tests/testthat/test-spectrogram.R
In gipso/actverse: Tools for Actigraphy Data Analysis
test_that("spectrogram() | general test", {
data <- dplyr::tibble(
index = seq(lubridate::as_datetime("2020-01-01 00:00:00"),
lubridate::as_datetime("2020-01-30 23:59:00"),
by = "min"),
x = rep(seq(1, 3600), times = 12)
) %>%
tsibble::tsibble(index = index)
object <- spectrogram(
data = data, col = "x", p_unit = "hours", p_min = 1, p_max = 100,
p_step = 1, int_unit = "days", int_n = 7, int_step = 5, alpha = 0.05,
print = TRUE) %>%
shush()
checkmate::expect_list(object, len = 2)
checkmate::expect_list(object$periodograms, len = 111)
expect_s3_class(object$spectrogram, "ggplot")
})
test_that("spectrogram() | error test", {
data_1 <- dplyr::tibble(
index = seq(lubridate::as_datetime("2020-01-01 00:00:00"),
lubridate::as_datetime("2020-01-10 00:00:00"),
by = "min"),
x = seq_along(index)
) %>%
tsibble::tsibble(index = index)
data_2 <- dplyr::tibble(index = 1:100, x = seq_along(index)) %>%
tsibble::tsibble(index = index)
data_3 <- dplyr::tibble(
index = c(lubridate::as_datetime(seq(0, 60 * 100, by = 60)),
lubridate::as_datetime(seq(6030, 6030 + (30 * 100),
by = 30))),
x = seq_along(index)
) %>%
tsibble::tsibble(index = index)
data_4 <- dplyr::tibble(
index = seq(as.POSIXct("2015-01-01"), as.POSIXct("2015-01-08"),
by = "min"),
x = ""
) %>%
tsibble::tsibble(index = index)
# assert_tsibble(data, min.rows = 2, min.cols = 2)
expect_error(spectrogram(
data = 1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'data' failed")
expect_error(spectrogram(
data = data_1[1, ], col = "x", p_unit = "minutes", p_min = 1,
p_max = 4600, int_unit = "days", int_n = 7, int_step = 720, p_step = 1,
alpha = 0.05, print = FALSE),
"Assertion on 'data' failed")
expect_error(spectrogram(
data = data_1[, 1], col = "x", p_unit = "minutes", p_min = 1,
p_max = 4600, int_unit = "days", int_n = 7, int_step = 720, p_step = 1,
alpha = 0.05, print = FALSE),
"Assertion on 'data' failed")
# assert_index_class(data, c("Date", "POSIXt"))
expect_error(spectrogram(
data = data_2, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'data' failed")
# assert_clear_epoch(data, 0.9)
expect_error(spectrogram(
data = data_3, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'data' failed")
# checkmate::assert_choice(col, names(data))
expect_error(spectrogram(
data = data_1, col = "a", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'col' failed")
# checkmate::assert_numeric(data[[col]])
expect_error(spectrogram(
data = data_4, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'data\\[\\[col\\]\\]' failed")
# checkmate::assert_choice(p_unit, p_unit_choices)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "a", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'p_unit' failed")
# assert_epoch_compatibility(data, p_unit)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "seconds", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'data' failed")
# checkmate::assert_int(p_min, lower = 1)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = "a",
p_max = 4600, int_unit = "days", int_n = 7, int_step = 720, p_step = 1,
alpha = 0.05, print = FALSE),
"Assertion on 'p_min' failed")
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = -1,
p_max = 4600, int_unit = "days", int_n = 7, int_step = 720, p_step = 1,
alpha = 0.05, print = FALSE),
"Assertion on 'p_min' failed")
# checkmate::assert_int(p_max, lower = 1)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = "a",
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'p_max' failed")
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = -1,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'p_max' failed")
# checkmate::assert_int(p_step, lower = 1)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = "a", int_unit = "days", int_n = 7, int_step = 720,
alpha = 0.05, print = FALSE),
"Assertion on 'p_step' failed")
