Nothing
tests/testthat/tests_flow_normalization.R
In EGRET: Exploration and Graphics for RivEr Trends
context("Flow normalization")
test_that("setupYears", {
testthat::skip_on_cran()
eList <- Choptank_eList
Daily <- getDaily(eList)
#Dec - Feb
AnnualResults <- setupYears(Daily, 4, 10)
expect_equal(nrow(AnnualResults), 32)
expect_equal(signif(AnnualResults$DecYear[1], digits = 7), 1979.917)
expect_equal(signif(AnnualResults$FNConc[1], digits = 7), 1.066795)
expect_equal(signif(AnnualResults$FNFlux[1], digits = 7), 264.495)
expect_equal(signif(AnnualResults$Conc[1], digits = 7), 0.9007685)
expect_equal(signif(AnnualResults$Flux[1], digits = 7), 359.9743)
expect_equal(signif(AnnualResults$Q[1], digits = 7), 5.02106)
AnnualResults_waterYear <- setupYears(Daily)
expect_equal(nrow(AnnualResults_waterYear), 32)
expect_equal(signif(AnnualResults_waterYear$DecYear[1], digits = 7), 1980.249)
expect_equal(signif(AnnualResults_waterYear$FNConc[1], digits = 7), 1.002724)
expect_equal(signif(AnnualResults_waterYear$FNFlux[1], digits = 7), 291.2176)
expect_equal(signif(AnnualResults_waterYear$Conc[1], digits = 7), 0.9485403)
expect_equal(signif(AnnualResults_waterYear$Flux[1], digits = 7), 316.0491)
expect_equal(signif(AnnualResults_waterYear$Q[1], digits = 7), 4.251937)
AnnualResults_calendarYear <- setupYears(Daily, paLong = 12, paStart = 1)
expect_equal(nrow(AnnualResults_calendarYear), 31)
expect_equal(signif(AnnualResults_calendarYear$DecYear[1], digits = 7), 1980.5)
expect_equal(signif(AnnualResults_calendarYear$FNConc[1], digits = 7), 0.9994875)
expect_equal(signif(AnnualResults_calendarYear$FNFlux[1], digits = 7), 292.0164)
expect_equal(signif(AnnualResults_calendarYear$Conc[1], digits = 7), 0.9979275)
expect_equal(signif(AnnualResults_calendarYear$Flux[1], digits = 7), 284.0979)
expect_equal(signif(AnnualResults_calendarYear$Q[1], digits = 7), 3.621384)
eList <- Choptank_eList
expect_equal(as.numeric(signif(eList$Daily$FNConc[1], digits = 6)), 0.972757)
})
test_that("setupYears", {
testthat::skip_on_cran()
eList <- Choptank_eList
tC <- tableChange(eList)
expect_null(tC)
tCS <- tableChangeSingle(eList)
expect_equal(ncol(tCS), 6)
expect_equal(tCS$Year1, c(rep(1981, 6), rep(1986, 5), rep(1991, 4),
rep(1996, 3), rep(2001, 2), 2006))
expect_equal(tCS$Year2, c(seq(from = 1986, to = 2011, by = 5),
seq(from = 1991, to = 2011, by = 5),
seq(from = 1996, to = 2011, by = 5),
seq(from = 2001, to = 2011, by = 5),
seq(from = 2006, to = 2011, by = 5),
2011))
expect_equal(tCS$`change[mg/L]`[1], 0.039)
expect_equal(tCS$`slope[mg/L/yr]`[1], 0.0079)
expect_equal(tCS$`change[%]`[1], 3.9)
expect_equal(tCS$`slope [%/yr]`[1], 0.79)
tR <- tableResults(eList)
expect_true(all(names(tR) %in% c("Year","Discharge [cms]",
"Conc [mg/L]","FN Conc [mg/L]",
"Flux [10^6kg/yr]","FN Flux [10^6kg/yr]")))
expect_equal(tR$Year[1], 1980)
expect_equal(tR$`Discharge [cms]`[1], 4.25)
expect_equal(tR$`Conc [mg/L]`[1], 0.949)
expect_equal(tR$`FN Conc [mg/L]`[1], 1.003)
expect_equal(tR$`Flux [10^6kg/yr]`[1], 0.1154)
expect_equal(tR$`FN Flux [10^6kg/yr]`[1], 0.106)
tR_2 <- tableResults(eList, fluxUnit = 'kgDay', qUnit = 'cms')
expect_true(all(names(tR_2) %in% c("Year","Discharge [cms]",
"Conc [mg/L]","FN Conc [mg/L]",
"Flux [kg/day]","FN Flux [kg/day]")))
eList <- Choptank_eList
tFC <- tableFlowChange(eList, istat=5, yearPoints=c(1985,1990,1995,2001,2005,2009))
expect_true(all(names(tFC) %in% c("year1","year2","change[cfs]","slope[cfs/yr]",
"change[%]","slope[%/yr]")))
expect_equal(tFC$`change[cfs]`[1], 7.4)
expect_equal(tFC$`slope[cfs/yr]`[1], 1.5)
expect_equal(tFC$`change[%]`[1], 6.6)
expect_equal(tFC$`slope[%/yr]`[1], 1.3)
printReturn <- printSeries(eList, 5)
expect_true(all(names(printReturn) %in% c("years","qActual","qSmooth")))
expect_equal(printReturn$qActual[2], 78.3)
expect_equal(printReturn$qSmooth[2], 109)
expect_equal(setSeasonLabelByUser(), "Water Year")
expect_equal(setSeasonLabelByUser(paStartInput = 12,paLongInput = 3), "Season Consisting of Dec Jan Feb")
})
test_that("getSurfaceEstimates",{
eList <- Choptank_eList
Daily_orig <- eList$Daily
Daily_new <- Daily_orig[,c("Date","Q","Julian","Month","Day",
"DecYear","MonthSeq","Qualifier","i",
"LogQ","Q7","Q30")]
eList <- as.egret(eList$INFO, Daily_new, eList$Sample, eList$surfaces)
daily_stuff <- EGRET:::getSurfaceEstimates(eList)
expect_equal(ncol(daily_stuff), 16)
expect_true(all(c("yHat","SE","ConcDay","FluxDay") %in% names(daily_stuff)))
expect_equal(round(head(daily_stuff$yHat),3),
c(-0.165,-0.180,-0.304,
-0.464, -0.487,-0.368))
expect_equal(round(head(daily_stuff$SE),3),
c(0.221,0.221,0.217,0.212,0.211,0.215))
expect_equal(round(head(daily_stuff$ConcDay),3),
c(0.875,0.860,0.764,0.654,0.638,0.721))
expect_equal(round(head(daily_stuff$FluxDay),3),
c(143.356,149.347,181.347,217.747,224.883,199.328))
})
test_that("bin_Qs",{
eList <- Choptank_eList
Daily_orig <- eList$Daily
allLogQsByDayOfYear <- EGRET:::bin_Qs(Daily_orig)
expect_length(allLogQsByDayOfYear, 366)
# This is 364 instead of 366 because 59 and 60 are special
expect_equal(364,sum(32 == sapply(allLogQsByDayOfYear, length)))
