added test skips in absence of JAGS

DESCRIPTION

@@ -47,9 +47,11 @@ Suggests:
     R2jags,
     roxygen2,
     testthat (>= 0.8.0)
+    BRCindicators
 VignetteBuilder: 
     knitr
 Encoding: UTF-8
+remotes: BiologicalRecordsCentre/BRCindicators
 LazyData: TRUE
 RoxygenNote: 7.2.3
 SystemRequirements: JAGS

tests/testthat/test-occurrenceChange.R

@@ -1,36 +1,43 @@
 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)))
+
+  # skip the test if jagsUI is not installed
+  if ((!requireNamespace("jagsUI", quietly = TRUE))) {
+    skip("jagsUI software not available")
+  }
+
+  # 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(
+  suppressWarnings(results <- occDetModel(
     taxa = taxa,
     site = site,
     survey = survey,
@@ -69,38 +76,44 @@ regions <- data.frame(site = unique(site),
 })
 
 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)))
+  # skip the test if jagsUI is not installed
+  if ((!requireNamespace("jagsUI", quietly = TRUE))) {
+    skip("jagsUI software not available")
+  }
+
+  # 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(
+  suppressWarnings(results <- occDetModel(
     taxa = taxa,
     site = site,
     survey = survey,