| nodeDist {windex} | R Documentation |
Plotting and/or retrieving distribution of divergence times of a pair of species from a set of phylogenetic trees.
Description
Plots and/or retrieves the distribution of age estimates of the most recent common ancestor of a specified pair of species across trees (for instance a posterior distribution).
Usage
nodeDist(trees,sp1,sp2,relTime=F,fillcol="blue",xlabel="Age (mya)",main="",
return.ages=F,plot=T,add=F,...)
Arguments
trees |
An object of class multiPhylo containing a set of time-calibrated trees. |
sp1 |
Name of one of the two species for which the divergence time is of interest. |
sp2 |
Name of the other of the two species for which the divergence time is of interest. |
relTime |
Logical whether to plot relative (to age of root) divergence times or absolute times (defaults to absolute times). |
fillcol |
Colour to plot distribution. |
xlabel |
Label for the x-axis. |
main |
Title for plot (if desired, defaults to no title). |
return.ages |
Logical whether to return a vector of the relative (to age of root) divergence times or absolute times (defaults to FALSE, i.e. only plotting the distribution). |
plot |
Logical whether to plot distribution of divergence times, either absolute or relative as controlled by relTime argument (defaults to TRUE). |
add |
Logical whether to overlay distribution on an existing plot (make sure xlim and ylim on original call are set to accomodate both distributions). |
... |
Additional arguments to customise output, passed to plot. |
Value
Density plot of the distribution of relative or absolute divergence times across trees for the specified pair of species, and/or a vector of those divergence times.
Author(s)
Kevin Arbuckle
Examples
## Not run:
# Density plot of absolute divergence times
nodeDist(trees,"Naja_haje","Naja_nivea")
# Density plot of relative divergence times (root age for each tree set to 1)
nodeDist(trees,"Naja_haje","Naja_nivea",relTime=T,xlabel="Relative time")
## End(Not run)