tests/testthat/tests_userFriendly_fxns.R
In usgs/dataRetrieval: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data
context("Unit values")
test_that("Unit value data returns correct types", {
testthat::skip_on_cran()
siteNumber <- '05114000'
parameterCd <- '00060'
startDate <- "2014-10-10"
endDate <- "2014-10-10"
rawData <- readNWISuv(siteNumber,parameterCd,startDate,endDate)
rawData <- renameNWISColumns(rawData)
spreadOver120 <- readNWISuv(siteNumber,parameterCd,
as.Date(Sys.Date()-200),
Sys.Date())
expect_true(min(spreadOver120$dateTime) < as.POSIXct(Sys.Date(), tz="UTC"))
recent_uv <- readNWISuv(siteNumber,parameterCd,
as.Date(Sys.Date()-10),
Sys.Date())
expect_equal(grep(x = attr(recent_uv, "url"), pattern = "https://waterservices.usgs.gov/nwis/iv/"),1)
expect_equal(grep(x = attr(spreadOver120, "url"),pattern = "https://nwis.waterservices.usgs.gov/nwis/iv/"),1)
expect_equal(attr(rawData, "url"),"https://nwis.waterservices.usgs.gov/nwis/iv/?site=05114000&format=waterml,1.1&ParameterCd=00060&startDT=2014-10-10&endDT=2014-10-10")
timeZoneChange <- readNWISuv(c('04024430','04024000'),parameterCd,
"2013-11-03","2013-11-03",
tz="America/Chicago")
timeZoneChange <- renameNWISColumns(timeZoneChange)
expect_is(rawData$dateTime, 'POSIXct')
expect_is(rawData$Flow_Inst, 'numeric')
expect_equal(attr(rawData, "url"), "https://nwis.waterservices.usgs.gov/nwis/iv/?site=05114000&format=waterml,1.1&ParameterCd=00060&startDT=2014-10-10&endDT=2014-10-10")
# #First switchover to standard time:
# expect_that(as.numeric(timeZoneChange[which(timeZoneChange$tz_cd == "America/Chicago")[1],"dateTime"]),
# equals(as.numeric(as.POSIXct("2013-11-03 01:00:00", tz="UTC")+60*60*6)))
site <- "04087170"
pCode <- "63680"
startDate <- "2012-07-10"
endDate <- "2012-07-17"
dd_2 <- readNWISuv(site, pCode, startDate, endDate)
expect_true(any(names(dd_2) %in% c("agency_cd","site_no",
"dateTime",
"X_63680_00000","X_63680_00000_cd",
"X_.YSI.6136.UP._63680_00000",
"X_.YSI.6136.UP._63680_00000_cd",
"tz_cd")))
noData <- readNWISuv("01196500","00010", "2016-06-15", "2016-06-15")
# expect_equal(noData$X_00010_00000[1], as.numeric(NA))
})
context("Peak, rating, meas, site")
test_that("peak, rating curves, surface-water measurements", {
testthat::skip_on_cran()
siteNumbers <- c('01594440','040851325')
data <- readNWISpeak(siteNumbers)
expect_is(data$agency_cd, 'character')
#Rating curvs:
siteNumber <- '01594440'
data <- readNWISrating(siteNumber, "base")
expect_that(length(attr(data, "RATING")),equals(7))
#Surface meas:
siteNumbers <- c('01594440','040851325')
data <- readNWISmeas(siteNumbers)
expect_is(data$agency_cd, 'character')
siteINFO <- readNWISsite('05114000')
expect_is(siteINFO$agency_cd, 'character')
siteINFOMulti <- readNWISsite(c('05114000','09423350'))
expect_true(nrow(siteINFOMulti) == 2)
Meas07227500.ex <- readNWISmeas("07227500",expanded=TRUE)
expect_is(Meas07227500.ex$measurement_dt, 'Date')
expect_is(Meas07227500.ex$measurement_dateTime, 'POSIXct')
