tests/testthat/testoccDetFunc.r
In BiologicalRecordsCentre/sparta: Trend Analysis for Unstructured Data
context("Test occDetFunc")
# 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)
# set up regions for some testing
regionsDF <- 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))
)
# format data
suppressWarnings({
visitData <- formatOccData(
taxa = taxa, site = site,
survey = survey
)
})
## additional data for testing missing years
# remove one years
time_period_missing <- sub("2018-", "2019-", survey)
time_period_missing <- as.Date(time_period_missing)
# remove a second year
time_period_missing2 <- sub("2017-", "2019-", time_period_missing)
time_period_missing2 <- as.Date(time_period_missing2)
# format data
suppressWarnings({
visitData_missing <- formatOccData(
taxa = taxa, site = site,
survey = time_period_missing
)
})
suppressWarnings({
visitData_missing2 <- formatOccData(
taxa = taxa, site = site,
survey = time_period_missing2
)
})
# additional data for testing species lost after nyr filter
taxa_filterError <- c(taxa, "aa")
site_filterError <- c(site, "B1")
survey_filterError <- c(survey, sample(rDates, size = 1, TRUE))
suppressWarnings({
visitData_filterError <- formatOccData(
taxa = taxa_filterError, site = site_filterError,
survey = survey_filterError
)
})
test_that("Test occDetFunc errors", {
# skip the test if jagsUI is not installed
if ((!requireNamespace("jagsUI", quietly = TRUE))) {
skip("jagsUI software not available")
}
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 500,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111
),
"must not be larger that the number of iteration"
)
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
criterion = "OnlyGoodData",
seed = 111
),
"Criterion must be either an integer, `EqualWt` or `HighSpec`"
)
expect_error(
results <- occDetFunc(
taxa_name = "apple",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
criterion = "EqualWt",
seed = 111
),
"taxa_name is not the name of a taxa in spp_vis"
)
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData_missing$occDetdata,
spp_vis = visitData_missing$spp_vis,
write_results = FALSE,
criterion = "HighSpec",
seed = 111
),
"There are no visits in year 2018. This means there is no data, for any species in this year. BUGS cannot run if there is a year with no data. Quitting..."
)
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData_missing2$occDetdata,
spp_vis = visitData_missing2$spp_vis,
write_results = FALSE,
seed = 111
),
"There are 2 years with no visits, including 2017. This means there is no data, for any species in these years. BUGS cannot run if any year has no data. Quitting..."
)
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
max_year = "2028",
write_results = FALSE,
seed = 111
),
"max_year should be a numeric value"
)
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
max_year = 2028,
write_results = FALSE,
seed = 111
),
"max_year should be greater than the final year of available data"
)
})
test_that("Test occDetFunc with defaults", {
# 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"
))
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111
)
sink()
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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"
)
)
})
test_that("Test occDetFunc with model types", {
# 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"
))
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"indran", "centering",
"halfcauchy"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"indran", "centering",
"inversegamma"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c("indran", "intercept")
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"indran", "intercept",
"halfcauchy"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"indran", "intercept",
"inversegamma"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"ranwalk", "centering",
"halfcauchy"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"ranwalk", "centering",
"inversegamma"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c("ranwalk", "intercept")
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"ranwalk", "intercept",
"halfcauchy"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"ranwalk", "intercept",
"inversegamma"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"ranwalk",
"halfcauchy"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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"
)
)
sink()
})
test_that("Test occDetFunc with julian date", {
# 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({
visitData <- formatOccData(
taxa = taxa, site = site,
survey = survey,
includeJDay = TRUE
)
})
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"ranwalk", "intercept",
"inversegamma", "jul_date"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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"
)
)
expect_true("beta1" %in% row.names(results$BUGSoutput$summary))
expect_true("beta2" %in% row.names(results$BUGSoutput$summary))
expect_true("beta3" %in% row.names(results$BUGSoutput$summary))
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"indran", "centering",