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = -1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'p_step' failed")
# assert_leq(p_min + p_step, p_max)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 2,
p_step = 2, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'p_min \\+ p_step' failed")
# checkmate::assert_choice(int_unit, p_unit_choices)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "hours", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'int_unit' failed")
# checkmate::assert_int(int_n, lower = 1)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = "", int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'int_n' failed")
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = -1, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'int_n' failed")
# checkmate::assert_int(int_step, lower = 1)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = "", alpha = 0.05,
print = FALSE),
"Assertion on 'int_step' failed")
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = -1, alpha = 0.05,
print = FALSE),
"Assertion on 'int_step' failed")
# checkmate::assert_number(alpha, lower = 0.001, upper = 0.999)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = -1,
print = FALSE),
"Assertion on 'alpha' failed")
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 2,
print = FALSE),
"Assertion on 'alpha' failed")
# checkmate::assert_flag(print)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = 1),
"Assertion on 'print' failed")
# if (which(p_unit_choices == int_unit) <= which(p_unit_choices == p_unit))
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "seconds", int_n = 7, int_step = 720,
alpha = 0.05, print = FALSE))
# if (as.numeric(data_int) < as.numeric(string_to_period(int_unit))) {
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "years", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE))
# if (data_int <= lubridate::as.interval(
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 1000, int_step = 720,
alpha = 0.05, print = FALSE))
# if (int_step >= int_max_n_epoch) {
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "hours", p_min = 1, p_max = 100,
p_step = 1, int_unit = "days", int_n = 1, int_step = 1000000,
alpha = 0.05, print = FALSE))
})
test_that("spectrogram() | warning/message test", {
data_1 <- dplyr::tibble(
index = c(lubridate::as_datetime(seq(0, 60 * 1000, by = 60)),
lubridate::as_datetime(seq(60030, 60030 + (30 * 100),
by = 30))),
x = seq_along(index)
) %>%
tsibble::tsibble(index = index)
data_2 <- dplyr::tibble(
index = lubridate::as_datetime(seq(0, 60 * 1000, by = 60)),
x = c(1:500, rep(as.numeric(NA), length(index) - 500))
) %>%
tsibble::tsibble(index = index)
# warn_regularity(data, 0.99)
expect_message(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 100,
p_step = 1, int_unit = "hours", int_n = 1, int_step = 59, alpha = 0.05,
print = FALSE))
# warn_any_missing(data[[col]])
expect_message(spectrogram(
data = data_2, col = "x", p_unit = "minutes", p_min = 1, p_max = 100,
p_step = 1, int_unit = "hours", int_n = 1, int_step = 59, alpha = 0.05,
print = FALSE))
})
test_that("find_spectrogram_intervals() | general test", {
data <- dplyr::tibble(
index = seq(lubridate::as_datetime("2020-01-01 00:00:00"),
lubridate::as_datetime("2020-01-30 23:59:00"),
by = "min"),
x = rep(seq(1, 3600), times = 12)
) %>%
tsibble::tsibble(index = index)
object <- find_spectrogram_intervals(
data = data, int_unit = "days", int_n = 7, int_step = 720) %>%
shush()
expect_equal(dplyr::last(object),
lubridate::interval("2020-01-23 12:00:00",
"2020-01-30 12:00:00"))
})
test_that("find_spectrogram_intervals() | error test", {
data_1 <- dplyr::tibble(
index = seq(lubridate::as_datetime("2020-01-01 00:00:00"),
lubridate::as_datetime("2020-01-10 00:00:00"),
by = "min"),
x = seq_along(index)
) %>%
tsibble::tsibble(index = index)
data_2 <- dplyr::tibble(index = 1:100, x = seq_along(index)) %>%
tsibble::tsibble(index = index)
data_3 <- dplyr::tibble(
index = seq(as.POSIXct("2015-01-01"), as.POSIXct("2015-01-08"),