expect_error(whatNWISdata(siteNumber = "10312000",parameterCd = "50286"))
url <- "https://waterservices.usgs.gov/nwis/site/?format=rdb&seriesCatalogOutput=true&sites=05114000"
x <- importRDB1(url)
})
context("qw")
test_that("NWIS qw tests", {
testthat::skip_on_cran()
siteNumbers <- c('04024430','04024000')
startDate <- '2010-01-01'
endDate <- ''
parameterCd <- c('34247','30234','32104','34220')
rawNWISqwData <- readNWISqw(siteNumbers,parameterCd,startDate,endDate)
expect_is(rawNWISqwData$startDateTime, 'POSIXct')
rawNWISqwDataReshaped <- readNWISqw(siteNumbers,parameterCd,
startDate,endDate,reshape=TRUE)
expect_is(rawNWISqwDataReshaped$startDateTime, 'POSIXct')
expect_gt(ncol(rawNWISqwDataReshaped), ncol(rawNWISqwData))
expect_lt(nrow(rawNWISqwDataReshaped), nrow(rawNWISqwData))
parameterCd <- "all"
rawNWISall <- readNWISqw(siteNumbers,parameterCd,
startDate,"2011-01-01",reshape=TRUE)
expect_is(rawNWISall$startDateTime, 'POSIXct')
pgroup <- c("NUT")
rawNWISNutrients <- readNWISqw(siteNumbers,pgroup,
startDate,endDate)
expect_is(rawNWISNutrients$startDateTime, 'POSIXct')
qwret <- readNWISqw("413437087150601", parameterCd = c("NUT","INN"),startDate = "",endDate = "")
expect_true(nrow(qwret) == 0)
siteNumber <- '455638089034501'
wy_start <- paste0(2014, "-10-01")
wy_end <- paste0(2015, "-09-30")
#No data test:
no.data <- readNWISqw(siteNumbers = siteNumber,
parameterCd = '00060',
startDate = wy_start,
endDat = wy_end)
expect_true(nrow(no.data) == 0)
})
context("dv")
test_that("NWIS dv tests", {
testthat::skip_on_cran()
siteNumber <- '04085427'
startDate <- '2012-01-01'
endDate <- '2012-06-30'
pCode <- '00060'
rawDailyQ <- readNWISdv(siteNumber,pCode, startDate, endDate)
expect_is(rawDailyQ$Date, 'Date')
rawDailyQAndTempMeanMax <- readNWISdv(siteNumber,c('00010','00060'),
startDate, endDate, statCd=c('00001','00003'))
expect_true(length(grep("00060", names(rawDailyQAndTempMeanMax))) >= 2 &
length(grep("00010", names(rawDailyQAndTempMeanMax))) >= 2)
rawDailyMultiSites<- readNWISdv(c("01491000","01645000"),c('00010','00060'),
startDate, endDate, statCd=c('00001','00003'))
expect_true(length(unique(rawDailyMultiSites$site_no)) > 1)
# # Site with no data:
# x <- readNWISdv("10258500","00060", "2015-02-08", "2015-02-14")
# expect_true(sum(is.na(x$X_00060_00003)) > 0)
site <- "05212700"
notActive <- readNWISdv(site, "00060", "2014-01-01","2014-01-07")
expect_true(nrow(notActive) == 0)
})
test_that("WQP qw tests", {
testthat::skip_on_cran()
nameToUse <- 'Specific conductance'
pcodeToUse <- '00095'
INFO_WQP <- readWQPqw('USGS-04024315',pcodeToUse, startDate = "", endDate = "")
expect_is(INFO_WQP$ActivityStartDateTime, 'POSIXct')
INFO2 <- readWQPqw('WIDNR_WQX-10032762',nameToUse, startDate = "", endDate = "")
expect_is(INFO2$ActivityStartDateTime, 'POSIXct')
})
context("readNWISstat tests")
test_that("readNWISstat tests", {
testthat::skip_on_cran()
data <- readNWISstat(siteNumbers=c("02171500"),parameterCd=c("00010","00060"),
statReportType="daily",statType=c("mean","p75","p25"),startDate="2000",endDate="2010")
