tests/testthat/test_statistics.R
In USGS-R/HASP: Hydrologic AnalySis Package
context("Compute Statistical Tests")
test_that("Kendall Seasonal Trend", {
gw_level_data <- L2701_example_data$Discrete
less_data <- dplyr::filter(gw_level_data,
lev_dt > as.Date("2010-01-01"),
lev_dt < as.Date("2014-01-01"))
test1 <- trend_test(NULL,
gwl_data = gw_level_data,
parameter_cd = "62610",
days_required_per_month = 0)
test2 <- expect_message(trend_test(NULL,
less_data,
parameter_cd = "62610",
days_required_per_month = 0))
expect_true(all(c("test", "tau", "pValue", "slope", "intercept", "trend") %in% names(test1)))
expect_true(all(c("test", "tau", "pValue", "slope", "intercept", "trend") %in% names(test2)))
expect_true(all(is.na(c(test2$tau, test2$pValue, test2$slope, test2$intercept))))
expect_true(-0.163 == signif(test1$tau[2], digits = 3))
expect_true(1.08e-05 == signif(test1$pValue[2], digits = 3))
expect_true(-0.22 == signif(test1$slope[2], digits = 3))
expect_true(415 == signif(test1$intercept[2], digits = 3))
expect_true("Down" == test1$trend[2])
#both:
test1 <- trend_test(L2701_example_data$Daily,
gwl_data = gw_level_data,
parameter_cd = "62610",
days_required_per_month = 0)
expect_true(all(c("test", "tau", "pValue", "slope", "intercept", "trend") %in% names(test1)))
expect_equal(test1$trend, c("Up", "Down"))
#only dv:
test1 <- trend_test(L2701_example_data$Daily,
gwl_data = NULL,
parameter_cd = "62610",
days_required_per_month = 0)
expect_true(all(c("test", "tau", "pValue", "slope", "intercept", "trend") %in% names(test1)))
expect_equal(test1$trend, c("Up", "Down"))
test3 <- trend_test(gw_level_dv = NULL,
gwl_data = gw_level_data,
parameter_cd = "62610")
expect_true(-0.163 == signif(test3$tau[2], digits = 3))
qw_data <- L2701_example_data$QW
test4 <- trend_test(NULL,
qw_data,
approved_col = "ResultStatusIdentifier",
date_col = "ActivityStartDateTime",
value_col = "ResultMeasureValue")
expect_true(23.3 == signif(test4$slope[1], digits = 3))
expect_true(2 == signif(test4$slope[2], digits = 3))
test1 <- trend_test(L2701_example_data$Daily,
gwl_data = gw_level_data,
parameter_cd = "62610",
POR_trend = FALSE,
days_required_per_month = 0)
expect_true(all(c("test", "tau", "pValue", "slope", "intercept", "trend") %in% names(test1)))
expect_equal(test1$trend, c("Up"))
})
test_that("Weekly frequency table", {
wft <- weekly_frequency_table(L2701_example_data$Daily,
NULL,
date_col = "Date",
value_col = "X_62610_00001",
approved_col = "X_62610_00001_cd")
expect_equal(as.numeric(head(wft$p25, 6)), c(-28.7, -29.1, -29.3, -29.7, -29.8, -29.1), tolerance = 0.05)
expect_equal(as.numeric(head(wft$nYears, 6)), c(41, 42, 42, 42, 43, 43))
expect_equal(tail(wft$minMed, 6), c(-42.2, -42.4, -42.8, -42.7, -42.5, -40.9), tolerance = 0.05)
wft2 <- weekly_frequency_table(L2701_example_data$Daily,
L2701_example_data$Discrete,
parameter_cd = "62610")
expect_equal(as.numeric(head(wft2$p25, 6)), c(-28.7, -29.1, -29.3, -29.7, -29.8, -29.1), tolerance = 0.05)
expect_equal(as.numeric(head(wft2$nYears, 6)), c(41, 42, 42, 42, 43, 43))
expect_equal(tail(wft2$minMed, 6), c(-42.2, -42.4, -42.8, -42.7, -42.5, -40.9), tolerance = 0.05)