"halfcauchy", "jul_date"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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"
)
)
expect_true("beta1" %in% row.names(results$BUGSoutput$summary))
expect_true("beta2" %in% row.names(results$BUGSoutput$summary))
expect_true("beta3" %in% row.names(results$BUGSoutput$summary))
sink()
})
test_that("Test occDetFunc with catagorical list length", {
# 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({
visitData <- formatOccData(
taxa = taxa, site = site,
survey = survey,
includeJDay = TRUE
)
})
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"ranwalk", "intercept",
"inversegamma", "catlistlength"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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"
)
)
expect_true("dtype2.p" %in% row.names(results$BUGSoutput$summary))
expect_true("dtype3.p" %in% row.names(results$BUGSoutput$summary))
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"indran", "centering",
"halfcauchy", "catlistlength"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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"
)
)
expect_true("dtype2.p" %in% row.names(results$BUGSoutput$summary))
expect_true("dtype3.p" %in% row.names(results$BUGSoutput$summary))
sink()
})
test_that("Test occDetFunc using regions and region aggregates", {
# 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"
))
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = regionsDF,
region_aggs = list(agg1 = c("region1", "region2"))
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
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",
"regions", "region_aggs"
)
)
expect_identical(
results$regions,
c("region1", "region2", "region3")
)
expect_identical(names(results$region_aggs), "agg1")
RNs <- row.names(results$BUGSoutput$summary)
expect_true("a_region1[1]" %in% RNs)
expect_true("a_region2[1]" %in% RNs)
expect_true("a_region3[1]" %in% RNs)
expect_true("psi.fs.r_region1[1]" %in% RNs)
expect_true("psi.fs.r_region2[1]" %in% RNs)
expect_true("psi.fs.r_region3[1]" %in% RNs)
expect_true("psi.fs.r_agg1[1]" %in% RNs)
# test with a region with no data
regionsempty <- regionsDF
regionsempty$region4 <- 0
expect_warning(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = regionsempty,
region_aggs = list(agg1 = c("region1", "region2"))
),
"The following regions have no data and should not be modelled: region4 - These regions will not be included in the model"
)
# test with regional_codes not as a dataframe
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = as.matrix(regionsDF),
region_aggs = list(agg1 = c("region1", "region2"))
),
"regional_codes should be a data.frame"
)
# test with NAs in regional_codes
regionsNA <- regionsDF
regionsNA[1, 3] <- NA
expect_warning(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = regionsNA,
region_aggs = list(agg1 = c("region1", "region2"))
),
"NAs are present in regional_codes, these will be replaced with 0s"
)
# test with sites in multiple regions
regionsmulti <- regionsDF
regionsmulti[1, 3] <- 1
expect_warning(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = regionsmulti,
region_aggs = list(agg1 = c("region1", "region2"))
),
"1 sites are assigned to more than one region in regional_codes and will be removed"
)
# test with sites in no regions
regionsmulti <- regionsDF
regionsmulti[1, 2] <- 0
expect_warning(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = regionsmulti,
region_aggs = list(agg1 = c("region1", "region2"))
),
"1 sites are not assigned to a region in regional_codes and will be removed"
)
# test for sites in occurence data but not regions
regionsmissing <- regionsDF[2:50, ]
expect_warning(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = regionsmissing,
region_aggs = list(agg1 = c("region1", "region2"))
),
"1 sites are in occurrence data but not in regional_codes and will be removed"
)
# test for regional aggregate containing unknown region
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = regionsDF,
region_aggs = list(agg1 = c("region1", "region2", "region4"))
),
"Aggregate members [region4] not in regional_codes column names [region1, region2, region3]",
fixed = TRUE
)
# test for regional aggregate without regional_codes
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = NULL,
region_aggs = list(agg1 = c("region1", "region2"))
),
"Cannot use regional aggregates if regional_codes is not supplied"
)
sink()
})
test_that("Test occDetFunc with empty species post nyr filter", {
# skip the test if jagsUI is not installed
if ((!requireNamespace("jagsUI", quietly = TRUE))) {
skip("jagsUI software not available")
}
sink(file = ifelse(Sys.info()["sysname"] == "Windows",
"NUL",
"/dev/null"
))
expect_warning(
results <- occDetFunc(
taxa_name = "aa",
n_iterations = 50,
burnin = 15,
occDetdata = visitData_filterError$occDetdata,
spp_vis = visitData_filterError$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy")
),
"aa has insufficient data after site filtering. Either decrease nyr or change the criterion"
)
sink()
})
BiologicalRecordsCentre/sparta documentation built on June 12, 2024, 4:11 a.m.
