tests/testthat/test-SHLITR_risk_ode.R

In idmodelr: Infectious Disease Model Library and Utilities

context("SHLITR_risk_ode")



## initialise
inits <- c(
  # General population
  S = 800,
  H = 0,
  L = 0,
  I = 0,
  Tr = 0,
  R = 0,
  ## High risk population
  S_H = 199,
  H_H = 0,
  L_H = 0,
  I_H = 1,
  Tr_H = 0,
  R_H = 0
)

parameters <- c(
  beta = 3, # Rate of transmission
  beta_H = 6, # High risk rate of transmission
  gamma_H = 1/5, # Rate of progression to active symptoms from high risk latent
  nu = 1/2, #Rate of progression from high to low risk latent
  gamma_L = 1/100, # Rate of progression to active symptoms for low risk latent
  epsilon = 1/3, # Rate of treatment
  tau = 1/2, # Rate of recovery
  p = 0.2, # proportion of new births that are high risk
  M = 0.2 # Between group mixing
)

test <- SHLITR_risk_ode(1, inits, parameters)


test_that("SHLITR_risk_ode can correctly return rates of change over one timestep", {
  skip_on_cran()
  expect_known_output(test, file = "../../tests/test-files/SHLITR_risk_ode/test-01.rds")
})