expect_equal(round(head(allLogQsByDayOfYear[[1]]),3),
c(1.041,0.425,1.118,0.830,1.773,-0.009))
})
test_that("dateInfo",{
dateInfoA <- makeDateInfo(windowSide = 7,
surfaceStart = "1980-10-01",
surfaceEnd = "1981-09-30",
firstQDate0 = "1970-10-01",
lastQDate0 = "2017-09-30")
expect_equal(nrow(dateInfoA), 1)
expect_equal(dateInfoA[["flowNormStart"]][1], as.Date("1973-10-01"))
expect_equal(dateInfoA[["flowNormEnd"]][1], as.Date("1988-09-30"))
expect_equal(dateInfoA[["flowStart"]][1], as.Date("1980-10-01"))
expect_equal(dateInfoA[["flowEnd"]][1], as.Date("1981-09-30"))
dateInfoB <- makeDateInfo(windowSide = 7,
surfaceStart = "1980-10-01",
surfaceEnd = "2017-09-30",
firstQDate0 = "1970-10-01",
lastQDate0 = "2017-09-30")
expect_equal(dateInfoB[["flowNormStart"]][1], as.Date("1973-10-01"))
expect_equal(dateInfoB[["flowNormStart"]][37], as.Date("2002-10-01"))
expect_equal(dateInfoB[["flowNormEnd"]][1], as.Date("1988-09-30"))
expect_equal(dateInfoB[["flowNormEnd"]][37], as.Date("2017-09-30"))
expect_equal(dateInfoB[["flowStart"]][1], as.Date("1980-10-01"))
expect_equal(dateInfoB[["flowStart"]][37], as.Date("2016-10-01"))
expect_equal(dateInfoB[["flowEnd"]][1], as.Date("1981-09-30"))
expect_equal(dateInfoB[["flowEnd"]][37], as.Date("2017-09-30"))
dateInfoC <- makeDateInfo(windowSide = 7,
surfaceStart = "1980-02-01",
surfaceEnd = "1984-01-31",
firstQDate0 = "1970-10-01",
lastQDate0 = "2017-09-30")
expect_equal(nrow(dateInfoC), 4)
expect_equal(dateInfoC[["flowNormStart"]][1], as.Date("1973-02-01"))
expect_equal(dateInfoC[["flowNormStart"]][4], as.Date("1976-02-01"))
expect_equal(dateInfoC[["flowNormEnd"]][1], as.Date("1988-01-31"))
expect_equal(dateInfoC[["flowNormEnd"]][4], as.Date("1991-01-31"))
expect_equal(dateInfoC[["flowStart"]][1], as.Date("1980-02-01"))
expect_equal(dateInfoC[["flowStart"]][4], as.Date("1983-02-01"))
expect_equal(dateInfoC[["flowEnd"]][1], as.Date("1981-01-31"))
expect_equal(dateInfoC[["flowEnd"]][4], as.Date("1984-01-31"))
dateInfoD <- makeDateInfo(windowSide = 50,
surfaceStart = "1980-02-01",
surfaceEnd = "1984-01-31",
firstQDate0 = "1970-10-01",
lastQDate0 = "2017-09-30")
expect_equal(nrow(dateInfoD), 4)
expect_equal(dateInfoD[["flowNormStart"]][1], as.Date("1970-10-01"))
expect_equal(dateInfoD[["flowNormStart"]][4], as.Date("1970-10-01"))
# expect_equal(dateInfoD[["flowNormEnd"]][1], as.Date("2017-09-30"))
# expect_equal(dateInfoD[["flowNormEnd"]][4], as.Date("2017-09-30"))
expect_equal(dateInfoD[["flowStart"]][1], as.Date("1980-02-01"))
expect_equal(dateInfoD[["flowStart"]][4], as.Date("1983-02-01"))
expect_equal(dateInfoD[["flowEnd"]][1], as.Date("1981-01-31"))
expect_equal(dateInfoD[["flowEnd"]][4], as.Date("1984-01-31"))
})
test_that("getConcFluxFromSurface",{
eList <- Choptank_eList
localDaily <- eList$Daily
# Calculate "flow-normalized" concentration and flux:
allLogQsByDayOfYear <- EGRET:::bin_Qs(localDaily)
concFlux_list <- EGRET:::getConcFluxFromSurface(eList, allLogQsByDayOfYear, localDaily)
expect_length(concFlux_list, 3)
expect_type(concFlux_list, "list")
expect_equal(round(head(concFlux_list[["allFluxReplicated"]]),3),
c(143.356,100.241,88.592,47.434,88.592,92.699))
expect_equal(round(head(concFlux_list[["allConcReplicated"]]),3),
c(0.875,1.024,1.065,1.212,1.065,1.052))
expect_equal(round(head(concFlux_list[["allDatesReplicated"]]),3),
c(1979.75,1979.75,1979.75,1979.75,1979.75,1979.75))
})
test_that("flexFN",{
skip_on_cran()
eList <- Choptank_eList
eList <- setUpEstimation(eList)
flowNormStart <- c("1979-10-01","1990-01-01","1992-10-10")
flowNormEnd <- c("1995-06-06","2004-03-03","2011-09-29")
flowStart <- c("1979-10-01","1995-06-07","2004-03-04")
flowEnd <- c("1995-06-06","2004-03-03","2011-09-29")
dateInfo <- data.frame(flowNormStart,
flowNormEnd,
flowStart,
flowEnd,
stringsAsFactors = FALSE)
newEList <- flexFN(eList, dateInfo)
expect_true("segmentInfo" %in% names(attributes(newEList$INFO)))
segmentInfo <- attr(newEList$INFO, "segmentInfo")
expect_equal(segmentInfo, dateInfo)
expect_true(!(all(eList$Daily$FNFlux == newEList$Daily$FNFlux)))
})
test_that("runPairs",{
skip_on_cran()
eList <- Choptank_eList
year1 <- 1985
year2 <- 2010
#Option 1:
pairOut_1 <- runPairs(eList, year1, year2, windowSide = 0)
pairOut_1_orig <- runPairs(eList, year1, year2, windowSide = 0, oldSurface = TRUE)
expect_equal(attr(pairOut_1, "dateInfo"), attr(pairOut_1_orig, "dateInfo"))
expect_equal(attr(pairOut_1, "yearPair"), attr(pairOut_1_orig, "yearPair"))
expect_true(all(names(pairOut_1) %in% c("TotalChange","CQTC","QTC","x10","x11","x20","x22")))
expect_equal(round(pairOut_1$TotalChange[1], digits = 4), 0.429)
expect_equal(round(attr(pairOut_1, "Other")[["PercentChangeConc"]][["Total Percent Change"]],digits = 2),
42.27)
expect_equal(round(attr(pairOut_1, "Other")[["PercentChangeConc"]][["CQTC Percent"]],digits = 2),
42.27)
expect_equal(round(attr(pairOut_1, "Other")[["PercentChangeConc"]][["QTC Percent"]],digits = 2),
0)
expect_equal(round(attr(pairOut_1, "Other")[["PercentChangeFlux"]][["Total Percent Change"]],digits = 2),
29.44)
expect_equal(round(attr(pairOut_1, "Other")[["PercentChangeFlux"]][["CQTC Percent"]],digits = 2),
