tests/testthat/test_createStandards.R

In hugomflavio/actel: Acoustic Telemetry Data Analysis

skip_on_cran()
oldtz <- Sys.getenv('TZ', unset = NA)
Sys.setenv(TZ = 'UTC')

tests.home <- getwd()
setwd(tempdir())
dir.create("detections")
aux <- split(example.detections, example.detections$Receiver)
for (i in names(aux)[1:3]) {
  write.csv(aux[[i]], paste0("detections/", i, ".csv"), row.names = FALSE)
}

det <- loadDetections(start.time = NULL, stop.time = NULL, tz = "Europe/Copenhagen", force = FALSE)
unlink("detections", recursive = TRUE)

write.csv(example.spatial, "spatial.csv", row.names = FALSE)
spatial <- loadSpatial()
file.remove("spatial.csv")

fakedot <- paste(unique(spatial$Array[spatial$Type == "Hydrophone"]), collapse = "--")
recipient <- loadDot(string = fakedot, spatial = spatial, disregard.parallels = TRUE)
dot <- recipient$dot
arrays <- recipient$arrays
dotmat <- recipient$dotmat
paths <- recipient$paths

first.array <- names(arrays)[unlist(lapply(arrays, function(a) is.null(a$before)))]
spatial <- transformSpatial(spatial = spatial, bio = example.biometrics, arrays = arrays, dotmat = dotmat, first.array = first.array) # Finish structuring the spatial file

write.csv(example.deployments, "deployments.csv", row.names = FALSE)
dep <- loadDeployments(input = "deployments.csv", tz = "Europe/Copenhagen")
dep <- createUniqueSerials(input = dep)
file.remove("deployments.csv")

test_that("createStandards is working as expected", {
	expect_warning(output <- createStandards(detections = det, spatial = spatial, deployments = dep),
		"No detections were found for receiver(s) 132907, 132915, 132916, 132917, 132918, 133205, 133206, 133209, 133210, 133215, 133220, 133221, 133222, 133224.", fixed = TRUE)
	expect_equal(colnames(output), c('Timestamp', 'Receiver', 'CodeSpace', 'Signal', 'Sensor.Value', 'Sensor.Unit', 'Transmitter', 'Valid', 'Standard.name', 'Array', 'Section'))
	expect_equal(as.character(unique(output$Standard.name)), c("St.2", "St.6", "St.8"))
})

write.csv(example.deployments, "deployments.csv", row.names = FALSE)
dep <- loadDeployments(input = "deployments.csv", tz = "Europe/Copenhagen")
dep$Start[2] <- dep$Start[2] + 3600 * 24 * 30
dep <- createUniqueSerials(input = dep)
file.remove("deployments.csv")

test_that("createStandards removes detections outside deployments", {
	sink("temp.txt")
	expect_message(suppressWarnings(output <- createStandards(detections = det, spatial = spatial, deployments = dep)),
		"Error: 232 detections for receiver 132908 do not fall within deployment periods.", fixed = TRUE)
	sink()
	expect_equal(colnames(output), c('Timestamp', 'Receiver', 'CodeSpace', 'Signal', 'Sensor.Value', 'Sensor.Unit', 'Transmitter', 'Valid', 'Standard.name', 'Array', 'Section'))
	expect_equal(as.character(unique(output$Standard.name)), c("St.2", "St.6", "St.8"))
})
# b

unlink("detections", recursive = TRUE)
setwd(tests.home)

if (is.na(oldtz)) Sys.unsetenv("TZ") else Sys.setenv(TZ = oldtz)

rm(list = ls())