context("Two-year trend")
library(EGRET)
eList <- Choptank_eList
test_that("trendSetUp",{
caseSetUp <- trendSetUp(eList,
year1=1990,
year2=2012,
nBoot = 50,
bootBreak = 39,
blockLength = 200)
df <- data.frame(year1 = 1990,
yearData1 = 1980,
year2 = 2012,
yearData2 = 2011,
numSamples = 606,
nBoot = 50,
bootBreak = 39,
blockLength = 200,
confStop = 0.7)
expect_equal(caseSetUp, df)
expect_error( caseSetUp <- trendSetUp(eList,
year1=1970,
year2=2012,
nBoot = 50,
bootBreak = 39,
blockLength = 200))
expect_error( caseSetUp <- trendSetUp(eList,
year1=1980,
year2=2013,
nBoot = 50,
bootBreak = 39,
blockLength = 200))
})
test_that("setForBoot", {
INFO <- eList$INFO
eList <- setForBoot(eList, caseSetUp)
INFO2 <- eList$INFO
expect_gt(ncol(INFO2),ncol(INFO))
expect_true(all(c("DecLow","DecHigh") %in% names(INFO2)))
})
test_that("wordLike", {
likeList <- c(0.01, 0.5, 0.55, 0.99)
Trends <- wordLike(likeList)
expect_equal(Trends, c("Upward trend in concentration is highly unlikely",
"Downward trend in concentration is about as likely as not",
"Upward trend in flux is about as likely as not",
"Downward trend in flux is highly likely"))
})
test_that("blockSample", {
skip_on_cran()
Sample <- eList$Sample
suppressWarnings(RNGversion("3.5.0"))
set.seed(1)
bsReturn <- blockSample(Sample, 25)
expect_equal(bsReturn$ConcLow[1], 0.62)
expect_equal(bsReturn$Date[1], as.Date("1979-10-24"))
})
test_that("pVal", {
s <- c(0.01, 0.5, 0.55, 0.99)
pValue <- pVal(s)
expect_equal(pValue, 0.4)
})
test_that("makeTwoYearsResults", {
testthat::skip_on_cran()
twoResultsWaterYear <- EGRETci:::makeTwoYearsResults(eList, 1985, 2005)
expect_equal(floor(twoResultsWaterYear[1:2]), c(1,0))
})
test_that("makeCombo", {
surfaces1 <- c(1,2,3)
surfaces2 <- c(4, NA, 5)
surfaces <- EGRETci:::makeCombo(surfaces1, surfaces2)
expect_equal(surfaces, c(5,2,8))
})
test_that("paVector", {
year <- 2000
paStart <- 10
paLong <- 12
vectorYear <- c(seq(1999,2001,0.0833))
paIndexWaterYear <- paVector(year, paStart, paLong, vectorYear)
expect_equal(paIndexWaterYear, 10:21)
paStart <- 11
paLong <- 3
paIndexWinter <- paVector(year, paStart, paLong, vectorYear)
expect_equal(paIndexWinter, 11:13)
paStart <- 6
paLong <- 3
paIndexSummer <- paVector(year, paStart, paLong, vectorYear)
expect_equal(paIndexSummer, 18:20)
paStart <- 10
paLong <- 3
paIndexLate <- paVector(year, paStart, paLong, vectorYear)
expect_equal(paIndexLate, 22:24)
paCalendarYear <- paVector(year, 1, 12, vectorYear)
expect_equal(paCalendarYear, 14:24)
})
test_that("estSliceSurfacesSimpleAlt", {
testthat::skip_on_cran()
eList <- Choptank_eList
caseSetUp <- trendSetUp(eList,
year1=1990,
year2=2012,
nBoot = 50,
bootBreak = 39,
blockLength = 200)
eList <- setForBoot(eList,caseSetUp)
surfaces <- EGRETci:::estSliceSurfacesSimpleAlt(eList, 1990)
expect_equal(surfaces[1:14,1,3], as.numeric(rep(NA, 14)))
expect_equal(surfaces[1,173,1], 0.16541093)
})
test_that("wBT", {
testthat::skip_on_cran()
eList <- Choptank_eList
