Getting Started with MetaRVM

Introduction

MetaRVM is a comprehensive R package for simulating respiratory virus epidemics using meta-population compartmental models. This vignette describes the basic usage of the package.

Installation

The development version of MetaRVM can be installed from GitHub:

# install.packages("devtools")
devtools::install_github("RESUME-Epi/MetaRVM")

Loading the Package

library(MetaRVM)
library(ggplot2)
options(odin.verbose = FALSE)

Basic Example

This example shows how to run a basic meta-population simulation.

The metaRVM package includes a set of example files in its extdata directory. To run the example, these files must first be located. The system.file() function in R is the recommended way to do this, as it finds the files wherever the package is installed.

# Locate the example YAML configuration file
yaml_file <- system.file("extdata", "example_config.yaml", package = "MetaRVM")
print(yaml_file)
#> [1] "/tmp/RtmppE20dr/Rinst15c6d7215f780c/MetaRVM/extdata/example_config.yaml"

The yaml_file variable now holds the full path to the example configuration file. This file is set up to use the other example data files (also in the extdata directory) with relative paths. Below is the content of the yaml file.

run_id: ExampleRun
population_data:
  initialization: population_init_n24.csv
  vaccination: vaccination_n24.csv
mixing_matrix:
  weekday_day: m_weekday_day.csv
  weekday_night: m_weekday_night.csv
  weekend_day: m_weekend_day.csv
  weekend_night: m_weekend_night.csv
disease_params:
  ts: 0.5
  ve: 0.4
  dv: 180
  dp: 1
  de: 3
  da: 5
  ds: 6
  dh: 8
  dr: 180
  pea: 0.3
  psr: 0.95
  phr: 0.97
simulation_config:
  start_date: 01/01/2023 # m/d/Y
  length: 150
  nsim: 1
  nrep: 1
  simulation_mode: deterministic
  random_seed: 42

For a detailed explanation of all the configuration options, please see the yaml-configuration.html vignette.

Running the Simulation

Once the path to the configuration file is available, the simulation can be run using the metaRVM() function.

# Load the metaRVM library
library(MetaRVM)

# Run the simulation
sim_out <- metaRVM(yaml_file)
#> Loading required namespace: pkgbuild
#> Generating model in c
#> ℹ Re-compiling odin0ddd3654 (debug build)
#> ℹ Loading odin0ddd3654

print(sim_out)
#> MetaRVM Results Object
#> =====================
#> Instances: 1 
#> Populations: 
#> Date range: 2023-10-01 to 2024-02-27 
#> Parameter sets (nsim): 1 
#> Replicates per set (nrep): 1 
#> Simulation mode: deterministic 
#> Total observations: 388800 
#> Disease states: D, E, H, I_all, I_asymp, I_eff, I_presymp, I_symp, P, R, S, S_alloc, S_eff_prod, S_src_int, V, V_alloc, V_src_int, cum_V, mob_pop, n_EI, n_EIpresymp, n_HD, n_HR, n_HRD, n_IasympR, n_IsympH, n_IsympR, n_IsympRH, n_RS, n_SE, n_SE_eff, n_SV, n_VE, n_VS, n_preIsymp, p_HRD, p_RS, p_SE, p_VE
head(sim_out$results)
#>          date    age   race  zone disease_state        value instance
#>        <Date> <char> <char> <int>        <char>        <num>    <int>
#> 1: 2023-10-01   0-17      A    11             D 2.252583e-04        1
#> 2: 2023-10-01   0-17      A    11             E 1.365434e+01        1
#> 3: 2023-10-01   0-17      A    11             H 2.304447e-01        1
#> 4: 2023-10-01   0-17      A    11         I_all 2.742619e+01        1
#> 5: 2023-10-01   0-17      A    11       I_asymp 3.555784e-01        1
#> 6: 2023-10-01   0-17      A    11         I_eff 2.483657e+01        1

For more details on running metaRVM, refer to the running-a-simulation.html vignette.