wft2 <- weekly_frequency_table(L2701_example_data$Daily,
L2701_example_data$Discrete,
parameter_cd = "62610",
flip = TRUE)
expect_equal(as.numeric(head(wft2$p25, 6)),
c(-17.55, -17.50, -17.77, -18.28, -18.34, -18.82),
tolerance = 0.05)
expect_equal(as.numeric(head(wft2$nYears, 6)), c(41, 42, 42, 42, 43, 43))
expect_equal(tail(wft2$minMed, 6),
c(-4.91, -4.71, -4.89, -4.71, -4.86, -5.11), tolerance = 0.05)
})
test_that("Monthly frequency table", {
mft <- monthly_frequency_table(L2701_example_data$Daily,
NULL,
date_col = "Date",
value_col = "X_62610_00001",
approved_col = "X_62610_00001_cd")
expect_equal(as.numeric(head(mft$p75, 6)),
c(-18.0575, -19.0500, -20.2625, -22.0500, -23.5100, -21.0200),
tolerance = 0.05)
expect_equal(as.numeric(head(mft$nYears, 6)),
c(42, 43, 42, 42, 42, 41))
expect_equal(tail(mft$maxMed, 6),
c(-6.790, -4.820, -3.240, -4.800, -4.535, -4.860),
tolerance = 0.05)
mft2 <- monthly_frequency_table(L2701_example_data$Daily,
L2701_example_data$Discrete,
parameter_cd = "62610")
expect_equal(as.numeric(head(mft2$p75, 6)),
c(-18.0575, -19.0500, -20.2625, -22.0500, -23.5100, -21.0200),
tolerance = 0.05)
expect_equal(as.numeric(head(mft2$nYears, 6)),
c(43, 43, 43, 42, 42, 41))
expect_equal(tail(mft2$maxMed, 6),
c(-6.790, -4.820, -3.240, -4.800, -4.535, -4.860),
tolerance = 0.05)
mft2 <- monthly_frequency_table(L2701_example_data$Daily,
L2701_example_data$Discrete,
parameter_cd = "62610",
flip = TRUE)
expect_equal(as.numeric(head(mft2$p75, 6)),
c(-29.1325, -29.2400, -30.0975, -32.6600, -35.0900, -33.0800),
tolerance = 0.05)
expect_equal(as.numeric(head(mft2$nYears, 6)),
c(43, 43, 43, 42, 42, 41))
expect_equal(tail(mft2$maxMed, 6),
c(-37.515, -32.360, -32.670, -36.155, -41.400, -42.450),
tolerance = 0.05)
})
test_that("Daily summary table", {
daily_summary_table <- daily_gwl_summary(L2701_example_data$Daily,
NULL,
parameter_cd = "62610")
expect_equal(nrow(daily_summary_table), 1)
expect_equal(daily_summary_table$percent_complete, 96)
expect_equal(daily_summary_table$begin_date, as.Date("1978-10-01"))
expect_equal(daily_summary_table$p25, -28.4, tolerance = 0.005)
expect_equal(daily_summary_table$highest_level, -2.81, tolerance = 0.05)
daily_summary_table2 <- daily_gwl_summary(L2701_example_data$Daily,
L2701_example_data$Discrete,
parameter_cd = "62610")
expect_equal(nrow(daily_summary_table2), 1)
expect_equal(daily_summary_table2$percent_complete, 99)
expect_equal(daily_summary_table2$begin_date, as.Date("1978-10-01"))
expect_equal(daily_summary_table2$p25, -28.4, tolerance = 0.005)
expect_equal(daily_summary_table2$highest_level, -2.81, tolerance = 0.05)
})
test_that("Daily frequency table", {
daily_frequency_table <- daily_frequency_table(L2701_example_data$Daily,
gwl_data = NULL,
date_col = "Date",
value_col = "X_62610_00001",
approved_col = "X_62610_00001_cd")
expect_equal(daily_frequency_table$max[1], -5.29, tolerance = 0.005)
expect_equal(daily_frequency_table$min[365], -42.2, tolerance = 0.05)
expect_equal(daily_frequency_table$mean[183], -24.3, tolerance = 0.05)
daily_frequency_table2 <- daily_frequency_table(L2701_example_data$Daily,
gwl_data = L2701_example_data$Discrete,
parameter_cd = "62610")