caseSetUp <- trendSetUp(eList,
year1=1985,
year2=2005,
nBoot = 5,
bootBreak = 39,
blockLength = 200)
eList <- setForBoot(eList,caseSetUp)
eBoot <- wBT(eList,caseSetUp,saveOutput = FALSE)
bootOut <- eBoot$bootOut
expect_true(bootOut$rejectC)
expect_equal(signif(bootOut$lowC, digits = 6), 0.298427)
expect_equal(signif(bootOut$likeCUp, digits = 6), 0.916667)
expect_true(bootOut$rejectF)
expect_equal(eBoot$wordsOut, c("Upward trend in concentration is very likely" ,
"Downward trend in concentration is very unlikely",
"Upward trend in flux is very likely",
"Downward trend in flux is very unlikely"))
expect_equal(signif(eBoot$xConc, digits = 2), c(0.31,0.35,0.30,0.34,0.31))
expect_equal(signif(eBoot$pFlux, digits = 2), c(18,30,31,21,18))
expect_equal(signif(eBoot$xFlux, digits = 2), c(0.022,0.034,0.034,0.025,0.021))
expect_equal(signif(eBoot$pConc, digits = 2), c(30,35,30,33,31))
})
test_that("runPairsBoot", {
testthat::skip_on_cran()
eList <- EGRET::Choptank_eList
year1 <- 1985
year2 <- 2009
pairOut_2 <- EGRET::runPairs(eList, year1, year2, windowSide = 7)
boot_pair_out <- runPairsBoot(eList, pairOut_2, nBoot = 3, jitterOn = TRUE)
expect_true(all(c("bootOut","wordsOut","xConc","xFlux",
"pConc","pFlux","startSeed") %in% names(boot_pair_out)))
expect_true(boot_pair_out$bootOut$rejectC)
expect_true(all(c("Upward trend in concentration is likely",
"Downward trend in concentration is unlikely",
"Upward trend in flux is likely",
"Downward trend in flux is unlikely") %in% boot_pair_out$wordsOut))
expect_equal(round(boot_pair_out$xConc[1:2], digits = 2), c(0.38,0.40))
expect_equal(round(boot_pair_out$xFlux[1:2], digits = 2), c(0.05,0.06))
expect_equal(round(boot_pair_out$pConc[1:2], digits = 2), c(36.68,40.19))
expect_equal(round(boot_pair_out$pFlux[1:2], digits = 2), c(48.39,56.03))
})
test_that("runGroupBoot", {
testthat::skip_on_cran()
eList <- EGRET::Choptank_eList
year1 <- 1985
year2 <- 2009
groupResults <- EGRET::runGroups(eList,
group1firstYear = 1995,
group1lastYear = 2004,
group2firstYear = 2005,
group2lastYear = 2014,
windowSide = 7, wall = TRUE,
sample1EndDate = "2004-10-30",
paStart = 4, paLong = 2,
verbose = FALSE)
boot_group_out <- suppressWarnings(runGroupsBoot(eList, groupResults, nBoot = 3,
jitterOn = TRUE))
expect_true(all(c("bootOut","wordsOut","xConc","xFlux",
"pConc","pFlux","startSeed") %in% names(boot_group_out)))
expect_true(boot_group_out$bootOut$rejectC)
expect_true(all(c("Upward trend in concentration is likely",
"Downward trend in concentration is unlikely",
"Upward trend in flux is likely",
"Downward trend in flux is unlikely") %in% boot_group_out$wordsOut))
expect_equal(round(boot_group_out$xConc[1:2], digits = 2), c(0.1,0.21))
expect_equal(round(boot_group_out$xFlux[1:2], digits = 2), c(0.00,0.01))
expect_equal(round(boot_group_out$pConc[1:2], digits = 2), c(8.24,18.73))
expect_equal(round(boot_group_out$pFlux[1:2], digits = 2), c(0.08,7.75))
})
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.