## 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