All functions
b	Regression slope of recipient on donor values in an epidemic simulated with the toyepidemic R-package.
boxplot	A box-plot of phenotypic distances against phylogenetic distances from a PP analysis
boxplotTraitAlongTree	Box plots of trait values along a tree
chld	Node indices of the direct descendants of n in the phylogeny tree.
corrProfile	Generate a correlation profile for a given tree and data at the tips
cutUltrametric	Cut a tree to the largest ultrametric subtree not exceeding maxNTips tips
edgesFrom	Edge indices of the edges in tree starting from n
estimateH2	Estimate the heritability of a continuous trait in a phylogenetically linked population.
extendTipEdges	Make the ending edges of a tree longer/shorter by addLength
extractPP	Extract phylogenetic pairs from a phylogeny, i.e. mutually closest pairs from a distance matrix.
extractTipPairs	Extract tip pairs from a phylogeny.
groupByRootDist	Group tips according to distance from the root
infectionCouples	Infection couples given a tree and ids of all tips and nodes
nodeTimes	Calculate the time from the root to each node of the tree
plot	A basic ggplot of a PP analysis
plot	Plot the summary of a PP analysis
plotCorrProfile	Plot a correlation profile
PP	Perform phylogenetic pair analysis
R2adj	Broad-sense heritability of a pathogen trait
rA	Estimating intraclass correlation (ICC) through ANOVA
rAboot	Bootstrap ANOVA
sampleCorrsPairs	Sample from the distribution of Pearson correlation indices between possible source-recipient couples given an infectious tree.
sampleNodeIds	One (out of many possible) identifications of the nodes and root with tips in the tree.
sampleTransmissionPairs	get a sample list of possible transmission pair assignments
scatterPlotPPs	Scatter plot of phylogenetic pairs
summary	Summarize the estimates from a call to estimateH2
summary	Summarize the results of a PP-call in a data.table