fiber.plot: 'fiber.plot' (fibrously) plots a phylogeny
In willpearse/willeerd: Will's Eco-Evo R coDe

Description Usage Arguments Details Value Author(s) Examples

fiber.plot (fibrously) plots a phylogeny

1 2	fiber.plot(tree, gif, slices = NULL, colours = NULL, pca = NULL, clade.mat = NULL, delay = 0.2)

`tree`	a phylogeny (of class phylo) you wish to plot
`gif`	name of GIF you would like to create
`slices`	the time slices you would like to plot out; NULL (default) means one every unit time
`colours`	colours for each speciation event (thus must be same length as 'slices'); NULL (default) uses 'rainbow'
`pca`	PCA (of class prcomp) of phylogenetic dissimilarity matrix; NULL calculates one, I recommend you use the output from a previous run to speed things up
`clade.mat`	clade matrix (of class clade.matrix) of phylogeny; NULL calculates one, I recommend you use the output from a previous run to speed things up
`delay`	the delay between each slice's frame in the output GID; default 0.2 seconds

Probably best to just plot it out and see what happens. There are much smater ways of plotting out what species goes where, but this is what I've done... As with everything I have written, this is very much unchecked! Beware!!!

The data that were plotted last, the PCA and clade.matrix to speed later plots, and the colours used.

Will Pearse

## Not run: 
data(perissodactyla)
output <- fiber.plot(perissodactyla.tree, "test.gif")
fiber.plot(perissodactyla.tree, "test.gif", clade.mat=output$clade.mat, pca=output$pca)
#...that was much quicker (...on bigger phylogenies...), because we used the PCA and clade.matrix from last time

## End(Not run)