tests/testthat/test_simulation.R

In Mamie/PILAF: PILAF: Phylodynamics InfLuenzA Forecast

context("Test simulation of coalescent, sampling, ILI counts")

library(PILAF)

# test_that("Simulation code and forecasting runs", {
#   n = 10
#   lim = c(0, 100)
#   flu.Ne = PILAF:::YearlyLogisticTraj
#   flu.sampNum = 100
#   ILI.sampNum = 1000
#   sim.data = PILAF::SimulateILISampCoalCountsN(n, lim, flu.Ne, flu.sampNum, ILI.sampNum)
#   plot(sim.data)
#   train.time = seq(0, 90)
#   test.time = seq(91, 100)
#   sim.train = sim.data[sim.data$time %in% train.time,]
#   sim.test = sim.data[!sim.data$time %in% train.time,]
#   sim.fitted = forecast(sim.train, test.time)
#   AE = evaluate(sim.fitted, sim.test)
#   # plot(sim.fitted, sim.train)
#   expect_equal_to_reference(sim.fitted, "test_simulation.rds")
# })
#
# test_that("A single simulation iteration does not give NA in ILI", {
#   n = 1
#   lim = c(0, 100)
#   flu.Ne = PILAF:::YearlyLogisticTraj
#   flu.sampNum = 100
#   ILI.sampNum = 1000
#   sim.data = PILAF::SimulateILISampCoalCounts(lim, flu.Ne, flu.sampNum, ILI.sampNum)
# })