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"
)
)
})
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