tests/testthat/test_detectionHistory.R
In jniedballa/camtrapR: Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses
context("detectionHistory")
library(camtrapR)
# load station information
data(camtraps)
# create camera operation matrix
camop_no_problem <- cameraOperation(CTtable = camtraps,
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
hasProblems = FALSE,
dateFormat = "%d/%m/%Y"
)
data(recordTableSample) # load the record history
# compute detection history for a species
# without trapping effort
DetHist1 <- detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "station",
datesAsOccasionNames = FALSE,
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"
)
# with effort / using base R to define recordDateTimeFormat
DetHist2 <- detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "station",
datesAsOccasionNames = FALSE,
includeEffort = TRUE,
scaleEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"
)
DetHist2a <- detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "station",
datesAsOccasionNames = FALSE,
includeEffort = TRUE,
scaleEffort = TRUE,
timeZone = "Asia/Kuala_Lumpur"
)
# with effort / using lubridate package to define recordDateTimeFormat
DetHist2_lub <- detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "ymd HMS",
species = "VTA",
occasionLength = 7,
day1 = "station",
datesAsOccasionNames = FALSE,
includeEffort = TRUE,
scaleEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"
)
DetHist1day <- detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 1,
day1 = "station",
datesAsOccasionNames = F,
includeEffort = T,
scaleEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"
)
# day1 = "survey", datesAsOccasionNames = TRUE
DetHist1day_survey <- detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 1,
day1 = "survey",
datesAsOccasionNames = TRUE,
includeEffort = TRUE,
scaleEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"
)
# multi-season detection history
# load multi-season data
data(camtrapsMultiSeason)
data(recordTableSampleMultiSeason)
# multi-season camera operation matrix
camop_season <- cameraOperation(CTtable = camtrapsMultiSeason,
stationCol = "Station",
setupCol = "Setup_date",
sessionCol = "session",
retrievalCol = "Retrieval_date",
hasProblems = TRUE,
dateFormat = "%d/%m/%Y"
)
# multi-season detection history
DetHist_multi <- detectionHistory(recordTable = recordTableSampleMultiSeason,
camOp = camop_season,
stationCol = "Station",
speciesCol = "Species",
species = "VTA",
occasionLength = 10,
day1 = "station",
recordDateTimeCol = "DateTimeOriginal",
includeEffort = TRUE,
scaleEffort = FALSE,
timeZone = "UTC",
unmarkedMultFrameInput = TRUE
)
# multi, unmarkedMultFrameInput = FALSE
DetHist_multi2 <- detectionHistory(recordTable = recordTableSampleMultiSeason,
camOp = camop_season,
stationCol = "Station",
speciesCol = "Species",
species = "VTA",
occasionLength = 10,
day1 = "station",
recordDateTimeCol = "DateTimeOriginal",
includeEffort = TRUE,
scaleEffort = FALSE,
timeZone = "UTC",
unmarkedMultFrameInput = FALSE
)
# multi, occasionLength = 1, day1 = "survey"
DetHist_multi3 <- detectionHistory(recordTable = recordTableSampleMultiSeason,
camOp = camop_season,
stationCol = "Station",
speciesCol = "Species",
species = "VTA",
occasionLength = 1,
day1 = "survey",
recordDateTimeCol = "DateTimeOriginal",
includeEffort = TRUE,
scaleEffort = FALSE,
timeZone = "UTC",
datesAsOccasionNames = TRUE,
unmarkedMultFrameInput = TRUE
)
# Test section
test_that("recordTable output has correct class and names", {
expect_is(DetHist1, "list")
expect_is(DetHist2, "list")
expect_is(DetHist2a, "list")
expect_is(DetHist2_lub, "list")
expect_is(DetHist_multi, "list")
expect_equal(length(DetHist1), 1)
expect_equal(length(DetHist2), 2)
expect_equal(length(DetHist2a), 3)
expect_equal(length(DetHist2_lub), 2)
expect_equal(length(DetHist_multi), 2)
expect_equal(names(DetHist1), "detection_history")
expect_equal(names(DetHist2), c("detection_history", "effort"))
expect_equal(names(DetHist2a), c("detection_history", "effort", "effort_scaling_parameters"))
expect_equal(names(DetHist2_lub), c("detection_history", "effort"))
expect_equal(names(DetHist_multi), c("detection_history", "effort"))
})
test_that("detectionHistory output has correct dimensions", {
expect_equal(dim(DetHist1$detection_history), c(3,7))
expect_equal(dim(DetHist2$detection_history), c(3,7))
expect_equal(dim(DetHist2$effort), c(3,7))
expect_equal(dim(DetHist_multi$detection_history), c(4,16))
expect_equal(dim(DetHist_multi$effort), c(4,16))