by = "min"),
x = ""
) %>%
tsibble::tsibble(index = index)
# assert_tsibble(data, min.rows = 2, min.cols = 2)
expect_error(find_spectrogram_intervals(
data = 1, int_unit = "days", int_n = 7, int_step = 720),
"Assertion on 'data' failed")
expect_error(find_spectrogram_intervals(
data = data_1[1, ], int_unit = "days", int_n = 7, int_step = 720),
"Assertion on 'data' failed")
expect_error(find_spectrogram_intervals(
data = data_1[, 1], int_unit = "days", int_n = 7, int_step = 720),
"Assertion on 'data' failed")
# assert_index_class(data, c("Date", "POSIXt"))
expect_error(find_spectrogram_intervals(
data = data_2, int_unit = "days", int_n = 7, int_step = 720),
"Assertion on 'data' failed")
# checkmate::assert_choice(int_unit, int_choices)
expect_error(find_spectrogram_intervals(
data = data_1, int_unit = "", int_n = 7, int_step = 720),
"Assertion on 'int_unit' failed")
# checkmate::assert_int(int_n, lower = 1)
expect_error(find_spectrogram_intervals(
data = data_1, int_unit = "days", int_n = "", int_step = 720),
"Assertion on 'int_n' failed")
expect_error(find_spectrogram_intervals(
data = data_1, int_unit = "days", int_n = -1, int_step = 720),
"Assertion on 'int_n' failed")
# checkmate::assert_int(int_step, lower = 1)
expect_error(find_spectrogram_intervals(
data = data_1, int_unit = "days", int_n = 7, int_step = ""),
"Assertion on 'int_step' failed")
expect_error(find_spectrogram_intervals(
data = data_1, int_unit = "days", int_n = 7, int_step = -1),
"Assertion on 'int_step' failed")
})
test_that("compute_interval_periodogram() | general test", {
data <- dplyr::tibble(
index = seq(lubridate::as_datetime("2020-01-01 00:00:00"),
lubridate::as_datetime("2020-01-30 23:59:00"),
by = "min"),
x = rep(seq(1, 3600), times = 12)
) %>%
tsibble::tsibble(index = index)
envir <- environment()
cli::cli_progress_bar(total = 1, clear = FALSE, .envir = envir)
object <- compute_interval_periodogram(
data = data, col = "x",
int_i = lubridate::interval("2020-01-01 00:00:00",
"2020-01-03 00:00:00"),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = envir)
checkmate::expect_list(object, len = 10)
checkmate::expect_string(object$p_unit)
checkmate::expect_numeric(object$p_seq, len = 1501)
expect_equal(object$int, lubridate::interval("2020-01-01 00:00:00",
"2020-01-03 00:00:00"))
checkmate::expect_number(object$alpha)
checkmate::expect_numeric(object$a_p, len = 1501)
checkmate::expect_numeric(object$q_p, len = 1501)
checkmate::expect_numeric(object$q_p_critical, len = 1501)
checkmate::expect_numeric(object$q_p_rel, len = 1501)
checkmate::expect_numeric(object$q_p_pvalue, len = 1501)
checkmate::expect_tibble(object$q_p_peaks)
})
test_that("compute_interval_periodogram() | error test", {
data_1 <- dplyr::tibble(
index = seq(lubridate::as_datetime("2020-01-01 00:00:00"),
lubridate::as_datetime("2020-01-10 00:00:00"),
by = "min"),
x = seq_along(index)
) %>%
tsibble::tsibble(index = index)
data_2 <- dplyr::tibble(index = 1:100, x = seq_along(index)) %>%
tsibble::tsibble(index = index)
data_3 <- dplyr::tibble(
index = seq(as.POSIXct("2015-01-01"), as.POSIXct("2015-01-08"),
by = "min"),
x = ""
) %>%
tsibble::tsibble(index = index)
# assert_tsibble(data, min.rows = 2, min.cols = 2)
expect_error(compute_interval_periodogram(
data = 1, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'data' failed")
expect_error(compute_interval_periodogram(
data = data_1[1, ], col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'data' failed")
expect_error(compute_interval_periodogram(
data = data_1[, 1], col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'data' failed")
# assert_index_class(data, c("Date", "POSIXt"))
expect_error(compute_interval_periodogram(
data = data_2, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'data' failed")
# checkmate::assert_choice(col, names(data))
expect_error(compute_interval_periodogram(
