treepplr is the R Interface to TreePPL, a probabilistic programming language for phylogenetics.
treepplr converts data to a format readable by TreePPL, reads the TreePPL output, and connects to downstream analyses in model-specific packages, such as the evolnets package for the host repertoire evolution model.
See the package's documentation here. There you will find all package functions under Reference, and basic examples of running various models under Articles.
You can install treepplr like so:
if(!require("devtools", quietly = TRUE)) {
install.packages("devtools")
library(devtools)
} else {
library(devtools)
}
devtools::install_github("treeppl/treepplr")This will only install the R package. The TreePPL compiler will not be downloaded and installed until you run your first analysis, and the TreePPL compiler is called. During the download, you will see a message like this
[xx%] Downloaded xxxxxx bytes...
In subsequent analyses, the TreePPL compiler will be called directly, skipping this step.