29.44)
expect_equal(round(attr(pairOut_1, "Other")[["PercentChangeFlux"]][["QTC Percent"]],digits = 2),
0)
# Option 2:
pairOut_2 <- runPairs(eList, year1, year2, windowSide = 7)
expect_true(all(names(pairOut_2) %in% c("TotalChange","CQTC","QTC","x10","x11","x20","x22")))
expect_equal(round(pairOut_2$TotalChange[1], digits = 4), 0.3968)
expect_equal(round(pairOut_1$TotalChange[1], digits = 4), 0.429)
expect_equal(round(attr(pairOut_2, "Other")[["PercentChangeConc"]][["Total Percent Change"]],digits = 2),
38.56)
expect_equal(round(attr(pairOut_2, "Other")[["PercentChangeConc"]][["CQTC Percent"]],digits = 2),
41.7)
expect_equal(round(attr(pairOut_2, "Other")[["PercentChangeConc"]][["QTC Percent"]],digits = 2),
-3.13)
expect_equal(round(attr(pairOut_2, "Other")[["PercentChangeFlux"]][["Total Percent Change"]],digits = 2),
50.68)
expect_equal(round(attr(pairOut_2, "Other")[["PercentChangeFlux"]][["CQTC Percent"]],digits = 2),
31.94)
expect_equal(round(attr(pairOut_2, "Other")[["PercentChangeFlux"]][["QTC Percent"]],digits = 2),
18.74)
# Option 3:
pairOut_3 <- runPairs(eList, year1, year2,
windowSide = 0, flowBreak = TRUE,
Q1EndDate = "1990-09-30")
expect_true(all(names(pairOut_3) %in% c("TotalChange","CQTC","QTC","x10","x11","x20","x22")))
expect_equal(round(pairOut_3$TotalChange[1], digits = 4), 0.4081)
expect_equal(round(attr(pairOut_3, "Other")[["PercentChangeConc"]][["Total Percent Change"]],digits = 2),
39.77)
expect_equal(round(attr(pairOut_3, "Other")[["PercentChangeConc"]][["CQTC Percent"]],digits = 2),
41.81)
expect_equal(round(attr(pairOut_3, "Other")[["PercentChangeConc"]][["QTC Percent"]],digits = 2),
-2.04)
expect_equal(round(attr(pairOut_3, "Other")[["PercentChangeFlux"]][["Total Percent Change"]],digits = 2),
45.81)
expect_equal(round(attr(pairOut_3, "Other")[["PercentChangeFlux"]][["CQTC Percent"]],digits = 2),
31.89)
expect_equal(round(attr(pairOut_3, "Other")[["PercentChangeFlux"]][["QTC Percent"]],digits = 2),
13.91)
# Option 4:
pairOut_4 <- runPairs(eList, year1, year2,
windowSide = 7, flowBreak = TRUE,
Q1EndDate = "1990-09-30")
expect_true(all(names(pairOut_4) %in% c("TotalChange","CQTC","QTC","x10","x11","x20","x22")))
expect_equal(round(pairOut_4$TotalChange[1], digits = 4), 0.3995)
expect_equal(round(attr(pairOut_4, "Other")[["PercentChangeConc"]][["Total Percent Change"]],digits = 2),
38.93)
expect_equal(round(attr(pairOut_4, "Other")[["PercentChangeConc"]][["CQTC Percent"]],digits = 2),
41.81)
expect_equal(round(attr(pairOut_4, "Other")[["PercentChangeConc"]][["QTC Percent"]],digits = 2),
-2.88)
expect_equal(round(attr(pairOut_4, "Other")[["PercentChangeFlux"]][["Total Percent Change"]],digits = 2),
50.44)
expect_equal(round(attr(pairOut_4, "Other")[["PercentChangeFlux"]][["CQTC Percent"]],digits = 2),
31.89)
expect_equal(round(attr(pairOut_4, "Other")[["PercentChangeFlux"]][["QTC Percent"]],digits = 2),
18.55)
})
test_that("runSeries", {
skip_on_cran()
eList <- Choptank_eList
#Option 1:
seriesOut_1 <- runSeries(eList, windowSide = 0)
seriesOut_1_orig <- runSeries(eList, windowSide = 0, oldSurface = TRUE)
expect_equal(class(seriesOut_1),"egret")
expect_equal(class(seriesOut_1_orig),"egret")
expect_true(attr(seriesOut_1, "runSeries"))
expect_true(attr(seriesOut_1_orig, "runSeries"))
expect_equal(round(attr(seriesOut_1$surfaces, "LogQ")[1], digits = 2), -4.66)
expect_equal(round(attr(seriesOut_1$surfaces, "Year")[1], digits = 2), 1979.69)
# Option 2:
seriesOut_2 <- runSeries(eList, windowSide = 7, oldSurface = TRUE)
expect_equal(class(seriesOut_2),"egret")
expect_true(attr(seriesOut_2, "runSeries"))
# Option 3:
seriesOut_3 <- runSeries(eList,
windowSide = 0,
flowBreak = TRUE,
Q1EndDate = "1990-09-30")
expect_equal(class(seriesOut_3),"egret")
expect_true(attr(seriesOut_3, "runSeries"))
expect_equal(round(attr(seriesOut_3$surfaces, "LogQ")[1], digits = 2), -4.66)
expect_equal(round(attr(seriesOut_3$surfaces, "Year")[1], digits = 2), 1979.69)
# Option 4:
seriesOut_4 <- runSeries(eList,
windowSide = 7, flowBreak = TRUE,
Q1EndDate = "1990-09-30")
expect_equal(class(seriesOut_4),"egret")
expect_true(attr(seriesOut_4, "runSeries"))
expect_equal(round(attr(seriesOut_4$surfaces, "LogQ")[1], digits = 2), -4.66)
expect_equal(round(attr(seriesOut_4$surfaces, "Year")[1], digits = 2), 1979.69)
})
test_that("runGroups", {
skip_on_cran()
eList <- Choptank_eList
groupOut_1 <- runGroups(eList, windowSide = 0,
group1firstYear = 1980, group1lastYear = 1990,
group2firstYear = 1995, group2lastYear = 2005)
expect_true(all(names(groupOut_1) %in% c("TotalChange","CQTC","QTC","x10",
"x11","x20","x22")))
expect_true(all(round(groupOut_1$TotalChange, digits = 3) %in% c(0.226,0.022)))
expect_true(all(round(groupOut_1$CQTC, digits = 3) %in% c(0.226,0.022)))
expect_true(all(round(groupOut_1$QTC, digits = 3) %in% c(0,0)))
expect_true(all(round(groupOut_1$x10, digits = 3) %in% c(1.019,0.116)))
expect_true(all(round(groupOut_1$x11, digits = 3) %in% c(1.019,0.116)))
expect_true(all(round(groupOut_1$x20, digits = 3) %in% c(1.245,0.138)))
expect_true(all(round(groupOut_1$x22, digits = 3) %in% c(1.245,0.138)))