expect_equal(daily_frequency_table2$max[1], -5.29, tolerance = 0.005)
expect_equal(daily_frequency_table2$min[365], -42.2, tolerance = 0.05)
expect_equal(daily_frequency_table2$mean[183], -24.3, tolerance = 0.05)
})
test_that("trend segments",{
gw_level_dv <- L2701_example_data$Daily
qw_data <- L2701_example_data$QW
trend_results <- trend_test(gw_level_dv = NULL,
gwl_data = qw_data,
parameter_cd = NA,
date_col = "ActivityStartDateTime",
value_col = "ResultMeasureValue",
approved_col = "ResultStatusIdentifier",
stat_cd = NA)
seg_df <- HASP:::create_segs(trend_results,
qw_data,
value_col = "ResultMeasureValue",
date_col = "ActivityStartDateTime")
expect_true(all(signif(seg_df$x1, digits = 5) == c(2011.3, 1978.7)))
expect_true(all(signif(seg_df$x2, digits = 5) == c(2021.3, 2021.3)))
expect_true(all(seg_df$years == c("10-year trend",
"Period of record")))
expect_true(all(seg_df$trend == c("Up", "Up")))
trend_results <- trend_test(gw_level_dv = gw_level_dv,
gwl_data = NULL,
parameter_cd = "62610",
stat_cd = "00001")
seg_df_dv <- HASP:::create_segs(trend_results,
gw_level_dv,
date_col = "Date",
value_col = "X_62610_00001")
expect_true(all(signif(seg_df$x1, digits = 5) == c(2011.3, 1978.7)))
expect_true(all(signif(seg_df$x2, digits = 5) == c(2021.3, 2021.3)))
expect_true(all(seg_df$years == c("10-year trend",
"Period of record")))
expect_true(all(seg_df$trend == c("Up", "Up")))
expect_true(all(signif(seg_df_dv$y1, digits = 3) == c(-30.1, -15.9)))
expect_true(all(signif(seg_df_dv$y2, digits = 3) == c(-15.4, -27.9)))
gw_monthly <- monthly_mean(gw_level_dv,
date_col = "Date",
value_col = "X_62610_00001")
expect_true(all(names(gw_monthly) %in% c("year", "month", "mean_va", "n_days",
"mid_date")))
expect_type(gw_monthly$year, "double")
expect_type(gw_monthly$month, "double")
expect_type(gw_monthly$mean_va, "double")
expect_type(gw_monthly$n_days, "integer")
expect_true(gw_monthly$mid_date[1] == as.Date("1978-10-15"))
seg_df_month <- HASP:::create_segs(trend_results,
gw_monthly,
date_col = "mid_date",
value_col = "mean_va")
expect_true(all(signif(seg_df_month$x1, digits = 5) == c(2011.7, 1978.8)))
expect_true(all(signif(seg_df_month$x2, digits = 5) == c(2021.7, 2021.7)))
expect_true(all(seg_df_month$years == c("10-year trend",
"Period of record")))
expect_true(all(seg_df_month$trend == c("Up", "Down")))
expect_true(all(signif(seg_df_month$y1, digits = 3) == c(-30.1, -15.9)))
expect_true(all(signif(seg_df_month$y2, digits = 3) == c(-15.4, -27.9)))
})
test_that("utils", {
no_zero <- HASP:::zero_on_top(c(1:10))
yes_zero <- HASP:::zero_on_top(c(-10:-2))
crosses_zero <- HASP:::zero_on_top(c(-10:5))
expect_false(no_zero)
expect_true(yes_zero)
expect_true(is.na(crosses_zero))
ld <- last_day(c("2020-12-28", "2020-02-15", "2019-02-15"))
expect_equal(as.Date(c("2020-12-31", "2020-02-29", "2019-02-28")),
ld)
md <- mid_month(c("2019-02-15", "2020-03-08", "2010-06-01"))
expect_equal(as.Date(c("2019-02-15", "2020-03-16", "2010-06-15")),
md)
fd <- first_day(c("2020-12-28", "2020-02-15", "2019-02-15"))
expect_equal(as.Date(c("2020-12-01", "2020-02-01", "2019-02-01")),
fd)
})