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context("Test occDetFunc")
# 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)
# set up regions for some testing
regionsDF <- 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))
)
# format data
suppressWarnings({
visitData <- formatOccData(
taxa = taxa, site = site,
survey = survey
)
})
## additional data for testing missing years
# remove one years
time_period_missing <- sub("2018-", "2019-", survey)
time_period_missing <- as.Date(time_period_missing)
# remove a second year
time_period_missing2 <- sub("2017-", "2019-", time_period_missing)
time_period_missing2 <- as.Date(time_period_missing2)
# format data
suppressWarnings({
visitData_missing <- formatOccData(
taxa = taxa, site = site,
survey = time_period_missing
)
})
suppressWarnings({
visitData_missing2 <- formatOccData(
taxa = taxa, site = site,
survey = time_period_missing2
)
})
# additional data for testing species lost after nyr filter
taxa_filterError <- c(taxa, "aa")
site_filterError <- c(site, "B1")
survey_filterError <- c(survey, sample(rDates, size = 1, TRUE))
suppressWarnings({
visitData_filterError <- formatOccData(
taxa = taxa_filterError, site = site_filterError,
survey = survey_filterError
)
})
test_that("Test occDetFunc errors", {
# skip the test if jagsUI is not installed
if ((!requireNamespace("jagsUI", quietly = TRUE))) {
skip("jagsUI software not available")
}
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 500,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111
),
"must not be larger that the number of iteration"
)
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
criterion = "OnlyGoodData",
seed = 111
),
"Criterion must be either an integer, `EqualWt` or `HighSpec`"
)
expect_error(
results <- occDetFunc(
taxa_name = "apple",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
criterion = "EqualWt",
seed = 111
),
"taxa_name is not the name of a taxa in spp_vis"
)
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData_missing$occDetdata,
spp_vis = visitData_missing$spp_vis,
write_results = FALSE,
criterion = "HighSpec",
seed = 111
),
"There are no visits in year 2018. This means there is no data, for any species in this year. BUGS cannot run if there is a year with no data. Quitting..."
)
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData_missing2$occDetdata,
spp_vis = visitData_missing2$spp_vis,
write_results = FALSE,
seed = 111
),
"There are 2 years with no visits, including 2017. This means there is no data, for any species in these years. BUGS cannot run if any year has no data. Quitting..."
)
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
max_year = "2028",
write_results = FALSE,
seed = 111
),
"max_year should be a numeric value"
)
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
max_year = 2028,
write_results = FALSE,
seed = 111
),
"max_year should be greater than the final year of available data"
)
})
test_that("Test occDetFunc with defaults", {
# skip the test if jagsUI is not installed
if ((!requireNamespace("jagsUI", quietly = TRUE))) {
skip("jagsUI software not available")
}
sink(file = ifelse(Sys.info()["sysname"] == "Windows",
"NUL",
"/dev/null"
))
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111
)
sink()
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version"
)
)
})
test_that("Test occDetFunc with model types", {
# skip the test if jagsUI is not installed
if ((!requireNamespace("jagsUI", quietly = TRUE))) {
skip("jagsUI software not available")
}
sink(file = ifelse(Sys.info()["sysname"] == "Windows",
"NUL",
"/dev/null"
))
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"indran", "centering",
"halfcauchy"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"indran", "centering",
"inversegamma"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c("indran", "intercept")
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"indran", "intercept",
"halfcauchy"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"indran", "intercept",
"inversegamma"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"ranwalk", "centering",
"halfcauchy"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"ranwalk", "centering",
"inversegamma"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c("ranwalk", "intercept")
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"ranwalk", "intercept",
"halfcauchy"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"ranwalk", "intercept",
"inversegamma"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version"
)
)
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"ranwalk",
"halfcauchy"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version"
)
)
sink()
})
test_that("Test occDetFunc with julian date", {
# skip the test if jagsUI is not installed
if ((!requireNamespace("jagsUI", quietly = TRUE))) {
skip("jagsUI software not available")
}
sink(file = ifelse(Sys.info()["sysname"] == "Windows",
"NUL",
"/dev/null"
))
suppressWarnings({
visitData <- formatOccData(
taxa = taxa, site = site,
survey = survey,
includeJDay = TRUE
)
})
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"ranwalk", "intercept",
"inversegamma", "jul_date"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version"
)
)
expect_true("beta1" %in% row.names(results$BUGSoutput$summary))
expect_true("beta2" %in% row.names(results$BUGSoutput$summary))
expect_true("beta3" %in% row.names(results$BUGSoutput$summary))
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"indran", "centering",
