tests/testthat/testoccDetModel.r

In BiologicalRecordsCentre/sparta: Trend Analysis for Unstructured Data

context("Test occDetModel")

# Create data
n <- 15000 # size of dataset
nyr <- 20 # number of years in data
nSamples <- 100 # set number of dates
nSites <- 50 # set number of sites
set.seed(125)

# Create somes dates
first <- as.Date(strptime("2010/01/01", "%Y/%m/%d"))
last <- as.Date(strptime(paste(2010 + (nyr - 1), "/12/31", sep = ""), "%Y/%m/%d"))
dt <- last - first
rDates <- first + (runif(nSamples) * dt)

# taxa are set as random letters
taxa <- sample(letters, size = n, TRUE)

# three sites are visited randomly
site <- sample(paste("A", 1:nSites, sep = ""), size = n, TRUE)

# the date of visit is selected at random from those created earlier
survey <- sample(rDates, size = n, TRUE)

df <- data.frame(taxa, site, survey)

test_that("Test occDetModel", {
  # skip the test if jagsUI is not installed
  if ((!requireNamespace("jagsUI", quietly = TRUE))) {
    skip("jagsUI software not available")
  }

  sink(file = ifelse(Sys.info()["sysname"] == "Windows",
    "NUL",
    "/dev/null"
  ))
  suppressWarnings(results <- occDetModel(
    taxa = df$taxa,
    write_results = FALSE,
    site = df$site,
    survey = df$survey,
    species_list = c("a", "m", "g"),
    n_iterations = 100,
    burnin = 10,
    thinning = 2,
    seed = 111
  ))
  sink()

  expect_identical(names(results), c("a", "m", "g"))
  expect_identical(
    names(results[[1]]),
    c(
      "model", "BUGSoutput", "parameters.to.save", "model.file",
      "n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
      "nsites", "nvisits", "species_observations", "sparta_version"
    )
  )
})