USGS-R/HASP documentation built on July 28, 2024, 7:53 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
context("Compute Statistical Tests")
test_that("Kendall Seasonal Trend", {
gw_level_data <- L2701_example_data$Discrete
less_data <- dplyr::filter(gw_level_data,
lev_dt > as.Date("2010-01-01"),
lev_dt < as.Date("2014-01-01"))
test1 <- trend_test(NULL,
gwl_data = gw_level_data,
parameter_cd = "62610",
days_required_per_month = 0)
test2 <- expect_message(trend_test(NULL,
less_data,
parameter_cd = "62610",
days_required_per_month = 0))
expect_true(all(c("test", "tau", "pValue", "slope", "intercept", "trend") %in% names(test1)))
expect_true(all(c("test", "tau", "pValue", "slope", "intercept", "trend") %in% names(test2)))
expect_true(all(is.na(c(test2$tau, test2$pValue, test2$slope, test2$intercept))))
expect_true(-0.163 == signif(test1$tau[2], digits = 3))
expect_true(1.08e-05 == signif(test1$pValue[2], digits = 3))
expect_true(-0.22 == signif(test1$slope[2], digits = 3))
expect_true(415 == signif(test1$intercept[2], digits = 3))
expect_true("Down" == test1$trend[2])
#both:
test1 <- trend_test(L2701_example_data$Daily,
gwl_data = gw_level_data,
parameter_cd = "62610",
days_required_per_month = 0)
expect_true(all(c("test", "tau", "pValue", "slope", "intercept", "trend") %in% names(test1)))
expect_equal(test1$trend, c("Up", "Down"))
#only dv:
test1 <- trend_test(L2701_example_data$Daily,
gwl_data = NULL,
parameter_cd = "62610",
days_required_per_month = 0)
expect_true(all(c("test", "tau", "pValue", "slope", "intercept", "trend") %in% names(test1)))
expect_equal(test1$trend, c("Up", "Down"))
test3 <- trend_test(gw_level_dv = NULL,
gwl_data = gw_level_data,
parameter_cd = "62610")
expect_true(-0.163 == signif(test3$tau[2], digits = 3))
qw_data <- L2701_example_data$QW
test4 <- trend_test(NULL,
qw_data,
approved_col = "ResultStatusIdentifier",
date_col = "ActivityStartDateTime",
value_col = "ResultMeasureValue")
expect_true(23.3 == signif(test4$slope[1], digits = 3))
expect_true(2 == signif(test4$slope[2], digits = 3))
test1 <- trend_test(L2701_example_data$Daily,
gwl_data = gw_level_data,
parameter_cd = "62610",
POR_trend = FALSE,
days_required_per_month = 0)
expect_true(all(c("test", "tau", "pValue", "slope", "intercept", "trend") %in% names(test1)))
expect_equal(test1$trend, c("Up"))
})
test_that("Weekly frequency table", {
wft <- weekly_frequency_table(L2701_example_data$Daily,
NULL,
date_col = "Date",
value_col = "X_62610_00001",
approved_col = "X_62610_00001_cd")
expect_equal(as.numeric(head(wft$p25, 6)), c(-28.7, -29.1, -29.3, -29.7, -29.8, -29.1), tolerance = 0.05)
expect_equal(as.numeric(head(wft$nYears, 6)), c(41, 42, 42, 42, 43, 43))
expect_equal(tail(wft$minMed, 6), c(-42.2, -42.4, -42.8, -42.7, -42.5, -40.9), tolerance = 0.05)
wft2 <- weekly_frequency_table(L2701_example_data$Daily,
L2701_example_data$Discrete,
parameter_cd = "62610")
expect_equal(as.numeric(head(wft2$p25, 6)), c(-28.7, -29.1, -29.3, -29.7, -29.8, -29.1), tolerance = 0.05)
expect_equal(as.numeric(head(wft2$nYears, 6)), c(41, 42, 42, 42, 43, 43))
expect_equal(tail(wft2$minMed, 6), c(-42.2, -42.4, -42.8, -42.7, -42.5, -40.9), tolerance = 0.05)
