Stubentiger

(STUdying Balancing Evolution (Nfds) To Investigate GEnome Replacement)

This is an R package to simulate and fit a population genetic model with parameters for vaccination effectiveness, negative frequency-dependent selection (NFDS) and immigration.

Installation

Install Stubentiger's dependencies, odin.dust, dust, and mcstate:

install.packages(
  "odin.dust", "dust", "mcstate",
  repos = c("https://mrc-ide.r-universe.dev", "https://cloud.r-project.org"))

Install devtools, and use it to install Stubentiger from its GitHub repository:

install.packages("devtools")
devtools::install_github("bacpop/Stubentiger")
# if you want to have access to the vignettes, you may want to use
devtools::install_github("bacpop/Stubentiger", build_vignettes = TRUE)

Usage

library(Stubentiger)
simulate_example() # simulate model with example inputs and default parameters and returns GPSC frequencies
simulate_example_serotypes() # simulate model with example inputs and default parameters and returns serotype frequencies
fit_example_to_sim_data() # simulates data and fits model to simulated data, using example inputs and default parameters

To fit to your own data, first follow the steps described in the ProcessDataForModel vignette. Then to simulate run

simulate_model(model_parameters, simulation_steps)

for simulated GPSC frequencies. And

simulate_model_serotypes(model_parameters, simulation_steps)

for simulated serotype frequencies. And for fitting/inference run

fit_model_to_data(data, fixed_parameters, steps_mcmc1 = 10, steps_mcmc2 = 50)