# Option 2: Use sliding window.
# In each case it is a 15 year window (15 = 1 + 2*7)
groupOut_2 <- runGroups(eList, windowSide = 7,
group1firstYear = 1980, group1lastYear = 1990,
group2firstYear = 1995, group2lastYear = 2005)
expect_true(all(names(groupOut_2) %in% c("TotalChange","CQTC","QTC","x10",
"x11","x20","x22")))
expect_true(all(round(groupOut_2$TotalChange, digits = 3) %in% c(0.200,0.039)))
expect_true(all(round(groupOut_2$CQTC, digits = 3) %in% c(0.226,0.022)))
expect_true(all(round(groupOut_2$QTC, digits = 3) %in% c(-0.025,0.017)))
expect_true(all(round(groupOut_2$x10, digits = 3) %in% c(1.019,0.116)))
expect_true(all(round(groupOut_2$x11, digits = 3) %in% c(1.034,0.107)))
expect_true(all(round(groupOut_2$x20, digits = 3) %in% c(1.245,0.138)))
expect_true(all(round(groupOut_2$x22, digits = 3) %in% c(1.234,0.146)))
# Option 3: Flow normalization is based on splitting the flow record at 1990-09-30
# But in years before the break it uses all flow data from before the break,
# and years after the break uses all flow data after the break
groupOut_3 <- runGroups(eList, windowSide = 0,
group1firstYear = 1980, group1lastYear = 1990,
group2firstYear = 1995, group2lastYear = 2005,
flowBreak = TRUE,
Q1EndDate = "1990-09-30")
expect_true(all(round(groupOut_3$TotalChange, digits = 3) %in% c(0.207,0.037)))
expect_true(all(round(groupOut_3$CQTC, digits = 3) %in% c(0.226,0.022)))
expect_true(all(round(groupOut_3$QTC, digits = 3) %in% c(-0.019,0.015)))
expect_true(all(round(groupOut_3$x10, digits = 3) %in% c(1.019,0.116)))
expect_true(all(round(groupOut_3$x11, digits = 3) %in% c(1.031,0.107)))
expect_true(all(round(groupOut_3$x20, digits = 3) %in% c(1.245,0.138)))
expect_true(all(round(groupOut_3$x22, digits = 3) %in% c(1.238,0.144)))
expect_true(all(names(groupOut_3) %in% c("TotalChange","CQTC","QTC","x10",
"x11","x20","x22")))
# Option 4: Flow normalization is based on splitting the flow record at 1990-09-30
# but before the break uses a 15 year window of years before the break
# after the break uses a 15 year window of years after the break
groupOut_4 <- runGroups(eList, windowSide = 7,
group1firstYear = 1980, group1lastYear = 1990,
group2firstYear = 1995, group2lastYear = 2005,
flowBreak = TRUE,
Q1EndDate = "1990-09-30")
expect_true(all(names(groupOut_4) %in% c("TotalChange","CQTC","QTC","x10",
"x11","x20","x22")))
expect_true(all(round(groupOut_4$TotalChange, digits = 3) %in% c(0.203,0.040)))
expect_true(all(round(groupOut_4$CQTC, digits = 3) %in% c(0.226,0.022)))
expect_true(all(round(groupOut_4$QTC, digits = 3) %in% c(-0.023,0.018)))
expect_true(all(round(groupOut_4$x10, digits = 3) %in% c(1.019,0.116)))
expect_true(all(round(groupOut_4$x11, digits = 3) %in% c(1.031,0.107)))
expect_true(all(round(groupOut_4$x20, digits = 3) %in% c(1.245,0.138)))
expect_true(all(round(groupOut_4$x22, digits = 3) %in% c(1.234,0.147)))
})
test_that("stitch", {
skip_on_cran()
eList <- Choptank_eList
surfaceStart <- "1986-10-01"
surfaceEnd <- "2012-09-30"
# Surface skips a few years:
sample1StartDate <- "1986-10-01"
sample1EndDate <- "1992-09-30"
sample2StartDate <- "1996-10-01"
sample2EndDate <- "2012-09-30"
surface_skip <- stitch(eList,
sample1StartDate, sample1EndDate,
sample2StartDate, sample2EndDate,
surfaceStart, surfaceEnd)
expect_true(all(names(attributes(surface_skip)) %in%
c("dim","surfaceIndex","Year","LogQ",
"surfaceStart","surfaceEnd","sample1StartDate",
"sample1EndDate","sample2StartDate","sample2EndDate")))
expect_equal(attr(surface_skip, "surfaceStart"), as.Date(surfaceStart))
expect_equal(attr(surface_skip, "sample1EndDate"), sample1EndDate)
expect_true(!(dim(surface_skip)[2] == dim(eList$surfaces)[2]))
expect_true(dim(surface_skip)[1] == dim(eList$surfaces)[1])
expect_true(dim(surface_skip)[3] == dim(eList$surfaces)[3])
# Surface overlaps a few years:
sample1StartDate <- "1986-10-01"
sample1EndDate <- "1996-09-30"
sample2StartDate <- "1992-10-01"
sample2EndDate <- "2012-09-30"
surface_overlap <- stitch(eList,
sample1StartDate, sample1EndDate,
sample2StartDate, sample2EndDate)
expect_equal(attr(surface_overlap, "sample1EndDate"), sample1EndDate)
expect_true(!(dim(surface_overlap)[2] == dim(eList$surfaces)[2]))
expect_true(dim(surface_overlap)[1] == dim(eList$surfaces)[1])
expect_true(dim(surface_overlap)[3] == dim(eList$surfaces)[3])
})
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context("Flow normalization")
test_that("setupYears", {
testthat::skip_on_cran()
eList <- Choptank_eList
Daily <- getDaily(eList)
#Dec - Feb
AnnualResults <- setupYears(Daily, 4, 10)
expect_equal(nrow(AnnualResults), 32)
expect_equal(signif(AnnualResults$DecYear[1], digits = 7), 1979.917)
expect_equal(signif(AnnualResults$FNConc[1], digits = 7), 1.066795)
expect_equal(signif(AnnualResults$FNFlux[1], digits = 7), 264.495)
expect_equal(signif(AnnualResults$Conc[1], digits = 7), 0.9007685)
expect_equal(signif(AnnualResults$Flux[1], digits = 7), 359.9743)
