a matrix of Partial Least Squares component loadings
BoxCox	Logical - Should Summary Statistics be Box-Cox transformed? Default is yes and is recommended

Details

You will need to compute PLS loadings using the package "pls" prior to running this function. MECCA performs extremely poorly if summaries are not PLS transformed. If Bayes Factors are to be computed to perform model selection (Leuenberger and Wegmann 2010), raw summaries will need to be used in the post-sampling adjustment step. However, PLS transformed summaries can still be used in the acceptance/rejection step of the MCMC and can also be used to determine which simulations to retain

Value

$tuning	a matrix containing starting values and proposal widths for trait evolution parameters
$startingBirth	Starting value for speciation
$startingDeath	Starting value for extinction
$dcrit	the criticial distance - simulated data must fall within this distance of the observed data in order to be accepted
$obsTraits	the observed data
$plsObserved	Partial Least Squared transformed observed data
$plsLoadings	Partial Least Squared componenent loadings - these are used to transform data during the MCMC

Author(s)

Graham Slater, Luke Harmon, Daniel Wegman

References

Slater GJ, Harmon LJ, Wegmann D, Joyce P, Revell LJ, Alfaro ME. in press Evolution, Leuenberger C, and Wegmann D. 2010. Genetics 184: 243-252., Wegmann D, Leuenberger C, Excoffier L. 2009. Genetics 182: 1207-1218.

Examples

example(mecca)

geiger documentation built on April 4, 2023, 1:07 a.m.