"halfcauchy", "jul_date"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version"
)
)
expect_true("beta1" %in% row.names(results$BUGSoutput$summary))
expect_true("beta2" %in% row.names(results$BUGSoutput$summary))
expect_true("beta3" %in% row.names(results$BUGSoutput$summary))
sink()
})
test_that("Test occDetFunc with catagorical list length", {
# skip the test if jagsUI is not installed
if ((!requireNamespace("jagsUI", quietly = TRUE))) {
skip("jagsUI software not available")
}
sink(file = ifelse(Sys.info()["sysname"] == "Windows",
"NUL",
"/dev/null"
))
suppressWarnings({
visitData <- formatOccData(
taxa = taxa, site = site,
survey = survey,
includeJDay = TRUE
)
})
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"ranwalk", "intercept",
"inversegamma", "catlistlength"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version"
)
)
expect_true("dtype2.p" %in% row.names(results$BUGSoutput$summary))
expect_true("dtype3.p" %in% row.names(results$BUGSoutput$summary))
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111, modeltype = c(
"indran", "centering",
"halfcauchy", "catlistlength"
)
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version"
)
)
expect_true("dtype2.p" %in% row.names(results$BUGSoutput$summary))
expect_true("dtype3.p" %in% row.names(results$BUGSoutput$summary))
sink()
})
test_that("Test occDetFunc using regions and region aggregates", {
# skip the test if jagsUI is not installed
if ((!requireNamespace("jagsUI", quietly = TRUE))) {
skip("jagsUI software not available")
}
sink(file = ifelse(Sys.info()["sysname"] == "Windows",
"NUL",
"/dev/null"
))
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = regionsDF,
region_aggs = list(agg1 = c("region1", "region2"))
)
expect_identical(results$SPP_NAME, "a")
expect_identical(results$n.iter, 50)
expect_identical(
names(results),
c(
"model", "BUGSoutput", "parameters.to.save", "model.file",
"n.iter", "DIC", "SPP_NAME", "min_year", "max_year", "sites_included",
"nsites", "nvisits", "species_observations", "sparta_version",
"regions", "region_aggs"
)
)
expect_identical(
results$regions,
c("region1", "region2", "region3")
)
expect_identical(names(results$region_aggs), "agg1")
RNs <- row.names(results$BUGSoutput$summary)
expect_true("a_region1[1]" %in% RNs)
expect_true("a_region2[1]" %in% RNs)
expect_true("a_region3[1]" %in% RNs)
expect_true("psi.fs.r_region1[1]" %in% RNs)
expect_true("psi.fs.r_region2[1]" %in% RNs)
expect_true("psi.fs.r_region3[1]" %in% RNs)
expect_true("psi.fs.r_agg1[1]" %in% RNs)
# test with a region with no data
regionsempty <- regionsDF
regionsempty$region4 <- 0
expect_warning(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = regionsempty,
region_aggs = list(agg1 = c("region1", "region2"))
),
"The following regions have no data and should not be modelled: region4 - These regions will not be included in the model"
)
# test with regional_codes not as a dataframe
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = as.matrix(regionsDF),
region_aggs = list(agg1 = c("region1", "region2"))
),
"regional_codes should be a data.frame"
)
# test with NAs in regional_codes
regionsNA <- regionsDF
regionsNA[1, 3] <- NA
expect_warning(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = regionsNA,
region_aggs = list(agg1 = c("region1", "region2"))
),
"NAs are present in regional_codes, these will be replaced with 0s"
)
# test with sites in multiple regions
regionsmulti <- regionsDF
regionsmulti[1, 3] <- 1
expect_warning(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = regionsmulti,
region_aggs = list(agg1 = c("region1", "region2"))
),
"1 sites are assigned to more than one region in regional_codes and will be removed"
)
# test with sites in no regions
regionsmulti <- regionsDF
regionsmulti[1, 2] <- 0
expect_warning(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = regionsmulti,
region_aggs = list(agg1 = c("region1", "region2"))
),
"1 sites are not assigned to a region in regional_codes and will be removed"
)
# test for sites in occurence data but not regions
regionsmissing <- regionsDF[2:50, ]
expect_warning(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = regionsmissing,
region_aggs = list(agg1 = c("region1", "region2"))
),
"1 sites are in occurrence data but not in regional_codes and will be removed"
)
# test for regional aggregate containing unknown region
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = regionsDF,
region_aggs = list(agg1 = c("region1", "region2", "region4"))
),
"Aggregate members [region4] not in regional_codes column names [region1, region2, region3]",
fixed = TRUE
)
# test for regional aggregate without regional_codes
expect_error(
results <- occDetFunc(
taxa_name = "a",
n_iterations = 50,
burnin = 15,
occDetdata = visitData$occDetdata,
spp_vis = visitData$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy"),
regional_codes = NULL,
region_aggs = list(agg1 = c("region1", "region2"))
),
"Cannot use regional aggregates if regional_codes is not supplied"
)
sink()
})
test_that("Test occDetFunc with empty species post nyr filter", {
# 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"
))
expect_warning(
results <- occDetFunc(
taxa_name = "aa",
n_iterations = 50,
burnin = 15,
occDetdata = visitData_filterError$occDetdata,
spp_vis = visitData_filterError$spp_vis,
write_results = FALSE,
seed = 111,
modeltype = c("ranwalk", "halfcauchy")
),
"aa has insufficient data after site filtering. Either decrease nyr or change the criterion"
)
sink()
})
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