expect_equal(dim(DetHist1day$detection_history), c(3,44))
expect_equal(dim(DetHist1day_survey$detection_history), c(3,46))
expect_equal(dim(DetHist_multi2$detection_history), c(7,8))
expect_equal(dim(DetHist_multi3$detection_history), c(4,884))
})
test_that("detectionHistory output has correct row names", {
expect_rownames <- c("StationA", "StationB", "StationC")
expect_rownames_multi <- c("StationA", "StationB", "StationC", "StationD")
expect_rownames_multi2 <- c("StationA__SESS_2009", "StationB__SESS_2009", "StationC__SESS_2009",
"StationA__SESS_2010", "StationB__SESS_2010", "StationC__SESS_2010", "StationD__SESS_2010")
expect_equal(rownames(DetHist1$detection_history), expect_rownames)
expect_equal(rownames(DetHist2$detection_history), expect_rownames)
expect_equal(rownames(DetHist2$effort), expect_rownames)
expect_equal(rownames(DetHist1day$detection_history), expect_rownames)
expect_equal(rownames(DetHist1day_survey$detection_history), expect_rownames)
expect_equal(rownames(DetHist_multi$detection_history), expect_rownames_multi)
expect_equal(rownames(DetHist_multi$effort), expect_rownames_multi)
expect_equal(rownames(DetHist_multi2$detection_history), expect_rownames_multi2)
expect_equal(rownames(DetHist_multi3$detection_history), expect_rownames_multi)
})
test_that("occasionLength error message works", {
expect_error(detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 47,
day1 = "station",
datesAsOccasionNames = FALSE,
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"),
"occasionLength must be smaller than the total number of days in camOp")
expect_error(detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 0,
day1 = "station",
datesAsOccasionNames = FALSE,
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"),
"occasionLength must be a positive integer and not 0")
})
test_that("Warnings when day1 is a date and there are records before day1", {
expect_warning(detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "2009-05-01",
datesAsOccasionNames = FALSE,
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"),
"4 records (out of 5) were removed because they were taken before day1", fixed = TRUE)
}
)
test_that("Error when day1 is after camera retrieval", {
expect_error(detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "2009-06-01",
datesAsOccasionNames = FALSE,
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"),
"day1 (2009-06-01) is after the last station's retrieval date (2009-05-17)", fixed = TRUE)
}
)
test_that("Error when day1 is before camera setup", {
expect_error(detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "2009-04-01",
maxNumberDays = 10,
datesAsOccasionNames = FALSE,
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"),
"day1 (2009-04-01) is before the first station's setup date (2009-04-02)", fixed = TRUE)
}
)
test_that("Warning when timeZone not defined", {
expect_warning(detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "station",
includeEffort = FALSE),
"timeZone is not specified. Assuming UTC", fixed = TRUE)
}
)
test_that("Error when includeEffort = TRUE but scaleEffort not defined", {
expect_error(detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "station",
includeEffort = TRUE,
timeZone = "Asia/Kuala_Lumpur"),
"scaleEffort must be defined if includeEffort is TRUE", fixed = TRUE)
}
)
test_that("Error when camOp is not a matrix", {
expect_error(detectionHistory(recordTable = recordTableSample,
camOp = "camop_no_problem",
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "station",
includeEffort = TRUE,
timeZone = "Asia/Kuala_Lumpur"),
"camOp must be a matrix", fixed = TRUE)
}
)
test_that("Error when NAs/blanks in DateTimeOriginal", {
recordTableSample_withNA <- recordTableSample_with_blank <- recordTableSample
recordTableSample_withNA$DateTimeOriginal[1] <- NA
recordTableSample_with_blank$DateTimeOriginal[1] <- ""
expect_error(detectionHistory(recordTable = recordTableSample_withNA,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "PBE",
occasionLength = 7,
day1 = "station",
datesAsOccasionNames = FALSE,
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"
),
"there are NAs in subset_species[, recordDateTimeCol]", fixed = TRUE)
expect_error(detectionHistory(recordTable = recordTableSample_with_blank,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "PBE",
occasionLength = 7,
day1 = "station",
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"),
"there are blank values in subset_species[, recordDateTimeCol]", fixed = TRUE)
}
)
