A series of R functions that allow users to "Roll back" phylogenies to earlier points of taxonomic knowledge and track a series of metrics, inclidind Pybus and Harvey's Gamma, Tree length, phylogenetic distance (PD) and average new branch lengths, as well as functions that provide frames of tree-growth through time, and model Pybus and Harvey's gamma forward from previous points in taxonomic knowledge.
report the number of newly described taxa per year, or block of years, within a phylogeny
plot the gamma values of rolled back tree. Also includes a simulated gamma for each time slice using the tree of same OTU number with a random set of taxa removed.
(Lineages Through Time Through Time) = create a series of sequential images of LTT plots for a range of years
reate a series of sequential images of trees for a range of years
plot the Phylogenetic distance of taxa described within a specific time-window, PD = total length of distance matrix: PDcorr= PD divided by number of taxa included in the tree: PDcorr2= PD divided by the total pairwise distance of the total tree.
plot the Treelength values of rolled back tree. Also includes a simulated treelength for each time slice using the tree of same OTU numebr with a random set of taxa removed.
plot the average and max min lengths of new Branchlengths between sucessive time slices)
predict the range of gama values of "final tree" run forward from various starting points throughout the taxonomic history
this adds X random tips to a tree n, where X is the differece in taxa between n and n+1
This function randomizes the taxonomic positions, and runs multiple Gammaplot itterations, comparing that to the itterated randomly removed specimens.
Modify branchlength distribution to match a particular value of Gamma
Idenitifies the phylogenetic signal (lambda) of X characters, simulated under Brownian motion, across a tree's taxonomic history.
Idenitifies the evolutioniary rate (mean PIC^2) of X characters, simulated under Brownian motion, across a tree's taxonomic history.