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")

Usage

library(Stubentiger)
simulate_example() # simulate model with example inputs and default parameters
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)

and for fitting/inference run

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