tests/testthat/test-make_flocker_data.R

In jsocolar/flocker: Flexible Occupancy Estimation with Stan

test_that("make_flocker_data works correctly", {
  example_data <- simulate_flocker_data()
  obs <- example_data$obs
  unit_covs <- example_data$unit_covs
  event_covs <- example_data$event_covs
  
  fd <- make_flocker_data(obs, unit_covs, event_covs)
  expect_equal(fd$type, "single")
  expect_equal(class(fd), c("list", "flocker_data"))
  expect_equal(names(fd), c("data", "n_rep", "type", "unit_covs", "event_covs"))
  expect_true(
    all(fd$data[1:1500, c("ff_rep_index1", "ff_rep_index2", 
                          "ff_rep_index3", "ff_rep_index4")] == 
          matrix(1:6000, ncol = 4))
    )  
  expect_equal(names(fd$data), c("ff_y", "uc1", "species", "ec1",
                                 "ff_n_unit", "ff_n_rep", "ff_Q", "ff_unit", "ff_rep_index1", 
                                 "ff_rep_index2", "ff_rep_index3", "ff_rep_index4"))
  expect_true(all(fd$data$y %in% c(0,1,-99)))
  
  event_covs[[1]] <- matrix(1:6000, ncol = 4)
  fd <- make_flocker_data(obs, unit_covs, event_covs)
  expect_equal(fd$data$ec1, 1:6000)
  
  
  obs[2,4] <- NA
  fd <- make_flocker_data(obs, unit_covs, event_covs)
  expect_equal(
    sum(fd$data[1:1500, c("ff_rep_index1", "ff_rep_index2", "ff_rep_index3")] - 
          matrix(1:4500, ncol = 3)), 0)
  expect_equal(fd$data$ff_rep_index4[1:1500], c(4501, -99, 4502:5999))
  expect_true(all(fd$data$ff_y %in% c(0,1)))
  expect_equal(fd$data$ec1[1:4500], 1:4500)
  expect_equal(fd$data$ec1[4501:5999], c(4501, 4503:6000))
  
  obs[,4] <- NA
  expect_error(fd <- make_flocker_data(obs),
                 "The final column of obs contains only NAs.")
  
  obs <- array(obs, dim = c(nrow(obs), ncol(obs), 1))
  expect_error(fd <- make_flocker_data(obs), 
               "in a single-season model, obs must have exactly two dimensions")
  obs <- rep(1, 3000)
  expect_error(fd <- make_flocker_data(obs), 
               "in a single-season model, obs must have exactly two dimensions")
  obs <- matrix(rep(1, 3000), ncol=1)
  expect_error(fd <- make_flocker_data(obs), 
               "obs must contain at least two columns.")
  obs <- example_data$obs
  obs[1,1] <- 2
  expect_error(fd <- make_flocker_data(obs))
  obs[1,1] <- NA
  expect_error(fd <- make_flocker_data(obs), 
               "obs has NAs in its first column")
  obs[1,1] <- 1
  obs[1,2] <- NA
  expect_error(fd <- make_flocker_data(obs), 
               "Some rows of obs have non-trailing NAs")

  # Still need to add checks for the rest of the error messages, and for proper error messages using rep-constant data
})