tests/testthat/testfrescalo.r

In BiologicalRecordsCentre/sparta: Trend Analysis for Unstructured Data

### Frescalo testing is currently skipped if not on a ###
### windows machine, or if libcurl is not supported.  ###

# Create data
n <- 1500 # 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("1980/01/01", "%Y/%m/%d"))
last <- as.Date(strptime(paste(1980 + (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", 11:(nSites + 10), sep = ""), size = n, TRUE)

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

df1 <- data.frame(
  taxa = taxa,
  site = site,
  year = as.numeric(format(time_period, "%Y")),
  startdate = time_period,
  enddate = time_period + 500
)

allsites <- sort(unique(site))

weights <- merge(allsites, allsites)
weights$W <- runif(n = nrow(weights), min = 0, max = 1)

frespath <- file.path(tempdir(), "fres.exe")

# Save the system info as an object
system_info <- Sys.info()

test_that("Does the function stop when the operating system is not mac or Windows", {

  if (system_info["sysname"] == "Darwin") {
    skip("Frescalo installation failures")
  }

    temp <- tempfile(pattern = "dir")
    dir.create(temp)

    with_mocked_bindings(
        "detect_os_compat" = function() FALSE,
        {
            expect_error(suppressWarnings(frescalo(
                Data = df1,
                Fres_weights = weights,
                frespath = frespath,
                time_periods = data.frame(start = c(1980, 1990), end = c(1989, 1999)),
                site_col = "site",
                sp_col = "taxa",
                year = "year",
                sinkdir = temp
            )), "Apologies, Frescalo is currently only avaiable on mac and Windows operating systems.")
        }
    )
})

 if (system_info["sysname"] == "Windows") {
    download.file(
      url = "https://github.com/BiologicalRecordsCentre/frescalo/raw/master/Frescalo_3a_windows.exe",
      destfile = frespath,
      method = "libcurl",
      mode = "wb", quiet = TRUE
    )
  } else if (system_info["sysname"] == "Darwin") {
    download.file(
      url = "https://github.com/BiologicalRecordsCentre/frescalo/raw/master/Frescalo_3a_linux.exe",
      destfile = frespath,
      method = "libcurl",
      quiet = TRUE
    )

    system(command = paste("chmod", "+x", normalizePath(frespath)))
    }

test_that("Test errors", {

  if (system_info["sysname"] == "Darwin") {
    skip("Frescalo installation failures")
  }

  temp <- tempfile(pattern = "dir")
  dir.create(temp)
  expect_error(
    suppressWarnings(frescalo(
      Data = df1,
      frespath = frespath,
      time_periods = data.frame(start = c(1980, 1990), end = c(1989, 1999)),
      site_col = "site",
      sp_col = "FOO",
      year = "year",
      sinkdir = temp
    )),
    "FOO is not the name of a column in data"
  )
  
    expect_error(
    suppressWarnings(frescalo(
      Data = df1,
      frespath = frespath,
      time_periods = c(1980, 1990, 1989, 1999),
      site_col = "site",
      sp_col = "taxa",
      year = "year",
      sinkdir = temp
    )),
    "time_periods should be a data.frame"
  )

  expect_error(
    suppressWarnings(frescalo(
      Data = df1,
      frespath = frespath,
      time_periods = data.frame(start = c(1980, 1850), end = c(1989, 1999)),
      site_col = "site",
      sp_col = "taxa",
      year = "year",
      sinkdir = temp
    )),
    "In time_periods year ranges should not overlap"
  )

  expect_error(
    suppressWarnings(frescalo(
      Data = df1,
      frespath = frespath,
      time_periods = data.frame(start = c(1980, 1990), end = c(1989, 1999)),
      site_col = "site",
      sp_col = "taxa",
      year = "year",
      sinkdir = temp
    )),
    "the sites in your data do not match those in your weights file"
  )
  
  })

test_that("Runs without error", {

  if (system_info["sysname"] == "Darwin") {
    skip("Frescalo installation failures")
  }

  if (!detect_os_compat()) {
    skip("Operating system incompatible with Frescalo")
  }

  # This first run is done using years
  temp <- tempfile(pattern = "dir")
  dir.create(temp)
  ##sink(file.path(temp, "null"))
  fres_try <- suppressWarnings(frescalo(
    Data = df1,
    Fres_weights = weights,
    frespath = frespath,
    time_periods = data.frame(start = c(1980, 1990), end = c(1989, 1999)),
    site_col = "site",
    sp_col = "taxa",
    year = "year",
    sinkdir = temp
  ))
  ##sink()
  unlink(temp, recursive = TRUE)

  expect_equal(class(fres_try), "frescalo")
  expect_true("paths" %in% names(fres_try) &
    "trend" %in% names(fres_try) &
    "stat" %in% names(fres_try) &
    "freq" %in% names(fres_try) &
    "log" %in% names(fres_try) &
    "lm_stats" %in% names(fres_try))