data = data_1, col = "a",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'col' failed")
# checkmate::assert_numeric(data[[col]])
expect_error(compute_interval_periodogram(
data = data_3, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'data\\[\\[col\\]\\]' failed")
# assert_interval(int_i, any.missing = FALSE)
expect_error(compute_interval_periodogram(
data = data_1, col = "x",
int_i = 1,
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'int_i' failed")
expect_error(compute_interval_periodogram(
data = data_1, col = "x",
int_i = lubridate::as.interval(NA),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'int_i' failed")
# checkmate::assert_string(p_unit)
expect_error(compute_interval_periodogram(
data = data_1, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = 1, p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'p_unit' failed")
# checkmate::assert_numeric(p_seq, min.len = 1)
expect_error(compute_interval_periodogram(
data = data_1, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = "a", alpha = 0.05, envir = environment()),
"Assertion on 'p_seq' failed")
expect_error(compute_interval_periodogram(
data = data_1, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = numeric(), alpha = 0.05,
envir = environment()),
"Assertion on 'p_seq' failed")
# checkmate::assert_number(alpha, lower = 0.001, upper = 0.999)
expect_error(compute_interval_periodogram(
data = data_1, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = -1,
envir = environment()),
"Assertion on 'alpha' failed")
expect_error(compute_interval_periodogram(
data = data_1, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 2,
envir = environment()),
"Assertion on 'alpha' failed")
# checkmate::assert_environment(envir, null.ok = TRUE)
expect_error(compute_interval_periodogram(
data = data_1, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = 1),
"Assertion on 'envir' failed")
})
test_that("plot_spectrogram() | general test", {
data <- dplyr::tibble(
index = seq(lubridate::as_datetime("2020-01-01 00:00:00"),
lubridate::as_datetime("2020-01-30 23:59:00"),
by = "min"),
x = rep(seq(1, 3600), times = 12)
) %>%
tsibble::tsibble(index = index)
per <- periodogram(data = data, col = "x", p_min = 1, p_max = 100,
print = FALSE) %>%
shush()
spec <- spectrogram(
data = data, col = "x", p_unit = "hours", p_min = 1, p_max = 100,
p_step = 1, int_unit = "days", int_n = 7, int_step = 5, alpha = 0.05,
print = FALSE) %>%
shush()
expect_s3_class(plot_spectrogram(
p_seq = per$p_seq, per_ints = spec$periodograms, peaks = per$q_p_peaks,
xlab = "Period", print = TRUE),
"ggplot")
})
test_that("plot_spectrogram() | error test", {
# checkmate::assert_numeric(p_seq, min.len = 1)
expect_error(plot_spectrogram(
p_seq = "a", per_ints = list(a = 1), peaks = dplyr::tibble(),
xlab = "", print = TRUE),
"Assertion on 'p_seq' failed")
expect_error(plot_spectrogram(
p_seq = numeric(), per_ints = list(a = 1), peaks = dplyr::tibble(),
xlab = "", print = TRUE),
"Assertion on 'p_seq' failed")
# checkmate::assert_list(per_ints, min.len = 1)
expect_error(plot_spectrogram(
p_seq = 1, per_ints = 1, peaks = dplyr::tibble(),
xlab = "", print = TRUE),
"Assertion on 'per_ints' failed")
expect_error(plot_spectrogram(
p_seq = 1, per_ints = list(), peaks = dplyr::tibble(),
xlab = "", print = TRUE),
"Assertion on 'per_ints' failed")
# checkmate::assert_tibble(peaks)
expect_error(plot_spectrogram(
p_seq = 1, per_ints = list(a = 1), peaks = 1,
xlab = "", print = TRUE),
"Assertion on 'peaks' failed")
# checkmate::assert_string(xlab)
expect_error(plot_spectrogram(
p_seq = 1, per_ints = list(a = 1), peaks = dplyr::tibble(),
xlab = 1, print = TRUE),
"Assertion on 'xlab' failed")
# checkmate::assert_flag(print)
expect_error(plot_spectrogram(
p_seq = 1, per_ints = list(a = 1), peaks = dplyr::tibble(),
xlab = "", print = 1),
"Assertion on 'print' failed")
})
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test_that("spectrogram() | general test", {
data <- dplyr::tibble(
