--- a
+++ b/tests/testthat/test_data.R
@@ -0,0 +1,161 @@
+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")
+
+  }
+
+})
+
+
+