test_that("Error when DateTimeOriginal can't be interpreted (format wrong)", {
# suppressWarnings is because parse_date_time() gives a warning too: All formats failed to parse. No formats found.
expect_error(suppressWarnings(detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "mdy HMS", # wrong format
species = "PBE",
occasionLength = 7,
day1 = "station",
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur")),
"Cannot read datetime format in subset_species[, recordDateTimeCol]. Output is all NA.\nexpected: mdy HMS\nactual: 2009-04-21 00:40:00", fixed = TRUE)
}
)
# PART 2: camera operation matrix with fraction days!
camtraps_hrs <- camtraps
camtraps_hrs$Setup_date <- paste(camtraps_hrs$Setup_date, "12")
camtraps_hrs$Retrieval_date <- paste(camtraps_hrs$Retrieval_date, "18")
camtraps_hrs$Problem1_from <- paste(camtraps_hrs$Problem1_from, "12")
camtraps_hrs$Problem1_to <- paste(camtraps_hrs$Problem1_to, "18")
# create camera operation matrix
camop_no_problem_frac <- cameraOperation(CTtable = camtraps_hrs,
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
hasProblems = FALSE,
dateFormat = "dmy H"
)
# add some records on incomplete days
recordTableSample_extra <- recordTableSample_extra2 <- recordTableSample[5,]
recordTableSample_extra$DateTimeOriginal <- "2009-04-02 05:07:00" # on first day / StationA
recordTableSample_extra2$DateTimeOriginal <- "2009-05-14 05:07:00" # on last day / StationA
recordTableSample2 <- rbind(recordTableSample_extra, recordTableSample, recordTableSample_extra2)
test_that("it works when camera operation matrix uses fraction of days & there's records on those days", {
DetHist2_lub_frac <- detectionHistory(recordTable = recordTableSample2,
camOp = camop_no_problem_frac,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "ymd HMS",
species = "VTA",
occasionLength = 7,
day1 = "station",
datesAsOccasionNames = FALSE,
includeEffort = TRUE,
scaleEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"
)
expect_type(DetHist2_lub_frac, type = "list")
})
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context("detectionHistory")
library(camtrapR)
# load station information
data(camtraps)
# create camera operation matrix
camop_no_problem <- cameraOperation(CTtable = camtraps,
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
hasProblems = FALSE,
dateFormat = "%d/%m/%Y"
)
data(recordTableSample) # load the record history
# compute detection history for a species
# without trapping effort
DetHist1 <- detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "station",
datesAsOccasionNames = FALSE,
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"
)
# with effort / using base R to define recordDateTimeFormat
DetHist2 <- detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "station",
datesAsOccasionNames = FALSE,
includeEffort = TRUE,
scaleEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"
)
DetHist2a <- detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "station",
datesAsOccasionNames = FALSE,
includeEffort = TRUE,
scaleEffort = TRUE,
timeZone = "Asia/Kuala_Lumpur"
)
# with effort / using lubridate package to define recordDateTimeFormat
DetHist2_lub <- detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "ymd HMS",
species = "VTA",
occasionLength = 7,
day1 = "station",
datesAsOccasionNames = FALSE,
includeEffort = TRUE,
scaleEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"
)
DetHist1day <- detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 1,
day1 = "station",
datesAsOccasionNames = F,
includeEffort = T,
scaleEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"
)
# day1 = "survey", datesAsOccasionNames = TRUE
DetHist1day_survey <- detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 1,
day1 = "survey",
datesAsOccasionNames = TRUE,
includeEffort = TRUE,
scaleEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"
)
# multi-season detection history
# load multi-season data
data(camtrapsMultiSeason)
data(recordTableSampleMultiSeason)
# multi-season camera operation matrix
camop_season <- cameraOperation(CTtable = camtrapsMultiSeason,
stationCol = "Station",
setupCol = "Setup_date",
sessionCol = "session",
retrievalCol = "Retrieval_date",
hasProblems = TRUE,
dateFormat = "%d/%m/%Y"
)
# multi-season detection history
DetHist_multi <- detectionHistory(recordTable = recordTableSampleMultiSeason,
camOp = camop_season,
stationCol = "Station",
speciesCol = "Species",