index = seq(lubridate::as_datetime("2020-01-01 00:00:00"),
lubridate::as_datetime("2020-01-30 23:59:00"),
by = "min"),
x = rep(seq(1, 3600), times = 12)
) %>%
tsibble::tsibble(index = index)
object <- spectrogram(
data = data, col = "x", p_unit = "hours", p_min = 1, p_max = 100,
p_step = 1, int_unit = "days", int_n = 7, int_step = 5, alpha = 0.05,
print = TRUE) %>%
shush()
checkmate::expect_list(object, len = 2)
checkmate::expect_list(object$periodograms, len = 111)
expect_s3_class(object$spectrogram, "ggplot")
})
test_that("spectrogram() | error test", {
data_1 <- dplyr::tibble(
index = seq(lubridate::as_datetime("2020-01-01 00:00:00"),
lubridate::as_datetime("2020-01-10 00:00:00"),
by = "min"),
x = seq_along(index)
) %>%
tsibble::tsibble(index = index)
data_2 <- dplyr::tibble(index = 1:100, x = seq_along(index)) %>%
tsibble::tsibble(index = index)
data_3 <- dplyr::tibble(
index = c(lubridate::as_datetime(seq(0, 60 * 100, by = 60)),
lubridate::as_datetime(seq(6030, 6030 + (30 * 100),
by = 30))),
x = seq_along(index)
) %>%
tsibble::tsibble(index = index)
data_4 <- dplyr::tibble(
index = seq(as.POSIXct("2015-01-01"), as.POSIXct("2015-01-08"),
by = "min"),
x = ""
) %>%
tsibble::tsibble(index = index)
# assert_tsibble(data, min.rows = 2, min.cols = 2)
expect_error(spectrogram(
data = 1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'data' failed")
expect_error(spectrogram(
data = data_1[1, ], col = "x", p_unit = "minutes", p_min = 1,
p_max = 4600, int_unit = "days", int_n = 7, int_step = 720, p_step = 1,
alpha = 0.05, print = FALSE),
"Assertion on 'data' failed")
expect_error(spectrogram(
data = data_1[, 1], col = "x", p_unit = "minutes", p_min = 1,
p_max = 4600, int_unit = "days", int_n = 7, int_step = 720, p_step = 1,
alpha = 0.05, print = FALSE),
"Assertion on 'data' failed")
# assert_index_class(data, c("Date", "POSIXt"))
expect_error(spectrogram(
data = data_2, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'data' failed")
# assert_clear_epoch(data, 0.9)
expect_error(spectrogram(
data = data_3, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'data' failed")
# checkmate::assert_choice(col, names(data))
expect_error(spectrogram(
data = data_1, col = "a", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'col' failed")
# checkmate::assert_numeric(data[[col]])
expect_error(spectrogram(
data = data_4, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'data\\[\\[col\\]\\]' failed")
# checkmate::assert_choice(p_unit, p_unit_choices)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "a", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'p_unit' failed")
# assert_epoch_compatibility(data, p_unit)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "seconds", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'data' failed")
# checkmate::assert_int(p_min, lower = 1)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = "a",
p_max = 4600, int_unit = "days", int_n = 7, int_step = 720, p_step = 1,
alpha = 0.05, print = FALSE),
"Assertion on 'p_min' failed")
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = -1,
p_max = 4600, int_unit = "days", int_n = 7, int_step = 720, p_step = 1,
alpha = 0.05, print = FALSE),
"Assertion on 'p_min' failed")
# checkmate::assert_int(p_max, lower = 1)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = "a",
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'p_max' failed")
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = -1,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'p_max' failed")
# checkmate::assert_int(p_step, lower = 1)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = "a", int_unit = "days", int_n = 7, int_step = 720,
alpha = 0.05, print = FALSE),
"Assertion on 'p_step' failed")
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = -1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'p_step' failed")