expect_equal(signif(AnnualResults$Q[1], digits = 7), 5.02106)
AnnualResults_waterYear <- setupYears(Daily)
expect_equal(nrow(AnnualResults_waterYear), 32)
expect_equal(signif(AnnualResults_waterYear$DecYear[1], digits = 7), 1980.249)
expect_equal(signif(AnnualResults_waterYear$FNConc[1], digits = 7), 1.002724)
expect_equal(signif(AnnualResults_waterYear$FNFlux[1], digits = 7), 291.2176)
expect_equal(signif(AnnualResults_waterYear$Conc[1], digits = 7), 0.9485403)
expect_equal(signif(AnnualResults_waterYear$Flux[1], digits = 7), 316.0491)
expect_equal(signif(AnnualResults_waterYear$Q[1], digits = 7), 4.251937)
AnnualResults_calendarYear <- setupYears(Daily, paLong = 12, paStart = 1)
expect_equal(nrow(AnnualResults_calendarYear), 31)
expect_equal(signif(AnnualResults_calendarYear$DecYear[1], digits = 7), 1980.5)
expect_equal(signif(AnnualResults_calendarYear$FNConc[1], digits = 7), 0.9994875)
expect_equal(signif(AnnualResults_calendarYear$FNFlux[1], digits = 7), 292.0164)
expect_equal(signif(AnnualResults_calendarYear$Conc[1], digits = 7), 0.9979275)
expect_equal(signif(AnnualResults_calendarYear$Flux[1], digits = 7), 284.0979)
expect_equal(signif(AnnualResults_calendarYear$Q[1], digits = 7), 3.621384)
eList <- Choptank_eList
expect_equal(as.numeric(signif(eList$Daily$FNConc[1], digits = 6)), 0.972757)
})
test_that("setupYears", {
testthat::skip_on_cran()
eList <- Choptank_eList
tC <- tableChange(eList)
expect_null(tC)
tCS <- tableChangeSingle(eList)
expect_equal(ncol(tCS), 6)
expect_equal(tCS$Year1, c(rep(1981, 6), rep(1986, 5), rep(1991, 4),
rep(1996, 3), rep(2001, 2), 2006))
expect_equal(tCS$Year2, c(seq(from = 1986, to = 2011, by = 5),
seq(from = 1991, to = 2011, by = 5),
seq(from = 1996, to = 2011, by = 5),
seq(from = 2001, to = 2011, by = 5),
seq(from = 2006, to = 2011, by = 5),
2011))
expect_equal(tCS$`change[mg/L]`[1], 0.039)
expect_equal(tCS$`slope[mg/L/yr]`[1], 0.0079)
expect_equal(tCS$`change[%]`[1], 3.9)
expect_equal(tCS$`slope [%/yr]`[1], 0.79)
tR <- tableResults(eList)
expect_true(all(names(tR) %in% c("Year","Discharge [cms]",
"Conc [mg/L]","FN Conc [mg/L]",
"Flux [10^6kg/yr]","FN Flux [10^6kg/yr]")))
expect_equal(tR$Year[1], 1980)
expect_equal(tR$`Discharge [cms]`[1], 4.25)
expect_equal(tR$`Conc [mg/L]`[1], 0.949)
expect_equal(tR$`FN Conc [mg/L]`[1], 1.003)
expect_equal(tR$`Flux [10^6kg/yr]`[1], 0.1154)
expect_equal(tR$`FN Flux [10^6kg/yr]`[1], 0.106)
tR_2 <- tableResults(eList, fluxUnit = 'kgDay', qUnit = 'cms')
expect_true(all(names(tR_2) %in% c("Year","Discharge [cms]",
"Conc [mg/L]","FN Conc [mg/L]",
"Flux [kg/day]","FN Flux [kg/day]")))
eList <- Choptank_eList
tFC <- tableFlowChange(eList, istat=5, yearPoints=c(1985,1990,1995,2001,2005,2009))
expect_true(all(names(tFC) %in% c("year1","year2","change[cfs]","slope[cfs/yr]",
"change[%]","slope[%/yr]")))
expect_equal(tFC$`change[cfs]`[1], 7.4)
expect_equal(tFC$`slope[cfs/yr]`[1], 1.5)
expect_equal(tFC$`change[%]`[1], 6.6)
expect_equal(tFC$`slope[%/yr]`[1], 1.3)
printReturn <- printSeries(eList, 5)
expect_true(all(names(printReturn) %in% c("years","qActual","qSmooth")))
expect_equal(printReturn$qActual[2], 78.3)
expect_equal(printReturn$qSmooth[2], 109)
expect_equal(setSeasonLabelByUser(), "Water Year")
expect_equal(setSeasonLabelByUser(paStartInput = 12,paLongInput = 3), "Season Consisting of Dec Jan Feb")
})
test_that("getSurfaceEstimates",{
eList <- Choptank_eList
Daily_orig <- eList$Daily
Daily_new <- Daily_orig[,c("Date","Q","Julian","Month","Day",
"DecYear","MonthSeq","Qualifier","i",
"LogQ","Q7","Q30")]
eList <- as.egret(eList$INFO, Daily_new, eList$Sample, eList$surfaces)
daily_stuff <- EGRET:::getSurfaceEstimates(eList)
expect_equal(ncol(daily_stuff), 16)
expect_true(all(c("yHat","SE","ConcDay","FluxDay") %in% names(daily_stuff)))
expect_equal(round(head(daily_stuff$yHat),3),
c(-0.165,-0.180,-0.304,
-0.464, -0.487,-0.368))
expect_equal(round(head(daily_stuff$SE),3),
c(0.221,0.221,0.217,0.212,0.211,0.215))
expect_equal(round(head(daily_stuff$ConcDay),3),
c(0.875,0.860,0.764,0.654,0.638,0.721))
expect_equal(round(head(daily_stuff$FluxDay),3),
c(143.356,149.347,181.347,217.747,224.883,199.328))
})
test_that("bin_Qs",{
eList <- Choptank_eList
Daily_orig <- eList$Daily
allLogQsByDayOfYear <- EGRET:::bin_Qs(Daily_orig)
expect_length(allLogQsByDayOfYear, 366)
# This is 364 instead of 366 because 59 and 60 are special
expect_equal(364,sum(32 == sapply(allLogQsByDayOfYear, length)))
expect_equal(round(head(allLogQsByDayOfYear[[1]]),3),
c(1.041,0.425,1.118,0.830,1.773,-0.009))
})
test_that("dateInfo",{
dateInfoA <- makeDateInfo(windowSide = 7,
surfaceStart = "1980-10-01",
surfaceEnd = "1981-09-30",
firstQDate0 = "1970-10-01",
lastQDate0 = "2017-09-30")
expect_equal(nrow(dateInfoA), 1)
expect_equal(dateInfoA[["flowNormStart"]][1], as.Date("1973-10-01"))
expect_equal(dateInfoA[["flowNormEnd"]][1], as.Date("1988-09-30"))
