rootToTipRegressionPlot: Plot evolutionary distance from root to sample times and...

In treedater: Fast Molecular Clock Dating of Phylogenetic Trees with Rate Variation

Description

If a range of sample times was given, these will be estimated. Red and black respectively indicate sample and internal nodes. This function will print statistics computed from the linear regression model.

Usage

rootToTipRegressionPlot(td, show.tip.labels = FALSE, textopts = NULL,
  pointopts = NULL, ...)

Arguments

td	A fitted treedater object
show.tip.labels	If TRUE, the names of each sample will be plotted at the their corresponding time and evoutionary distance
textopts	An optional list of parameters for plotted tip labels. Passed to the *text* function.
pointopts	An optional list of parameters for plotted points if showing tip labels. Passed to the *points* function.
...	Additional arguments are passed to plot

Value

The fitted linear model (class 'lm')

Examples

## simulate a random tree and sample times for demonstration
# make a random tree:
tre <- ape::rtree(50)
# sample times based on distance from root to tip:
sts <- setNames( ape::node.depth.edgelength( tre )[1:ape::Ntip(tre)], tre$tip.label)
# modify edge length to represent evolutionary distance with rate 1e-3:
tre$edge.length <- tre$edge.length * 1e-3
# treedater: 
td <- dater( tre, sts =sts, clock='strict', s = 1000, omega0=.0015 )
# root to tip regression: 
fit = rootToTipRegressionPlot( td )
summary(fit)

treedater documentation built on Jan. 27, 2020, 1:06 a.m.