# assert_leq(p_min + p_step, p_max)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 2,
p_step = 2, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'p_min \\+ p_step' failed")
# checkmate::assert_choice(int_unit, p_unit_choices)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "hours", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'int_unit' failed")
# checkmate::assert_int(int_n, lower = 1)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = "", int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'int_n' failed")
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = -1, int_step = 720, alpha = 0.05,
print = FALSE),
"Assertion on 'int_n' failed")
# checkmate::assert_int(int_step, lower = 1)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = "", alpha = 0.05,
print = FALSE),
"Assertion on 'int_step' failed")
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = -1, alpha = 0.05,
print = FALSE),
"Assertion on 'int_step' failed")
# checkmate::assert_number(alpha, lower = 0.001, upper = 0.999)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = -1,
print = FALSE),
"Assertion on 'alpha' failed")
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 2,
print = FALSE),
"Assertion on 'alpha' failed")
# checkmate::assert_flag(print)
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 7, int_step = 720, alpha = 0.05,
print = 1),
"Assertion on 'print' failed")
# if (which(p_unit_choices == int_unit) <= which(p_unit_choices == p_unit))
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "seconds", int_n = 7, int_step = 720,
alpha = 0.05, print = FALSE))
# if (as.numeric(data_int) < as.numeric(string_to_period(int_unit))) {
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "years", int_n = 7, int_step = 720, alpha = 0.05,
print = FALSE))
# if (data_int <= lubridate::as.interval(
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 4600,
p_step = 1, int_unit = "days", int_n = 1000, int_step = 720,
alpha = 0.05, print = FALSE))
# if (int_step >= int_max_n_epoch) {
expect_error(spectrogram(
data = data_1, col = "x", p_unit = "hours", p_min = 1, p_max = 100,
p_step = 1, int_unit = "days", int_n = 1, int_step = 1000000,
alpha = 0.05, print = FALSE))
})
test_that("spectrogram() | warning/message test", {
data_1 <- dplyr::tibble(
index = c(lubridate::as_datetime(seq(0, 60 * 1000, by = 60)),
lubridate::as_datetime(seq(60030, 60030 + (30 * 100),
by = 30))),
x = seq_along(index)
) %>%
tsibble::tsibble(index = index)
data_2 <- dplyr::tibble(
index = lubridate::as_datetime(seq(0, 60 * 1000, by = 60)),
x = c(1:500, rep(as.numeric(NA), length(index) - 500))
) %>%
tsibble::tsibble(index = index)
# warn_regularity(data, 0.99)
expect_message(spectrogram(
data = data_1, col = "x", p_unit = "minutes", p_min = 1, p_max = 100,
p_step = 1, int_unit = "hours", int_n = 1, int_step = 59, alpha = 0.05,
print = FALSE))
# warn_any_missing(data[[col]])
expect_message(spectrogram(
data = data_2, col = "x", p_unit = "minutes", p_min = 1, p_max = 100,
p_step = 1, int_unit = "hours", int_n = 1, int_step = 59, alpha = 0.05,
print = FALSE))
})
test_that("find_spectrogram_intervals() | general test", {
data <- dplyr::tibble(
index = seq(lubridate::as_datetime("2020-01-01 00:00:00"),
lubridate::as_datetime("2020-01-30 23:59:00"),
by = "min"),
x = rep(seq(1, 3600), times = 12)
) %>%
tsibble::tsibble(index = index)
object <- find_spectrogram_intervals(
data = data, int_unit = "days", int_n = 7, int_step = 720) %>%
shush()
expect_equal(dplyr::last(object),
lubridate::interval("2020-01-23 12:00:00",
"2020-01-30 12:00:00"))
})
test_that("find_spectrogram_intervals() | error test", {
data_1 <- dplyr::tibble(
index = seq(lubridate::as_datetime("2020-01-01 00:00:00"),
lubridate::as_datetime("2020-01-10 00:00:00"),
by = "min"),
x = seq_along(index)
) %>%
tsibble::tsibble(index = index)
data_2 <- dplyr::tibble(index = 1:100, x = seq_along(index)) %>%
tsibble::tsibble(index = index)
data_3 <- dplyr::tibble(
index = seq(as.POSIXct("2015-01-01"), as.POSIXct("2015-01-08"),