expect_is(data$begin_yr, 'numeric')
expect_true(length(data) > 3)
monthData <- readNWISstat(siteNumbers=c("02171500"),parameterCd=c("00010","00060"),
statReportType="monthly",startDate="2000",endDate="2010")
expect_is(monthData$mean_va, 'numeric')
annualData <- readNWISstat(siteNumbers=c("02171500"),parameterCd=c("00010","00060"),statReportType="annual",
startDate="2000",endDate="2010")
expect_gt(nrow(annualData),2)
})
context("readNWISuse tests")
test_that("readNWISuse tests", {
testthat::skip_on_cran()
dc <- readNWISuse(years=c(2000,2005,2010),stateCd = "DC", countyCd = NULL)
expect_true(nrow(dc)==3)
expect_is(dc$state_cd, 'character')
ohio <- readNWISuse(years=2005,stateCd="OH",countyCd="ALL")
expect_true(nrow(ohio)==88)
twoCounties <- readNWISuse(years=2010,stateCd="PA",countyCd=c("Cambria","Indiana"))
expect_true(nrow(twoCounties)==2)
})
context("state tests")
test_that("state county tests",{
testthat::skip_on_cran()
fullName <- stateCdLookup("wi", "fullName")
expect_equal(fullName, "Wisconsin")
abbriev <- stateCdLookup("Wisconsin", "postal")
expect_equal(abbriev, "WI")
id <- stateCdLookup("WI", "id")
expect_equal(id, 55)
name <- stateCdLookup(55, "fullName")
expect_equal(name, "Wisconsin")
multipleStates <- stateCdLookup(c("West Virginia", "Wisconsin", 55, "MN"))
expect_equal(multipleStates, c("WV","WI","WI","MN"))
id <- countyCdLookup(state = "WI", county = "Dane")
expect_equal(id, "025")
name <- countyCdLookup(state = "OH", county = 13, output = "fullName")
expect_equal(name, "Belmont County")
index <- countyCdLookup(state = "Pennsylvania", county = "ALLEGHENY COUNTY", output = "tableIndex")
expect_equal(index, 2246)
fromIDs <- countyCdLookup(state = 13, county = 5, output = "fullName")
expect_equal(fromIDs, "Bacon County")
counties <- c("51001","51003")
already_ready <- countyCdLookup(county = counties)
expect_equal(counties, already_ready)
})
context("water year column")
df_test <- data.frame(site_no = as.character(1:13),
dateTime = seq(as.Date("2010-01-01"),as.Date("2011-01-31"),
by="months"),
result_va = 1:13, stringsAsFactors = FALSE)
test_that("addWaterYear works with Date, POSIXct, character, but breaks with numeric", {
testthat::skip_on_cran()
df_date <- df_test
df_date_wy <- addWaterYear(df_date)
expect_equal(ncol(df_date_wy), ncol(df_date) + 1)
df_posixct <- df_test
df_posixct$dateTime <- as.POSIXct(df_posixct$dateTime)
df_posixct_wy <- addWaterYear(df_posixct)
expect_equal(ncol(df_posixct_wy), ncol(df_posixct) + 1)
df_char <- df_test
df_char$dateTime <- as.character(df_char$dateTime)
df_char_wy <- addWaterYear(df_char)
expect_equal(ncol(df_char_wy), ncol(df_char) + 1)
df_num <- df_test
df_num$dateTime <- as.numeric(df_num$dateTime)
dfnum2 <- addWaterYear(df_num)
expect_equal(dfnum2$waterYear, rep(NA, 13))
})
test_that("addWaterYear works for each column name", {
testthat::skip_on_cran()
nwisqw_style <- df_test
nwisqw_style_wy <- addWaterYear(nwisqw_style)
