The goal of BactDating is to perform Bayesian dating of the nodes of a bacterial phylogenetic tree. This typically involves simultaneous Bayesian estimation of the molecular clock rate and coalescent rate. Additional features include inference of root location, lost sampling dates and different evolutionary models.
You can install BactDating from github with:
devtools::install_github("xavierdidelot/BactDating")The package can then be loaded using:
library(BactDating)This is a basic example of usage. First we generate a coalescent tree with a single leaf per year between 1990 and 2010:
tree=simcoaltree(1990:2010)
plot(tree)
ape::axisPhylo(backward=F)
Next we generate an observed phylogeny based on this timed tree, and perform a root-to-tip analysis:
obsphy=simobsphy(tree)
r=roottotip(obsphy,1990:2010)
We can run the dating analysis on this phylogeny as follows:
res=bactdate(obsphy,1990:2010)
plot(res,'treeCI')
For more detailed examples of how to use BactDating, see the vignettes
here.
See also the help included in the package using the R command
help(package='BactDating').
If you have any problem or question please create an issue
here or get in
touch by emailing xavier.didelot@gmail.com