Package index • DiagnoDating

All functions

DiagnoDating: DiagnoDating: diagnostics for dated phylogenies in microbial population genetics

calcLikBranches(): Calculate likelihood of branches

calcResiduals(): Calculate normal residuals of branches

estimAlpha(): Estimation of the coalescent rate alpha

plot(<resDating>): Plotting methods

plotLikBranches(): Plot likelihood of branches

plotResid(): Plot residuals

postdistpvals(): Compute posterior distribution of p-values

ppcheck(): Perform posterior predictive check

print(<resDating>): Print function for resDating objects

resDating(): Constructor for the class resDating

resample(): Resample a dated tree using bactdate

runBactDating(): Date a tree using BactDating

runDating(): Run a dating analysis

runLSD(): Date a tree using LSD

runNodeDating(): Date a tree using node.dating

runTreeDater(): Date a tree using treedater

runTreeTime(): Date a tree using TreeTime

simMaster(): Simulation with structure using Master

simStructure(): Simulation with structure

takeSample(): Extract from BactDating output (r) the tree corresponding to a specific iteration in (w)

testImbalance(): Test to determine whether there are lineages with unbalanced dates For each node, perform a Kruskal-Wallis test for the dates on the left and on the right

testResid(): Test on residuals