PLD_loc_mrca: Location of Most Recent Common Ancestor

In phyloland: Modelling Competitive Exclusion and Limited Dispersal in a Statistical Phylogeographic Framework

Description

Function that returns the posterior distribution of the geographic locations of the Most Recent Common Ancestor of a set of tips. A barplot can be generated.

Usage

PLD_loc_mrca(x, tips, sub_sample = 0, plot_distrib = FALSE, col = NA)

Arguments

x	an object of class "phyloland" generated by a call to PLD_interface.
tips	a vector of character strings specifying the set of tips.
sub_sample	a vector of integers that specifies the indexes of the trees and locations to take into account. Default is 0, all the trees and locations are considered.
plot_distrib	a logical value, if TRUE a barplot is plotted. The default is FALSE.
col	a set of colors for the barplot.

Value

frequencies	matrix with 3 columns containing location latitudes, longitudes and frequencies.
locationsMRCA	vector containing all the sub_sample sampled locations for the tips Most Recent Common Ancestor.

Examples

data(Banza)
locations = PLD_loc_mrca(x = Banza, tips = Banza$tips, sub_sample = 100:200, plot_distrib = TRUE)
locations$frequencies

phyloland documentation built on May 2, 2019, 6:46 a.m.