Create Muller Plots of Evolutionary Dynamics
Modify a dataframe to enable plotting of populations instead of freque...
Add a row to the edges list to represent the root node (if not already...
Add rows to a population dataframe to ensure genotype starting points ...
Create a tree object of class "phylo" from an adjacency matrix
Add branches of length zero to get rid of single nodes in an adjacency...
Move to top of adjacency matrix
Get adjacency list of a tree.
Extract an adjacency matrix from a larger data frame
Create a data frame from which to create a Muller plot
Extract population data from a larger data frame
Move to daughter in adjacency matrix
Move to sibling in adjacency matrix
Move to parent in adjacency matrix
Draw a Muller plot of frequencies using ggplot2
Draw a Muller plot of population sizes using ggplot2
Faster way to record a path through all nodes of an adjacency matrix
Record a path through all nodes of an adjacency matrix
Reorder a Muller plot dataframe by a vector
Create plots that combine a phylogeny and frequency dynamics. Phylogenetic input can be a generic adjacency matrix or a tree of class "phylo". Inspired by similar plots in publications of the labs of RE Lenski and JE Barrick. Named for HJ Muller (who popularised such plots) and H Wickham (whose code this package exploits).