expect_equal(dateInfoA[["flowStart"]][1], as.Date("1980-10-01"))
expect_equal(dateInfoA[["flowEnd"]][1], as.Date("1981-09-30"))
dateInfoB <- makeDateInfo(windowSide = 7,
surfaceStart = "1980-10-01",
surfaceEnd = "2017-09-30",
firstQDate0 = "1970-10-01",
lastQDate0 = "2017-09-30")
expect_equal(dateInfoB[["flowNormStart"]][1], as.Date("1973-10-01"))
expect_equal(dateInfoB[["flowNormStart"]][37], as.Date("2002-10-01"))
expect_equal(dateInfoB[["flowNormEnd"]][1], as.Date("1988-09-30"))
expect_equal(dateInfoB[["flowNormEnd"]][37], as.Date("2017-09-30"))
expect_equal(dateInfoB[["flowStart"]][1], as.Date("1980-10-01"))
expect_equal(dateInfoB[["flowStart"]][37], as.Date("2016-10-01"))
expect_equal(dateInfoB[["flowEnd"]][1], as.Date("1981-09-30"))
expect_equal(dateInfoB[["flowEnd"]][37], as.Date("2017-09-30"))
dateInfoC <- makeDateInfo(windowSide = 7,
surfaceStart = "1980-02-01",
surfaceEnd = "1984-01-31",
firstQDate0 = "1970-10-01",
lastQDate0 = "2017-09-30")
expect_equal(nrow(dateInfoC), 4)
expect_equal(dateInfoC[["flowNormStart"]][1], as.Date("1973-02-01"))
expect_equal(dateInfoC[["flowNormStart"]][4], as.Date("1976-02-01"))
expect_equal(dateInfoC[["flowNormEnd"]][1], as.Date("1988-01-31"))
expect_equal(dateInfoC[["flowNormEnd"]][4], as.Date("1991-01-31"))
expect_equal(dateInfoC[["flowStart"]][1], as.Date("1980-02-01"))
expect_equal(dateInfoC[["flowStart"]][4], as.Date("1983-02-01"))
expect_equal(dateInfoC[["flowEnd"]][1], as.Date("1981-01-31"))
expect_equal(dateInfoC[["flowEnd"]][4], as.Date("1984-01-31"))
dateInfoD <- makeDateInfo(windowSide = 50,
surfaceStart = "1980-02-01",
surfaceEnd = "1984-01-31",
firstQDate0 = "1970-10-01",
lastQDate0 = "2017-09-30")
expect_equal(nrow(dateInfoD), 4)
expect_equal(dateInfoD[["flowNormStart"]][1], as.Date("1970-10-01"))
expect_equal(dateInfoD[["flowNormStart"]][4], as.Date("1970-10-01"))
# expect_equal(dateInfoD[["flowNormEnd"]][1], as.Date("2017-09-30"))
# expect_equal(dateInfoD[["flowNormEnd"]][4], as.Date("2017-09-30"))
expect_equal(dateInfoD[["flowStart"]][1], as.Date("1980-02-01"))
expect_equal(dateInfoD[["flowStart"]][4], as.Date("1983-02-01"))
expect_equal(dateInfoD[["flowEnd"]][1], as.Date("1981-01-31"))
expect_equal(dateInfoD[["flowEnd"]][4], as.Date("1984-01-31"))
})
test_that("getConcFluxFromSurface",{
eList <- Choptank_eList
localDaily <- eList$Daily
# Calculate "flow-normalized" concentration and flux:
allLogQsByDayOfYear <- EGRET:::bin_Qs(localDaily)
concFlux_list <- EGRET:::getConcFluxFromSurface(eList, allLogQsByDayOfYear, localDaily)
expect_length(concFlux_list, 3)
expect_type(concFlux_list, "list")
expect_equal(round(head(concFlux_list[["allFluxReplicated"]]),3),
c(143.356,100.241,88.592,47.434,88.592,92.699))
expect_equal(round(head(concFlux_list[["allConcReplicated"]]),3),
c(0.875,1.024,1.065,1.212,1.065,1.052))
expect_equal(round(head(concFlux_list[["allDatesReplicated"]]),3),
c(1979.75,1979.75,1979.75,1979.75,1979.75,1979.75))
})
test_that("flexFN",{
skip_on_cran()
eList <- Choptank_eList
eList <- setUpEstimation(eList)
flowNormStart <- c("1979-10-01","1990-01-01","1992-10-10")
flowNormEnd <- c("1995-06-06","2004-03-03","2011-09-29")
flowStart <- c("1979-10-01","1995-06-07","2004-03-04")
flowEnd <- c("1995-06-06","2004-03-03","2011-09-29")
dateInfo <- data.frame(flowNormStart,
flowNormEnd,
flowStart,
flowEnd,
stringsAsFactors = FALSE)
newEList <- flexFN(eList, dateInfo)
expect_true("segmentInfo" %in% names(attributes(newEList$INFO)))
segmentInfo <- attr(newEList$INFO, "segmentInfo")
expect_equal(segmentInfo, dateInfo)
expect_true(!(all(eList$Daily$FNFlux == newEList$Daily$FNFlux)))
})
test_that("runPairs",{
skip_on_cran()
eList <- Choptank_eList
year1 <- 1985
year2 <- 2010
#Option 1:
pairOut_1 <- runPairs(eList, year1, year2, windowSide = 0)
pairOut_1_orig <- runPairs(eList, year1, year2, windowSide = 0, oldSurface = TRUE)
expect_equal(attr(pairOut_1, "dateInfo"), attr(pairOut_1_orig, "dateInfo"))
expect_equal(attr(pairOut_1, "yearPair"), attr(pairOut_1_orig, "yearPair"))
expect_true(all(names(pairOut_1) %in% c("TotalChange","CQTC","QTC","x10","x11","x20","x22")))
expect_equal(round(pairOut_1$TotalChange[1], digits = 4), 0.429)
expect_equal(round(attr(pairOut_1, "Other")[["PercentChangeConc"]][["Total Percent Change"]],digits = 2),
42.27)
expect_equal(round(attr(pairOut_1, "Other")[["PercentChangeConc"]][["CQTC Percent"]],digits = 2),
42.27)
expect_equal(round(attr(pairOut_1, "Other")[["PercentChangeConc"]][["QTC Percent"]],digits = 2),
0)
expect_equal(round(attr(pairOut_1, "Other")[["PercentChangeFlux"]][["Total Percent Change"]],digits = 2),
29.44)
expect_equal(round(attr(pairOut_1, "Other")[["PercentChangeFlux"]][["CQTC Percent"]],digits = 2),
29.44)
expect_equal(round(attr(pairOut_1, "Other")[["PercentChangeFlux"]][["QTC Percent"]],digits = 2),
0)
# Option 2:
pairOut_2 <- runPairs(eList, year1, year2, windowSide = 7)