species = "VTA",
occasionLength = 10,
day1 = "station",
recordDateTimeCol = "DateTimeOriginal",
includeEffort = TRUE,
scaleEffort = FALSE,
timeZone = "UTC",
unmarkedMultFrameInput = TRUE
)
# multi, unmarkedMultFrameInput = FALSE
DetHist_multi2 <- detectionHistory(recordTable = recordTableSampleMultiSeason,
camOp = camop_season,
stationCol = "Station",
speciesCol = "Species",
species = "VTA",
occasionLength = 10,
day1 = "station",
recordDateTimeCol = "DateTimeOriginal",
includeEffort = TRUE,
scaleEffort = FALSE,
timeZone = "UTC",
unmarkedMultFrameInput = FALSE
)
# multi, occasionLength = 1, day1 = "survey"
DetHist_multi3 <- detectionHistory(recordTable = recordTableSampleMultiSeason,
camOp = camop_season,
stationCol = "Station",
speciesCol = "Species",
species = "VTA",
occasionLength = 1,
day1 = "survey",
recordDateTimeCol = "DateTimeOriginal",
includeEffort = TRUE,
scaleEffort = FALSE,
timeZone = "UTC",
datesAsOccasionNames = TRUE,
unmarkedMultFrameInput = TRUE
)
# Test section
test_that("recordTable output has correct class and names", {
expect_is(DetHist1, "list")
expect_is(DetHist2, "list")
expect_is(DetHist2a, "list")
expect_is(DetHist2_lub, "list")
expect_is(DetHist_multi, "list")
expect_equal(length(DetHist1), 1)
expect_equal(length(DetHist2), 2)
expect_equal(length(DetHist2a), 3)
expect_equal(length(DetHist2_lub), 2)
expect_equal(length(DetHist_multi), 2)
expect_equal(names(DetHist1), "detection_history")
expect_equal(names(DetHist2), c("detection_history", "effort"))
expect_equal(names(DetHist2a), c("detection_history", "effort", "effort_scaling_parameters"))
expect_equal(names(DetHist2_lub), c("detection_history", "effort"))
expect_equal(names(DetHist_multi), c("detection_history", "effort"))
})
test_that("detectionHistory output has correct dimensions", {
expect_equal(dim(DetHist1$detection_history), c(3,7))
expect_equal(dim(DetHist2$detection_history), c(3,7))
expect_equal(dim(DetHist2$effort), c(3,7))
expect_equal(dim(DetHist_multi$detection_history), c(4,16))
expect_equal(dim(DetHist_multi$effort), c(4,16))
expect_equal(dim(DetHist1day$detection_history), c(3,44))
expect_equal(dim(DetHist1day_survey$detection_history), c(3,46))
expect_equal(dim(DetHist_multi2$detection_history), c(7,8))
expect_equal(dim(DetHist_multi3$detection_history), c(4,884))
})
test_that("detectionHistory output has correct row names", {
expect_rownames <- c("StationA", "StationB", "StationC")
expect_rownames_multi <- c("StationA", "StationB", "StationC", "StationD")
expect_rownames_multi2 <- c("StationA__SESS_2009", "StationB__SESS_2009", "StationC__SESS_2009",
"StationA__SESS_2010", "StationB__SESS_2010", "StationC__SESS_2010", "StationD__SESS_2010")
expect_equal(rownames(DetHist1$detection_history), expect_rownames)
expect_equal(rownames(DetHist2$detection_history), expect_rownames)
expect_equal(rownames(DetHist2$effort), expect_rownames)
expect_equal(rownames(DetHist1day$detection_history), expect_rownames)
expect_equal(rownames(DetHist1day_survey$detection_history), expect_rownames)
expect_equal(rownames(DetHist_multi$detection_history), expect_rownames_multi)
expect_equal(rownames(DetHist_multi$effort), expect_rownames_multi)
expect_equal(rownames(DetHist_multi2$detection_history), expect_rownames_multi2)
expect_equal(rownames(DetHist_multi3$detection_history), expect_rownames_multi)
})
test_that("occasionLength error message works", {
expect_error(detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 47,
day1 = "station",
datesAsOccasionNames = FALSE,
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"),
"occasionLength must be smaller than the total number of days in camOp")
expect_error(detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 0,
day1 = "station",
datesAsOccasionNames = FALSE,
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"),
"occasionLength must be a positive integer and not 0")
})
test_that("Warnings when day1 is a date and there are records before day1", {
expect_warning(detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "2009-05-01",
datesAsOccasionNames = FALSE,
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"),
"4 records (out of 5) were removed because they were taken before day1", fixed = TRUE)
}
)
test_that("Error when day1 is after camera retrieval", {
expect_error(detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "2009-06-01",
datesAsOccasionNames = FALSE,
