All functions

b

Regression slope of recipient on donor values in an epidemic simulated with
the toyepidemic Rpackage. 
boxplot

A boxplot 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

Broadsense 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 sourcerecipient 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 PPcall in a data.table 