expect_true(all(names(pairOut_2) %in% c("TotalChange","CQTC","QTC","x10","x11","x20","x22")))
expect_equal(round(pairOut_2$TotalChange[1], digits = 4), 0.3968)
expect_equal(round(pairOut_1$TotalChange[1], digits = 4), 0.429)
expect_equal(round(attr(pairOut_2, "Other")[["PercentChangeConc"]][["Total Percent Change"]],digits = 2),
38.56)
expect_equal(round(attr(pairOut_2, "Other")[["PercentChangeConc"]][["CQTC Percent"]],digits = 2),
41.7)
expect_equal(round(attr(pairOut_2, "Other")[["PercentChangeConc"]][["QTC Percent"]],digits = 2),
-3.13)
expect_equal(round(attr(pairOut_2, "Other")[["PercentChangeFlux"]][["Total Percent Change"]],digits = 2),
50.68)
expect_equal(round(attr(pairOut_2, "Other")[["PercentChangeFlux"]][["CQTC Percent"]],digits = 2),
31.94)
expect_equal(round(attr(pairOut_2, "Other")[["PercentChangeFlux"]][["QTC Percent"]],digits = 2),
18.74)
# Option 3:
pairOut_3 <- runPairs(eList, year1, year2,
windowSide = 0, flowBreak = TRUE,
Q1EndDate = "1990-09-30")
expect_true(all(names(pairOut_3) %in% c("TotalChange","CQTC","QTC","x10","x11","x20","x22")))
expect_equal(round(pairOut_3$TotalChange[1], digits = 4), 0.4081)
expect_equal(round(attr(pairOut_3, "Other")[["PercentChangeConc"]][["Total Percent Change"]],digits = 2),
39.77)
expect_equal(round(attr(pairOut_3, "Other")[["PercentChangeConc"]][["CQTC Percent"]],digits = 2),
41.81)
expect_equal(round(attr(pairOut_3, "Other")[["PercentChangeConc"]][["QTC Percent"]],digits = 2),
-2.04)
expect_equal(round(attr(pairOut_3, "Other")[["PercentChangeFlux"]][["Total Percent Change"]],digits = 2),
45.81)
expect_equal(round(attr(pairOut_3, "Other")[["PercentChangeFlux"]][["CQTC Percent"]],digits = 2),
31.89)
expect_equal(round(attr(pairOut_3, "Other")[["PercentChangeFlux"]][["QTC Percent"]],digits = 2),
13.91)
# Option 4:
pairOut_4 <- runPairs(eList, year1, year2,
windowSide = 7, flowBreak = TRUE,
Q1EndDate = "1990-09-30")
expect_true(all(names(pairOut_4) %in% c("TotalChange","CQTC","QTC","x10","x11","x20","x22")))
expect_equal(round(pairOut_4$TotalChange[1], digits = 4), 0.3995)
expect_equal(round(attr(pairOut_4, "Other")[["PercentChangeConc"]][["Total Percent Change"]],digits = 2),
38.93)
expect_equal(round(attr(pairOut_4, "Other")[["PercentChangeConc"]][["CQTC Percent"]],digits = 2),
41.81)
expect_equal(round(attr(pairOut_4, "Other")[["PercentChangeConc"]][["QTC Percent"]],digits = 2),
-2.88)
expect_equal(round(attr(pairOut_4, "Other")[["PercentChangeFlux"]][["Total Percent Change"]],digits = 2),
50.44)
expect_equal(round(attr(pairOut_4, "Other")[["PercentChangeFlux"]][["CQTC Percent"]],digits = 2),
31.89)
expect_equal(round(attr(pairOut_4, "Other")[["PercentChangeFlux"]][["QTC Percent"]],digits = 2),
18.55)
})
test_that("runSeries", {
skip_on_cran()
eList <- Choptank_eList
#Option 1:
seriesOut_1 <- runSeries(eList, windowSide = 0)
seriesOut_1_orig <- runSeries(eList, windowSide = 0, oldSurface = TRUE)
expect_equal(class(seriesOut_1),"egret")
expect_equal(class(seriesOut_1_orig),"egret")
expect_true(attr(seriesOut_1, "runSeries"))
expect_true(attr(seriesOut_1_orig, "runSeries"))
expect_equal(round(attr(seriesOut_1$surfaces, "LogQ")[1], digits = 2), -4.66)
expect_equal(round(attr(seriesOut_1$surfaces, "Year")[1], digits = 2), 1979.69)
# Option 2:
seriesOut_2 <- runSeries(eList, windowSide = 7, oldSurface = TRUE)
expect_equal(class(seriesOut_2),"egret")
expect_true(attr(seriesOut_2, "runSeries"))
# Option 3:
seriesOut_3 <- runSeries(eList,
windowSide = 0,
flowBreak = TRUE,
Q1EndDate = "1990-09-30")
expect_equal(class(seriesOut_3),"egret")
expect_true(attr(seriesOut_3, "runSeries"))
expect_equal(round(attr(seriesOut_3$surfaces, "LogQ")[1], digits = 2), -4.66)
expect_equal(round(attr(seriesOut_3$surfaces, "Year")[1], digits = 2), 1979.69)
# Option 4:
seriesOut_4 <- runSeries(eList,
windowSide = 7, flowBreak = TRUE,
Q1EndDate = "1990-09-30")
expect_equal(class(seriesOut_4),"egret")
expect_true(attr(seriesOut_4, "runSeries"))
expect_equal(round(attr(seriesOut_4$surfaces, "LogQ")[1], digits = 2), -4.66)
expect_equal(round(attr(seriesOut_4$surfaces, "Year")[1], digits = 2), 1979.69)
})
test_that("runGroups", {
skip_on_cran()
eList <- Choptank_eList
groupOut_1 <- runGroups(eList, windowSide = 0,
group1firstYear = 1980, group1lastYear = 1990,
group2firstYear = 1995, group2lastYear = 2005)
expect_true(all(names(groupOut_1) %in% c("TotalChange","CQTC","QTC","x10",
"x11","x20","x22")))
expect_true(all(round(groupOut_1$TotalChange, digits = 3) %in% c(0.226,0.022)))
expect_true(all(round(groupOut_1$CQTC, digits = 3) %in% c(0.226,0.022)))
expect_true(all(round(groupOut_1$QTC, digits = 3) %in% c(0,0)))
expect_true(all(round(groupOut_1$x10, digits = 3) %in% c(1.019,0.116)))
expect_true(all(round(groupOut_1$x11, digits = 3) %in% c(1.019,0.116)))
expect_true(all(round(groupOut_1$x20, digits = 3) %in% c(1.245,0.138)))
expect_true(all(round(groupOut_1$x22, digits = 3) %in% c(1.245,0.138)))
