Rapid Calculation of Phylogenetic Information Content

Documentation for package ‘PhyInformR’ version 1.0

allmodel.signal.noise	A function to compute results of QIRP, QIHP, and QIPP accomodating uneven branch lengths and user defined substitution models or base frequency distributions
Approximator	Quantify Quartet Resolution Probabilities Using 2012 Formulation
cluster.signal.noise	Quantify Quartet Resolution Probabilities Using 2012 Formulation and MCMC approach
defined.multi.profile	A function to plot phylogenetic informativeness profiles based on site rate cutoffs by partition
informativeness.profile	A function to plot phylogenetic informativeness profiles
multi.profile	A function to plot phylogenetic informativeness profiles based on site rate cutoffs by rate
parallel.cluster.signal.noise	Quantify Quartet Resolution Probabilities Using 2012 Formulation and MCMC approach in parallel
Plot.Another.TreeSI	A function to visualize QIRP of additional data across a tree topology
plotPosterior	A function to visualize outputs of QIRP, QIHP, and QIPP computed across a distribution of trees
PlotTreeSI	A funtion to visualize QIRP across a tree topology
prumetalrates	Rates for prumetal dataset
rag1	Rates rag1 dataset
sample.rates	Simulated rates
sample.tree	Sample tree
sample.tree2	Another Sample tree
space.maker	Core Function required to assemble heatmaps of QIRP as in Prum et al. 2015
space.maker.narrow	Core Function required to assemble more fine-scale heatmaps of QIRP as in Prum et al. 2015
su.bayes	A function to compute results of QIRP, QIHP, and QIPP across a posterior distribution of trees