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"),
"day1 (2009-06-01) is after the last station's retrieval date (2009-05-17)", fixed = TRUE)
}
)
test_that("Error when day1 is before camera setup", {
expect_error(detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "2009-04-01",
maxNumberDays = 10,
datesAsOccasionNames = FALSE,
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"),
"day1 (2009-04-01) is before the first station's setup date (2009-04-02)", fixed = TRUE)
}
)
test_that("Warning when timeZone not defined", {
expect_warning(detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "station",
includeEffort = FALSE),
"timeZone is not specified. Assuming UTC", fixed = TRUE)
}
)
test_that("Error when includeEffort = TRUE but scaleEffort not defined", {
expect_error(detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "station",
includeEffort = TRUE,
timeZone = "Asia/Kuala_Lumpur"),
"scaleEffort must be defined if includeEffort is TRUE", fixed = TRUE)
}
)
test_that("Error when camOp is not a matrix", {
expect_error(detectionHistory(recordTable = recordTableSample,
camOp = "camop_no_problem",
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "VTA",
occasionLength = 7,
day1 = "station",
includeEffort = TRUE,
timeZone = "Asia/Kuala_Lumpur"),
"camOp must be a matrix", fixed = TRUE)
}
)
test_that("Error when NAs/blanks in DateTimeOriginal", {
recordTableSample_withNA <- recordTableSample_with_blank <- recordTableSample
recordTableSample_withNA$DateTimeOriginal[1] <- NA
recordTableSample_with_blank$DateTimeOriginal[1] <- ""
expect_error(detectionHistory(recordTable = recordTableSample_withNA,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "PBE",
occasionLength = 7,
day1 = "station",
datesAsOccasionNames = FALSE,
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"
),
"there are NAs in subset_species[, recordDateTimeCol]", fixed = TRUE)
expect_error(detectionHistory(recordTable = recordTableSample_with_blank,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
species = "PBE",
occasionLength = 7,
day1 = "station",
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"),
"there are blank values in subset_species[, recordDateTimeCol]", fixed = TRUE)
}
)
test_that("Error when DateTimeOriginal can't be interpreted (format wrong)", {
# suppressWarnings is because parse_date_time() gives a warning too: All formats failed to parse. No formats found.
expect_error(suppressWarnings(detectionHistory(recordTable = recordTableSample,
camOp = camop_no_problem,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "mdy HMS", # wrong format
species = "PBE",
occasionLength = 7,
day1 = "station",
includeEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur")),
"Cannot read datetime format in subset_species[, recordDateTimeCol]. Output is all NA.\nexpected: mdy HMS\nactual: 2009-04-21 00:40:00", fixed = TRUE)
}
)
# PART 2: camera operation matrix with fraction days!
camtraps_hrs <- camtraps
camtraps_hrs$Setup_date <- paste(camtraps_hrs$Setup_date, "12")
camtraps_hrs$Retrieval_date <- paste(camtraps_hrs$Retrieval_date, "18")
camtraps_hrs$Problem1_from <- paste(camtraps_hrs$Problem1_from, "12")
camtraps_hrs$Problem1_to <- paste(camtraps_hrs$Problem1_to, "18")
# create camera operation matrix
camop_no_problem_frac <- cameraOperation(CTtable = camtraps_hrs,
stationCol = "Station",
setupCol = "Setup_date",
retrievalCol = "Retrieval_date",
hasProblems = FALSE,
dateFormat = "dmy H"
)
# add some records on incomplete days
recordTableSample_extra <- recordTableSample_extra2 <- recordTableSample[5,]
recordTableSample_extra$DateTimeOriginal <- "2009-04-02 05:07:00" # on first day / StationA
recordTableSample_extra2$DateTimeOriginal <- "2009-05-14 05:07:00" # on last day / StationA
recordTableSample2 <- rbind(recordTableSample_extra, recordTableSample, recordTableSample_extra2)
test_that("it works when camera operation matrix uses fraction of days & there's records on those days", {
DetHist2_lub_frac <- detectionHistory(recordTable = recordTableSample2,
camOp = camop_no_problem_frac,
stationCol = "Station",
speciesCol = "Species",
recordDateTimeCol = "DateTimeOriginal",
recordDateTimeFormat = "ymd HMS",
species = "VTA",
occasionLength = 7,
day1 = "station",
datesAsOccasionNames = FALSE,
includeEffort = TRUE,
scaleEffort = FALSE,
timeZone = "Asia/Kuala_Lumpur"
)
expect_type(DetHist2_lub_frac, type = "list")
})
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