tests/testthat/test_find_imports.R

In reconhub/outbreaker2: Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

context("Test detection of imported cases")

## test various movements  ##
test_that("Test detection of imported cases", {
    ## skip on CRAN
    skip_on_cran()


    ## generate inputs
    data(fake_outbreak)
    data <- with(fake_outbreak,
                 outbreaker_data(dates = onset,
                                 w_dens = w,
                                 ctd = ctd,
                                 dna = dna))
    config <- create_config(data = data)
    data <- add_convolutions(data = data, config = config)
    temp <- create_param(data = data, config = config)
    param_current <- temp$current
    param_store <- temp$store

    ll <- custom_likelihoods()
    priors <- custom_priors()
    moves <- custom_moves()

    moves <- bind_moves(moves = moves,
                        config = config,
                        data = data,
                        likelihoods = ll,
                        priors = priors)

    ## detect imported cases
    out <- outbreaker_find_imports(moves = moves, data = data,
                                   param_current = param_current,
                                   param_store = param_store,
                                   config = config,
                                   likelihoods = ll)

    ## tests ##
    expect_identical(which(!out$config$move_alpha), which(!out$config$move_kappa))
    expect_identical(out$param_store$alpha[[1]], out$param_current$alpha)
    expect_identical(out$param_store$kappa[[1]], out$param_current$kappa)
    expect_equal(which(is.na(out$param_current$alpha)), c(1,4,28))
    expect_true(all(config$move_alpha==!is.na(param_current$alpha)))

})