context("Test outbreaker data and settings")

## test data ##

test_that("test: data are processed fine", {

  ## skip on CRAN

  skip_on_cran()

  ## get data

  x <- fake_outbreak

  out <- outbreaker_data(dates = x$onset, dna = x$dna, w_dens = x$w)

  out_nodna <- outbreaker_data(dates = x$onset, w_dens = x$w)

  ## check output

  expect_is(out, "list")

  expect_is(out$D, "matrix")

  expect_equal(out$max_range, 11)

  expect_equal(out_nodna$L, 0)

  expect_equal(out$L, 1e4)

  expect_equal(out$w_dens, out$f_dens)

  expect_equal(out$log_w_dens[1,], out$log_f_dens)

  expect_error(outbreaker_data(dates = 1, w_dens = c(0,-1)),

               "w_dens has negative entries")

  expect_error(outbreaker_data(dates = 1, w_dens = c(0,1), f_dens = c(0,-1)),

               "f_dens has negative entries")

  wrong_lab_dna <- x$dna

  rownames(wrong_lab_dna) <- paste0("host_", seq_len(nrow(wrong_lab_dna)))

  expect_error(outbreaker_data(dates = x$onset, dna = wrong_lab_dna, w_dens = x$w),

               "DNA sequence labels don't match case ids")

})

test_that("outbreaker_data accepts epicontacts and case labelling", {

  ## skip on CRAN

  skip_on_cran()

  ## outbreaker time, ctd, no DNA ##

  ## analysis

  set.seed(1)

  ## get data

  x <- fake_outbreak

  ids_char <- replicate(length(fake_outbreak$sample),

                        paste(sample(letters, 5, TRUE), collapse = ""))

  ids_num <- sample.int(1000, length(fake_outbreak$sample), FALSE)

  ## check for character and numeric ids

  for(ids in list(ids_char, ids_num)) {

    ## make epi_contacts object

    tTree <- data.frame(i = ids[x$ances],

                        j = ids[1:length(x$ances)])

    ctd <- sim_ctd(tTree, eps = 0.9, lambda = 0.1)

    epi_c <- suppressWarnings(epicontacts::make_epicontacts(linelist = data.frame(id = ids),

                                                            contacts = ctd,

                                                            directed = TRUE))

    data <- outbreaker_data(dates = x$onset,

                            dna = x$dna,

                            ctd = epi_c,

                            w_dens = x$w)

    ## test recursiveness

    data <- outbreaker_data(data = data)

    ## check correct contacts are labelled as 1 in matrix

    ctd_ind <- apply(ctd, 2, match, ids)

    expect_equal(rep(1, nrow(ctd)), data$contacts[ctd_ind[,c(2, 1)]])

    expect_equal(rep(0, nrow(ctd)), data$contacts[ctd_ind])

    ## check directionality is being passed

    config <- create_config(data = data)

    ## check ids are carried through

    expect_equal(data$ids, epi_c$linelist$id)

    ## make sure directionality is carried through

    expect_true(config$ctd_directed)

    ## case labelling via dates

    dates <- x$onset

    names(dates) <- ids

    data <- outbreaker_data(dates = dates,

                            dna = x$dna,

                            ctd = ctd,

                            w_dens = x$w)

    ## test recursiveness

    data <- outbreaker_data(data = data)

    ## check direcionality working

    config <- create_config(ctd_directed = TRUE,

                            data = data)

    ## check contact numbers are being updated

    data <- add_convolutions(data, config)

    ## check ids are carried through

    expect_equal(data$ids, as.character(ids))

    ## make sure directionality is carried through

    expect_true(config$ctd_directed)

    ## check the number of contacts are correct

    expect_equal(nrow(ctd), sum(data$contacts))

    ## toggle directionality

    data <- outbreaker_data(dates = dates,

                            dna = x$dna,

                            ctd = ctd,

                            w_dens = x$w)

    data <- outbreaker_data(data = data)

    config <- create_config(ctd_directed = FALSE)

    data <- add_convolutions(data, config)

    ## check the number of contacts are correct

    expect_equal(2*nrow(ctd), sum(data$contacts))

    ## check correct contacts are labelled as 1 in matrix

    ctd_ind <- apply(ctd, 2, match, ids)

    ctd_ind <- rbind(ctd_ind, ctd_ind[,c(2, 1)])

    expect_equal(rep(1, 2*nrow(ctd)), data$contacts[ctd_ind])

    ## make sure directionality is carried through

    expect_false(config$ctd_directed)

    ## identify non-matching labels

    wrong_dna <- x$dna

    rownames(wrong_dna) <- 1:length(x$onset)

    expect_error(data <- outbreaker_data(dates = dates,

                                         dna = wrong_dna,

                                         ctd = ctd,

                                         w_dens = x$w,

                                         ctd_directed = TRUE),

                 "DNA sequence labels don't match case ids")

  }

})