Host repertoire model example

library(treepplr)
library(ggplot2)
library(magrittr)
library(dplyr)
library(ape)

if(!require("evolnets", quietly = TRUE)) {
 library(devtools)
 if (!require("BiocManager", quietly = TRUE))
   install.packages("BiocManager")
 library(BiocManager)
 BiocManager::install("ggtree")
 devtools::install_github("maribraga/evolnets")
 library(ggtree)
 library(evolnets)
} else {
 library(evolnets)
}

This is a very simplified workflow in treepplr for analysis of host repertoire evolution. The data used here is simulated and the inference is too simple. A real analysis would include many other steps such as testing of different inference methods and check of convergence.

The purpose of this vignette is to show how to run TreePPL with treepplr, and how to process the output with evolnets.

Load model and data files

Load the 3-state host repertoire model and example data available within treepplr.

model <- tp_model("hostrep3states")
data <- tp_data("hostrep3states")

Load model and data files

Run treeppl