wft2 <- weekly_frequency_table(L2701_example_data$Daily,
L2701_example_data$Discrete,
parameter_cd = "62610",
flip = TRUE)
expect_equal(as.numeric(head(wft2$p25, 6)),
c(-17.55, -17.50, -17.77, -18.28, -18.34, -18.82),
tolerance = 0.05)
expect_equal(as.numeric(head(wft2$nYears, 6)), c(41, 42, 42, 42, 43, 43))
expect_equal(tail(wft2$minMed, 6),
c(-4.91, -4.71, -4.89, -4.71, -4.86, -5.11), tolerance = 0.05)
})
test_that("Monthly frequency table", {
mft <- monthly_frequency_table(L2701_example_data$Daily,
NULL,
date_col = "Date",
value_col = "X_62610_00001",
approved_col = "X_62610_00001_cd")
expect_equal(as.numeric(head(mft$p75, 6)),
c(-18.0575, -19.0500, -20.2625, -22.0500, -23.5100, -21.0200),
tolerance = 0.05)
expect_equal(as.numeric(head(mft$nYears, 6)),
c(42, 43, 42, 42, 42, 41))
expect_equal(tail(mft$maxMed, 6),
c(-6.790, -4.820, -3.240, -4.800, -4.535, -4.860),
tolerance = 0.05)
mft2 <- monthly_frequency_table(L2701_example_data$Daily,
L2701_example_data$Discrete,
parameter_cd = "62610")
expect_equal(as.numeric(head(mft2$p75, 6)),
c(-18.0575, -19.0500, -20.2625, -22.0500, -23.5100, -21.0200),
tolerance = 0.05)
expect_equal(as.numeric(head(mft2$nYears, 6)),
c(43, 43, 43, 42, 42, 41))
expect_equal(tail(mft2$maxMed, 6),
c(-6.790, -4.820, -3.240, -4.800, -4.535, -4.860),
tolerance = 0.05)
mft2 <- monthly_frequency_table(L2701_example_data$Daily,
L2701_example_data$Discrete,
parameter_cd = "62610",
flip = TRUE)
expect_equal(as.numeric(head(mft2$p75, 6)),
c(-29.1325, -29.2400, -30.0975, -32.6600, -35.0900, -33.0800),
tolerance = 0.05)
expect_equal(as.numeric(head(mft2$nYears, 6)),
c(43, 43, 43, 42, 42, 41))
expect_equal(tail(mft2$maxMed, 6),
c(-37.515, -32.360, -32.670, -36.155, -41.400, -42.450),
tolerance = 0.05)
})
test_that("Daily summary table", {
daily_summary_table <- daily_gwl_summary(L2701_example_data$Daily,
NULL,
parameter_cd = "62610")
expect_equal(nrow(daily_summary_table), 1)
expect_equal(daily_summary_table$percent_complete, 96)
expect_equal(daily_summary_table$begin_date, as.Date("1978-10-01"))
expect_equal(daily_summary_table$p25, -28.4, tolerance = 0.005)
expect_equal(daily_summary_table$highest_level, -2.81, tolerance = 0.05)
daily_summary_table2 <- daily_gwl_summary(L2701_example_data$Daily,
L2701_example_data$Discrete,
parameter_cd = "62610")
expect_equal(nrow(daily_summary_table2), 1)
expect_equal(daily_summary_table2$percent_complete, 99)
expect_equal(daily_summary_table2$begin_date, as.Date("1978-10-01"))
expect_equal(daily_summary_table2$p25, -28.4, tolerance = 0.005)
expect_equal(daily_summary_table2$highest_level, -2.81, tolerance = 0.05)
})
test_that("Daily frequency table", {
daily_frequency_table <- daily_frequency_table(L2701_example_data$Daily,
gwl_data = NULL,
date_col = "Date",
value_col = "X_62610_00001",
approved_col = "X_62610_00001_cd")
expect_equal(daily_frequency_table$max[1], -5.29, tolerance = 0.005)
expect_equal(daily_frequency_table$min[365], -42.2, tolerance = 0.05)
expect_equal(daily_frequency_table$mean[183], -24.3, tolerance = 0.05)
daily_frequency_table2 <- daily_frequency_table(L2701_example_data$Daily,
gwl_data = L2701_example_data$Discrete,
parameter_cd = "62610")
