tests/testthat/test-EpiInvert.R

In EpiInvert: Variational Techniques in Epidemiology

test_that("EpiInvert", {
  library(dplyr)
  data("incidence")
  data("festives")
  data("si_distr_data")
  
  # test EpiInvert using parametric serial interval 
  res <- EpiInvert(incidence$USA,
                   incidence$date[length(incidence$date)],
                   festives$USA
                   )
  x <- round(res$power_a+0.003,digits=2)
  expect_equal(x, 1.1)
  
  # test EpiInvert using non parametric serial interval 
  res <- EpiInvert(incidence$USA,
                   incidence$date[length(incidence$date)],
                   festives$USA,
                   EpiInvert::select_params(list(si_distr = si_distr_data,shift_si_distr=1)))
  x <- round(res$power_a+0.004,digits=2)
  expect_equal(x, 1.09)
  
  # test without using festive days
  res <- EpiInvert(
    incidence$USA,
    incidence$date[length(incidence$date)]
    )
  x <- round(res$power_a+0.007,digits=2)
  expect_equal(x, 1.07)
  
  # test EpiInvert using a different time interval 
  res <-  EpiInvert(incidence$USA,
                    incidence$date[length(incidence$date)],
                    festives$USA, 
                    EpiInvert::select_params(list(max_time_interval = 100))
                    )
  x <- round(res$power_a-0.005,digits=2)
  expect_equal(x, 0.59)
  
  # test EpiInvert using a different parametric serial interval 
  res <-  EpiInvert(incidence$USA,
                    incidence$date[length(incidence$date)],
                    festives$USA, 
                    
                    EpiInvert::select_params(list( mean_si = 11,sd_si=7,shift_si=-2))
                    )
  x <- round(res$power_a-0.003,digits=2)
  expect_equal(x,1.03)
  
  # test EpiInvert using different regularization values
  res <-  EpiInvert(incidence$USA,
                    incidence$date[length(incidence$date)],
                    festives$USA, 
                    EpiInvert::select_params(list( Rt_regularization_weight=10,seasonality_regularization_weight=20)))
  x <- round(res$power_a-0.003,digits=2)
  expect_equal(x,1.05)
  
  # test EpiInvert using weekly aggregated incidence 
  data(incidence_weekly_aggregated)
  res <- EpiInvert(incidence_weekly_aggregated$FRA,"2022-05-05",festives$FRA,
                    select_params(list(incidence_weekly_aggregated = TRUE)))
  x <- round(res$power_a-0.049315,digits=1)
  expect_equal(x,1.2)
  
  # test EpiInvertForecast
  data("restored_incidence_database")
  forecast <-  EpiInvertForecast(res,restored_incidence_database)
  x <- round(forecast$i_restored_forecast[1]/100-0.5,digits=0)
  expect_equal(x,359)
  
  # test EpiIndicators
  data("owid")
  sel <- dplyr::filter(owid,iso_code=="FRA")
  df<-data.frame(sel$date,sel$new_cases_restored_EpiInvert,sel$new_deaths_restored_EpiInvert)
  res <- EpiIndicators(df)
  x <- round(res$r[1]*10000-0.0588,digits=0)
  expect_equal(x,374)
})