  dir.create(temp)
  #sink(file.path(temp, "null"))
  fres_try <- suppressWarnings(frescalo(
    Data = df1,
    Fres_weights = weights,
    start_col = "startdate",
    end_col = "enddate",
    frespath = frespath,
    time_periods = data.frame(start = c(1980, 1990), end = c(1989, 1999)),
    site_col = "site",
    sp_col = "taxa",
    year = "year",
    sinkdir = temp
  ))
  #sink()
  unlink(temp, recursive = TRUE)

  expect_equal(class(fres_try), "frescalo")
  expect_true("paths" %in% names(fres_try) &
    "trend" %in% names(fres_try) &
    "stat" %in% names(fres_try) &
    "freq" %in% names(fres_try) &
    "log" %in% names(fres_try) &
    "lm_stats" %in% names(fres_try))

  # test a very low value of phi
  temp <- tempfile(pattern = "dir")
  dir.create(temp)
  #sink(file.path(temp, "null"))
  fres_try <- suppressWarnings(frescalo(
    Data = df1,
    phi = 0.51,
    Fres_weights = weights,
    frespath = frespath,
    time_periods = data.frame(start = c(1980, 1990), end = c(1989, 1999)),
    site_col = "site",
    sp_col = "taxa",
    year = "year",
    sinkdir = temp
  ))
  #sink()
  unlink(temp, recursive = TRUE)

  expect_equal(class(fres_try), "frescalo")
  expect_true("paths" %in% names(fres_try) &
    "trend" %in% names(fres_try) &
    "stat" %in% names(fres_try) &
    "freq" %in% names(fres_try) &
    "log" %in% names(fres_try) &
    "lm_stats" %in% names(fres_try))
})

# three sites are visited randomly
site <- sample(paste("SK", 11:(nSites + 10), sep = ""), size = n, TRUE)

df1 <- data.frame(
  taxa = taxa,
  site = site,
  year = as.numeric(format(time_period, "%Y")),
  startdate = time_period,
  enddate = time_period + 500
)

allsites <- sort(unique(site))

weights <- merge(allsites, allsites)
weights$W <- runif(n = nrow(weights), min = 0, max = 1)

test_that("Test plotting", {

  if (system_info["sysname"] == "Darwin") {
    skip("Frescalo installation failures")
  }

  if (!detect_os_compat()) {
    skip("Operating system incompatible with Frescalo")
  }

  # test plotting
  temp <- tempfile(pattern = "dir")
  dir.create(temp)
  #sink(file.path(temp, "null"))
  fres_try <- suppressWarnings(frescalo(
    Data = df1,
    Fres_weights = weights,
    frespath = frespath,
    time_periods = data.frame(start = c(1980, 1990), end = c(1989, 1999)),
    site_col = "site",
    sp_col = "taxa",
    year = "year",
    plot_fres = TRUE,
    sinkdir = temp
  ))
  #sink()
  unlink(temp, recursive = TRUE)

  expect_equal(class(fres_try), "frescalo")
  expect_true("paths" %in% names(fres_try) &
    "trend" %in% names(fres_try) &
    "stat" %in% names(fres_try) &
    "freq" %in% names(fres_try) &
    "log" %in% names(fres_try) &
    "lm_stats" %in% names(fres_try))
})

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

df1 <- data.frame(
  taxa = taxa,
  site = site,
  year = as.numeric(format(time_period, "%Y")),
  startdate = time_period,
  enddate = time_period + 500
)

allsites <- sort(unique(site))

weights <- merge(allsites, allsites)
weights$W <- runif(n = nrow(weights), min = 0, max = 1)

test_that("Runs high value of phi", {

  if (system_info["sysname"] == "Darwin") {
    skip("Frescalo installation failures")
  }

  if (!detect_os_compat()) {
    skip("Operating system incompatible with Frescalo")
  }

  # test a very low value of phi
  temp <- tempfile(pattern = "dir")
  dir.create(temp)
  #sink(file.path(temp, "null"))
  fres_try <- suppressWarnings(frescalo(
    Data = df1,
    Fres_weights = weights,
    phi = NULL,
    frespath = frespath,
    time_periods = data.frame(start = c(1980, 1990), end = c(1989, 1999)),
    site_col = "site",
    sp_col = "taxa",
    year = "year",
    sinkdir = temp
  ))
  #sink()
  unlink(temp, recursive = TRUE)

  expect_equal(class(fres_try), "frescalo")
  expect_true("paths" %in% names(fres_try) &
    "trend" %in% names(fres_try) &
    "stat" %in% names(fres_try) &
    "freq" %in% names(fres_try) &
    "log" %in% names(fres_try) &
    "lm_stats" %in% names(fres_try))
})