by = "min"),
x = ""
) %>%
tsibble::tsibble(index = index)
# assert_tsibble(data, min.rows = 2, min.cols = 2)
expect_error(find_spectrogram_intervals(
data = 1, int_unit = "days", int_n = 7, int_step = 720),
"Assertion on 'data' failed")
expect_error(find_spectrogram_intervals(
data = data_1[1, ], int_unit = "days", int_n = 7, int_step = 720),
"Assertion on 'data' failed")
expect_error(find_spectrogram_intervals(
data = data_1[, 1], int_unit = "days", int_n = 7, int_step = 720),
"Assertion on 'data' failed")
# assert_index_class(data, c("Date", "POSIXt"))
expect_error(find_spectrogram_intervals(
data = data_2, int_unit = "days", int_n = 7, int_step = 720),
"Assertion on 'data' failed")
# checkmate::assert_choice(int_unit, int_choices)
expect_error(find_spectrogram_intervals(
data = data_1, int_unit = "", int_n = 7, int_step = 720),
"Assertion on 'int_unit' failed")
# checkmate::assert_int(int_n, lower = 1)
expect_error(find_spectrogram_intervals(
data = data_1, int_unit = "days", int_n = "", int_step = 720),
"Assertion on 'int_n' failed")
expect_error(find_spectrogram_intervals(
data = data_1, int_unit = "days", int_n = -1, int_step = 720),
"Assertion on 'int_n' failed")
# checkmate::assert_int(int_step, lower = 1)
expect_error(find_spectrogram_intervals(
data = data_1, int_unit = "days", int_n = 7, int_step = ""),
"Assertion on 'int_step' failed")
expect_error(find_spectrogram_intervals(
data = data_1, int_unit = "days", int_n = 7, int_step = -1),
"Assertion on 'int_step' failed")
})
test_that("compute_interval_periodogram() | general test", {
data <- dplyr::tibble(
index = seq(lubridate::as_datetime("2020-01-01 00:00:00"),
lubridate::as_datetime("2020-01-30 23:59:00"),
by = "min"),
x = rep(seq(1, 3600), times = 12)
) %>%
tsibble::tsibble(index = index)
envir <- environment()
cli::cli_progress_bar(total = 1, clear = FALSE, .envir = envir)
object <- compute_interval_periodogram(
data = data, col = "x",
int_i = lubridate::interval("2020-01-01 00:00:00",
"2020-01-03 00:00:00"),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = envir)
checkmate::expect_list(object, len = 10)
checkmate::expect_string(object$p_unit)
checkmate::expect_numeric(object$p_seq, len = 1501)
expect_equal(object$int, lubridate::interval("2020-01-01 00:00:00",
"2020-01-03 00:00:00"))
checkmate::expect_number(object$alpha)
checkmate::expect_numeric(object$a_p, len = 1501)
checkmate::expect_numeric(object$q_p, len = 1501)
checkmate::expect_numeric(object$q_p_critical, len = 1501)
checkmate::expect_numeric(object$q_p_rel, len = 1501)
checkmate::expect_numeric(object$q_p_pvalue, len = 1501)
checkmate::expect_tibble(object$q_p_peaks)
})
test_that("compute_interval_periodogram() | error test", {
data_1 <- dplyr::tibble(
index = seq(lubridate::as_datetime("2020-01-01 00:00:00"),
lubridate::as_datetime("2020-01-10 00:00:00"),
by = "min"),
x = seq_along(index)
) %>%
tsibble::tsibble(index = index)
data_2 <- dplyr::tibble(index = 1:100, x = seq_along(index)) %>%
tsibble::tsibble(index = index)
data_3 <- dplyr::tibble(
index = seq(as.POSIXct("2015-01-01"), as.POSIXct("2015-01-08"),
by = "min"),
x = ""
) %>%
tsibble::tsibble(index = index)
# assert_tsibble(data, min.rows = 2, min.cols = 2)
expect_error(compute_interval_periodogram(
data = 1, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'data' failed")
expect_error(compute_interval_periodogram(
data = data_1[1, ], col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'data' failed")
expect_error(compute_interval_periodogram(
data = data_1[, 1], col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'data' failed")
# assert_index_class(data, c("Date", "POSIXt"))
expect_error(compute_interval_periodogram(
data = data_2, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'data' failed")
# checkmate::assert_choice(col, names(data))
expect_error(compute_interval_periodogram(
data = data_1, col = "a",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'col' failed")
