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Analysis of HBV data

Xavier Didelot

2026-01-21

Source: vignettes/HBV.Rmd
HBV.Rmd

Loading the data

In this vignette we demonstrate the usage of DiagnoDating on a dataset of Hepatitis B virus (HBV) published by Zoe Patterson Ross et al (2018). The data for this example can be loaded using the command data(HBV). This will load in your environment the object phy which is the phylogeny constructed using PhyML. To perform dating, we also need to know the dates of the samples. This is stored in labels of the tips of the phylogeny, and can be extracted as follows:

library(DiagnoDating,quietly=T)
set.seed(1)
data(HBV)
dates=as.numeric(gsub(".*_","",phy$tip.label))
names(dates)=phy$tip.label

Dating analysis

Let us perform a dating analysis using BactDating and the additive relaxed clock model (ARC):

r=runDating(unroot(phy),dates,model='arc')
print(r)
## Result from BactDating, model arc, clock rate 0.29, relaxation parameter 27.75, root date 1158.83

Diagnostics of the dating analysis

The posterior predictive check is not satisfied:

ppcheck(r,showPlot = T,showProgress = F)

## [1] 0.008

The residual analysis is also not satisfied:

ps=postdistpvals(r,showPlot = T)

## The posterior distribution of p-values has median 0.00 and 99.70% of values below 5%