# Option 2: Use sliding window.
# In each case it is a 15 year window (15 = 1 + 2*7)
groupOut_2 <- runGroups(eList, windowSide = 7,
group1firstYear = 1980, group1lastYear = 1990,
group2firstYear = 1995, group2lastYear = 2005)
expect_true(all(names(groupOut_2) %in% c("TotalChange","CQTC","QTC","x10",
"x11","x20","x22")))
expect_true(all(round(groupOut_2$TotalChange, digits = 3) %in% c(0.200,0.039)))
expect_true(all(round(groupOut_2$CQTC, digits = 3) %in% c(0.226,0.022)))
expect_true(all(round(groupOut_2$QTC, digits = 3) %in% c(-0.025,0.017)))
expect_true(all(round(groupOut_2$x10, digits = 3) %in% c(1.019,0.116)))
expect_true(all(round(groupOut_2$x11, digits = 3) %in% c(1.034,0.107)))
expect_true(all(round(groupOut_2$x20, digits = 3) %in% c(1.245,0.138)))
expect_true(all(round(groupOut_2$x22, digits = 3) %in% c(1.234,0.146)))
# Option 3: Flow normalization is based on splitting the flow record at 1990-09-30
# But in years before the break it uses all flow data from before the break,
# and years after the break uses all flow data after the break
groupOut_3 <- runGroups(eList, windowSide = 0,
group1firstYear = 1980, group1lastYear = 1990,
group2firstYear = 1995, group2lastYear = 2005,
flowBreak = TRUE,
Q1EndDate = "1990-09-30")
expect_true(all(round(groupOut_3$TotalChange, digits = 3) %in% c(0.207,0.037)))
expect_true(all(round(groupOut_3$CQTC, digits = 3) %in% c(0.226,0.022)))
expect_true(all(round(groupOut_3$QTC, digits = 3) %in% c(-0.019,0.015)))
expect_true(all(round(groupOut_3$x10, digits = 3) %in% c(1.019,0.116)))
expect_true(all(round(groupOut_3$x11, digits = 3) %in% c(1.031,0.107)))
expect_true(all(round(groupOut_3$x20, digits = 3) %in% c(1.245,0.138)))
expect_true(all(round(groupOut_3$x22, digits = 3) %in% c(1.238,0.144)))
expect_true(all(names(groupOut_3) %in% c("TotalChange","CQTC","QTC","x10",
"x11","x20","x22")))
# Option 4: Flow normalization is based on splitting the flow record at 1990-09-30
# but before the break uses a 15 year window of years before the break
# after the break uses a 15 year window of years after the break
groupOut_4 <- runGroups(eList, windowSide = 7,
group1firstYear = 1980, group1lastYear = 1990,
group2firstYear = 1995, group2lastYear = 2005,
flowBreak = TRUE,
Q1EndDate = "1990-09-30")
expect_true(all(names(groupOut_4) %in% c("TotalChange","CQTC","QTC","x10",
"x11","x20","x22")))
expect_true(all(round(groupOut_4$TotalChange, digits = 3) %in% c(0.203,0.040)))
expect_true(all(round(groupOut_4$CQTC, digits = 3) %in% c(0.226,0.022)))
expect_true(all(round(groupOut_4$QTC, digits = 3) %in% c(-0.023,0.018)))
expect_true(all(round(groupOut_4$x10, digits = 3) %in% c(1.019,0.116)))
expect_true(all(round(groupOut_4$x11, digits = 3) %in% c(1.031,0.107)))
expect_true(all(round(groupOut_4$x20, digits = 3) %in% c(1.245,0.138)))
expect_true(all(round(groupOut_4$x22, digits = 3) %in% c(1.234,0.147)))
})
test_that("stitch", {
skip_on_cran()
eList <- Choptank_eList
surfaceStart <- "1986-10-01"
surfaceEnd <- "2012-09-30"
# Surface skips a few years:
sample1StartDate <- "1986-10-01"
sample1EndDate <- "1992-09-30"
sample2StartDate <- "1996-10-01"
sample2EndDate <- "2012-09-30"
surface_skip <- stitch(eList,
sample1StartDate, sample1EndDate,
sample2StartDate, sample2EndDate,
surfaceStart, surfaceEnd)
expect_true(all(names(attributes(surface_skip)) %in%
c("dim","surfaceIndex","Year","LogQ",
"surfaceStart","surfaceEnd","sample1StartDate",
"sample1EndDate","sample2StartDate","sample2EndDate")))
expect_equal(attr(surface_skip, "surfaceStart"), as.Date(surfaceStart))
expect_equal(attr(surface_skip, "sample1EndDate"), sample1EndDate)
expect_true(!(dim(surface_skip)[2] == dim(eList$surfaces)[2]))
expect_true(dim(surface_skip)[1] == dim(eList$surfaces)[1])
expect_true(dim(surface_skip)[3] == dim(eList$surfaces)[3])
# Surface overlaps a few years:
sample1StartDate <- "1986-10-01"
sample1EndDate <- "1996-09-30"
sample2StartDate <- "1992-10-01"
sample2EndDate <- "2012-09-30"
surface_overlap <- stitch(eList,
sample1StartDate, sample1EndDate,
sample2StartDate, sample2EndDate)
expect_equal(attr(surface_overlap, "sample1EndDate"), sample1EndDate)
expect_true(!(dim(surface_overlap)[2] == dim(eList$surfaces)[2]))
expect_true(dim(surface_overlap)[1] == dim(eList$surfaces)[1])
expect_true(dim(surface_overlap)[3] == dim(eList$surfaces)[3])
})
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