# checkmate::assert_numeric(data[[col]])
expect_error(compute_interval_periodogram(
data = data_3, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'data\\[\\[col\\]\\]' failed")
# assert_interval(int_i, any.missing = FALSE)
expect_error(compute_interval_periodogram(
data = data_1, col = "x",
int_i = 1,
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'int_i' failed")
expect_error(compute_interval_periodogram(
data = data_1, col = "x",
int_i = lubridate::as.interval(NA),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'int_i' failed")
# checkmate::assert_string(p_unit)
expect_error(compute_interval_periodogram(
data = data_1, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = 1, p_seq = seq(1000, 2500), alpha = 0.05,
envir = environment()),
"Assertion on 'p_unit' failed")
# checkmate::assert_numeric(p_seq, min.len = 1)
expect_error(compute_interval_periodogram(
data = data_1, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = "a", alpha = 0.05, envir = environment()),
"Assertion on 'p_seq' failed")
expect_error(compute_interval_periodogram(
data = data_1, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = numeric(), alpha = 0.05,
envir = environment()),
"Assertion on 'p_seq' failed")
# checkmate::assert_number(alpha, lower = 0.001, upper = 0.999)
expect_error(compute_interval_periodogram(
data = data_1, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = -1,
envir = environment()),
"Assertion on 'alpha' failed")
expect_error(compute_interval_periodogram(
data = data_1, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 2,
envir = environment()),
"Assertion on 'alpha' failed")
# checkmate::assert_environment(envir, null.ok = TRUE)
expect_error(compute_interval_periodogram(
data = data_1, col = "x",
int_i = lubridate::as.interval(1, as.Date("2020-01-01")),
p_unit = "minutes", p_seq = seq(1000, 2500), alpha = 0.05,
envir = 1),
"Assertion on 'envir' failed")
})
test_that("plot_spectrogram() | general test", {
data <- dplyr::tibble(
index = seq(lubridate::as_datetime("2020-01-01 00:00:00"),
lubridate::as_datetime("2020-01-30 23:59:00"),
by = "min"),
x = rep(seq(1, 3600), times = 12)
) %>%
tsibble::tsibble(index = index)
per <- periodogram(data = data, col = "x", p_min = 1, p_max = 100,
print = FALSE) %>%
shush()
spec <- spectrogram(
data = data, col = "x", p_unit = "hours", p_min = 1, p_max = 100,
p_step = 1, int_unit = "days", int_n = 7, int_step = 5, alpha = 0.05,
print = FALSE) %>%
shush()
expect_s3_class(plot_spectrogram(
p_seq = per$p_seq, per_ints = spec$periodograms, peaks = per$q_p_peaks,
xlab = "Period", print = TRUE),
"ggplot")
})
test_that("plot_spectrogram() | error test", {
# checkmate::assert_numeric(p_seq, min.len = 1)
expect_error(plot_spectrogram(
p_seq = "a", per_ints = list(a = 1), peaks = dplyr::tibble(),
xlab = "", print = TRUE),
"Assertion on 'p_seq' failed")
expect_error(plot_spectrogram(
p_seq = numeric(), per_ints = list(a = 1), peaks = dplyr::tibble(),
xlab = "", print = TRUE),
"Assertion on 'p_seq' failed")
# checkmate::assert_list(per_ints, min.len = 1)
expect_error(plot_spectrogram(
p_seq = 1, per_ints = 1, peaks = dplyr::tibble(),
xlab = "", print = TRUE),
"Assertion on 'per_ints' failed")
expect_error(plot_spectrogram(
p_seq = 1, per_ints = list(), peaks = dplyr::tibble(),
xlab = "", print = TRUE),
"Assertion on 'per_ints' failed")
# checkmate::assert_tibble(peaks)
expect_error(plot_spectrogram(
p_seq = 1, per_ints = list(a = 1), peaks = 1,
xlab = "", print = TRUE),
"Assertion on 'peaks' failed")
# checkmate::assert_string(xlab)
expect_error(plot_spectrogram(
p_seq = 1, per_ints = list(a = 1), peaks = dplyr::tibble(),
xlab = 1, print = TRUE),
"Assertion on 'xlab' failed")
# checkmate::assert_flag(print)
expect_error(plot_spectrogram(
p_seq = 1, per_ints = list(a = 1), peaks = dplyr::tibble(),
xlab = "", print = 1),
"Assertion on 'print' failed")
})
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