fix of test errors

tests/testthat/test-occurrenceChange.R

@@ -0,0 +1,147 @@
+test_that("Test errors and warnings", {
+
+# Create a small dataset
+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(seed = 648)
+
+# 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', 1:nSites, sep=''), size = n, TRUE)
+
+# the date of visit is selected at random from those created earlier
+survey <- sample(rDates, size = n, TRUE)
+
+# run with regions
+# Create region definitions
+regions <- data.frame(site = unique(site),
+                      region1 = c(rep(1, 20), rep(0, 30)),
+                      region2 = c(rep(0, 20), rep(1, 15), rep(0, 15)),
+                      region3 = c(rep(0, 20), rep(0, 15), rep(1, 15)))
+
+  # run the model with these data for one species
+ suppressWarnings(results <- occDetModel(
+    taxa = taxa,
+    site = site,
+    survey = survey,
+    species_list = c("a"),
+    write_results = FALSE,
+    n_iterations = 200,
+    burnin = 10,
+    thinning = 2,
+    regional_codes = regions
+  ))
+
+  expect_error(
+    occurrenceChange(firstYear = 1900, lastYear = 1990, bayesOut = results$a),
+    "firstYear must be in the year range of the data"
+  )
+  expect_error(
+    occurrenceChange(firstYear = 1990, lastYear = 2050, bayesOut = results$a),
+    "lastYear must be in the year range of the data"
+  )
+  expect_error(
+    occurrenceChange(firstYear = 1990, lastYear = 1990, bayesOut = results$a, change = results$a),
+    "Change must be a character string identifying the change metric.  Either: difference, percentdif, growthrate or lineargrowth"
+  )
+  expect_error(
+    occurrenceChange(firstYear = 1990, lastYear = 1990, bayesOut = results$a, change = as.character("Galina")),
+    "The change metric must be one of the following: difference, percentdif, growthrate or lineargrowth"
+  )
+  expect_error(
+    occurrenceChange(firstYear = 1990, lastYear = 1990, bayesOut = results$a, region = results$a),
+    "region must be a character string identifying the regional estimates that change is to be calculated for."
+  )
+  expect_error(
+    occurrenceChange(firstYear = 1990, lastYear = 1990, bayesOut = results$a, region = as.character("Galina")),
+    "region must match that used in the model output file, check spelling."
+  )
+})
+
+test_that("Test occurrenceChange functionality", {
+
+# Create a small dataset
+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(seed = 648)
+
+# 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', 1:nSites, sep=''), size = n, TRUE)
+
+# the date of visit is selected at random from those created earlier
+survey <- sample(rDates, size = n, TRUE)
+
+# run with regions
+# Create region definitions
+regions <- data.frame(site = unique(site),
+                      region1 = c(rep(1, 20), rep(0, 30)),
+                      region2 = c(rep(0, 20), rep(1, 15), rep(0, 15)),
+                      region3 = c(rep(0, 20), rep(0, 15), rep(1, 15)))
+
+  # run the model with these data for one species
+ suppressWarnings(results <- occDetModel(
+    taxa = taxa,
+    site = site,
+    survey = survey,
+    species_list = c("a"),
+    write_results = FALSE,
+    n_iterations = 200,
+    burnin = 10,
+    thinning = 2,
+    regional_codes = regions
+  ))
+
+  # estimate the growthrate (default change measure) for one species ('a')
+  changeGrowthrate <- occurrenceChange(firstYear = 1990, lastYear = 1999, bayesOut = results$a, change = "growthrate")
+
+  # estimate the lineargrowth for one species ('a')
+  changeLineargrowth <- occurrenceChange(firstYear = 1990, lastYear = 1999, bayesOut = results$a, change = "lineargrowth")
+
+  # estimate the difference for one species ('a')
+  changeDifference <- occurrenceChange(firstYear = 1990, lastYear = 1999, bayesOut = results$a, change = "difference")
+
+  # estimate the percentdif for one species ('a')
+  changePercentdif <- occurrenceChange(firstYear = 1990, lastYear = 1999, bayesOut = results$a, change = "percentdif")
+
+  # growthrate
+  expect_equal(nrow(changeGrowthrate$data[, 1]), nrow(changeGrowthrate$data[, 2]), nrow(changeGrowthrate$data[, 3]))
+  expect_true(all(changeGrowthrate$data[, 1:2] <= 1))
+  expect_equal(length(changeGrowthrate), 4)
+  expect_equal((((changeGrowthrate$data[, 2] / changeGrowthrate$data[, 1])^(1 / 10)) - 1) * 100, changeGrowthrate$data[, 3])
+  # Lineargrowth
+  expect_equal(nrow(changeLineargrowth$data[, 1]), nrow(changeLineargrowth$data[, 2]), nrow(changeLineargrowth$data[, 3]))
+  expect_true(all(changeLineargrowth$data[, 1:2] <= 1))
+  expect_equal(length(changeLineargrowth), 4)
+  expect_equal(((changeLineargrowth$data[, 2] - changeLineargrowth$data[, 1]) / changeLineargrowth$data[, 1]), changeLineargrowth$data[, 3])
+  # Difference
+  expect_equal(nrow(changeDifference$data[, 1]), nrow(changeDifference$data[, 2]), nrow(changeDifference$data[, 3]))
+  expect_true(all(changeDifference$data[, 1:2] <= 1))
+  expect_equal(length(changeDifference), 4)
+  expect_equal(changeDifference$data[, 2] - changeDifference$data[, 1], changeDifference$data[, 3])
+  # percentdif
+  expect_equal(nrow(changePercentdif$data[, 1]), nrow(changePercentdif$data[, 2]), nrow(changePercentdif$data[, 3]))
+  expect_true(all(changePercentdif$data[, 1:2] <= 1))
+  expect_equal(length(changePercentdif), 4)
+  expect_equal((((changePercentdif$data[, 2] - changePercentdif$data[, 1]) / changePercentdif$data[, 1]) * 100), changePercentdif$data[, 3])
+})

tests/testthat/test-plot_DetectionPhenology.r

@@ -1,4 +1,9 @@
 test_that("Test plot_DetectionPhenology", {
+
+  # 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",