expect_equal(daily_frequency_table2$max[1], -5.29, tolerance = 0.005)
expect_equal(daily_frequency_table2$min[365], -42.2, tolerance = 0.05)
expect_equal(daily_frequency_table2$mean[183], -24.3, tolerance = 0.05)
})
test_that("trend segments",{
gw_level_dv <- L2701_example_data$Daily
qw_data <- L2701_example_data$QW
trend_results <- trend_test(gw_level_dv = NULL,
gwl_data = qw_data,
parameter_cd = NA,
date_col = "ActivityStartDateTime",
value_col = "ResultMeasureValue",
approved_col = "ResultStatusIdentifier",
stat_cd = NA)
seg_df <- HASP:::create_segs(trend_results,
qw_data,
value_col = "ResultMeasureValue",
date_col = "ActivityStartDateTime")
expect_true(all(signif(seg_df$x1, digits = 5) == c(2011.3, 1978.7)))
expect_true(all(signif(seg_df$x2, digits = 5) == c(2021.3, 2021.3)))
expect_true(all(seg_df$years == c("10-year trend",
"Period of record")))
expect_true(all(seg_df$trend == c("Up", "Up")))
trend_results <- trend_test(gw_level_dv = gw_level_dv,
gwl_data = NULL,
parameter_cd = "62610",
stat_cd = "00001")
seg_df_dv <- HASP:::create_segs(trend_results,
gw_level_dv,
date_col = "Date",
value_col = "X_62610_00001")
expect_true(all(signif(seg_df$x1, digits = 5) == c(2011.3, 1978.7)))
expect_true(all(signif(seg_df$x2, digits = 5) == c(2021.3, 2021.3)))
expect_true(all(seg_df$years == c("10-year trend",
"Period of record")))
expect_true(all(seg_df$trend == c("Up", "Up")))
expect_true(all(signif(seg_df_dv$y1, digits = 3) == c(-30.1, -15.9)))
expect_true(all(signif(seg_df_dv$y2, digits = 3) == c(-15.4, -27.9)))
gw_monthly <- monthly_mean(gw_level_dv,
date_col = "Date",
value_col = "X_62610_00001")
expect_true(all(names(gw_monthly) %in% c("year", "month", "mean_va", "n_days",
"mid_date")))
expect_type(gw_monthly$year, "double")
expect_type(gw_monthly$month, "double")
expect_type(gw_monthly$mean_va, "double")
expect_type(gw_monthly$n_days, "integer")
expect_true(gw_monthly$mid_date[1] == as.Date("1978-10-15"))
seg_df_month <- HASP:::create_segs(trend_results,
gw_monthly,
date_col = "mid_date",
value_col = "mean_va")
expect_true(all(signif(seg_df_month$x1, digits = 5) == c(2011.7, 1978.8)))
expect_true(all(signif(seg_df_month$x2, digits = 5) == c(2021.7, 2021.7)))
expect_true(all(seg_df_month$years == c("10-year trend",
"Period of record")))
expect_true(all(seg_df_month$trend == c("Up", "Down")))
expect_true(all(signif(seg_df_month$y1, digits = 3) == c(-30.1, -15.9)))
expect_true(all(signif(seg_df_month$y2, digits = 3) == c(-15.4, -27.9)))
})
test_that("utils", {
no_zero <- HASP:::zero_on_top(c(1:10))
yes_zero <- HASP:::zero_on_top(c(-10:-2))
crosses_zero <- HASP:::zero_on_top(c(-10:5))
expect_false(no_zero)
expect_true(yes_zero)
expect_true(is.na(crosses_zero))
ld <- last_day(c("2020-12-28", "2020-02-15", "2019-02-15"))
expect_equal(as.Date(c("2020-12-31", "2020-02-29", "2019-02-28")),
ld)
md <- mid_month(c("2019-02-15", "2020-03-08", "2010-06-01"))
expect_equal(as.Date(c("2019-02-15", "2020-03-16", "2010-06-15")),
md)
fd <- first_day(c("2020-12-28", "2020-02-15", "2019-02-15"))
expect_equal(as.Date(c("2020-12-01", "2020-02-01", "2019-02-01")),
fd)
})
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.