expect_equal(ncol(nwisqw_style_wy), ncol(nwisqw_style) + 1)
nwisdata_style <- df_test
names(nwisdata_style)[2] <- "Date"
nwisdata_style_wy <- addWaterYear(nwisdata_style)
expect_equal(ncol(nwisdata_style_wy), ncol(nwisdata_style) + 1)
wqp_style <- df_test
names(wqp_style)[2] <- "ActivityStartDate"
wqp_style[['ActivityEndDate']] <- wqp_style[["ActivityStartDate"]]
wqp_style_wy <- addWaterYear(wqp_style)
expect_equal(ncol(wqp_style_wy), ncol(wqp_style) + 2)
userspecified_style <- df_test
names(userspecified_style)[2] <- "MyDateCol"
expect_error(addWaterYear(userspecified_style),
"specified date column does not exist in supplied data frame")
})
test_that("addWaterYear correctly calculates the WY and is numeric", {
testthat::skip_on_cran()
df_test_wy <- addWaterYear(df_test)
expect_is(df_test_wy[['waterYear']], "numeric")
expect_true(all(df_test_wy[['waterYear']][1:9] == 2010))
expect_true(all(df_test_wy[['waterYear']][10:13] == 2011))
})
test_that("addWaterYear adds column next to dateTime", {
testthat::skip_on_cran()
df_test_wy <- addWaterYear(df_test)
dateTime_col <- which(names(df_test_wy) == "dateTime")
expect_equal(names(df_test_wy)[dateTime_col + 1], "waterYear")
})
test_that("addWaterYear can be used with pipes", {
testthat::skip_on_cran()
df_test_wy <- df_test
df_test_wy <- addWaterYear(df_test_wy)
expect_equal(ncol(df_test_wy), ncol(df_test) + 1)
})
test_that("addWaterYear doesn't add another WY column if it exists", {
testthat::skip_on_cran()
df_test_wy <- addWaterYear(df_test)
expect_equal(ncol(df_test_wy), ncol(df_test) + 1)
df_test_wy2 <- addWaterYear(df_test_wy)
expect_equal(ncol(df_test_wy2), ncol(df_test_wy))
})
test_that("calcWaterYear can handle missing values", {
dateVec <- seq(as.Date("2010-01-01"),as.Date("2011-01-31"), by="months")
dateVec[c(3,7,12)] <- NA
wyVec <- dataRetrieval:::calcWaterYear(dateVec)
expect_is(wyVec, "numeric")
expect_true(all(is.na(wyVec[c(3,7,12)])))
})
context("Construct NWIS urls")
test_that("Construct NWIS urls", {
testthat::skip_on_cran()
siteNumber <- '01594440'
startDate <- '1985-01-01'
endDate <- ''
pCode <- c("00060","00010")
url_daily <- constructNWISURL(siteNumber,pCode,
startDate,endDate,'dv',statCd=c("00003","00001"))
expect_equal(url_daily, "https://waterservices.usgs.gov/nwis/dv/?site=01594440&format=waterml,1.1&ParameterCd=00060,00010&StatCd=00003,00001&startDT=1985-01-01")
url_unit <- constructNWISURL(siteNumber,pCode,"2012-06-28","2012-06-30",'iv')
expect_equal(url_unit, "https://nwis.waterservices.usgs.gov/nwis/iv/?site=01594440&format=waterml,1.1&ParameterCd=00060,00010&startDT=2012-06-28&endDT=2012-06-30")
url_qw_single <- constructNWISURL(siteNumber,"01075",startDate,endDate,'qw')
expect_equal(url_qw_single, "https://nwis.waterdata.usgs.gov/nwis/qwdata?search_site_no=01594440&search_site_no_match_type=exact&multiple_parameter_cds=01075¶m_cd_operator=AND&list_of_search_criteria=search_site_no,multiple_parameter_cds&group_key=NONE&sitefile_output_format=html_table&column_name=agency_cd&column_name=site_no&column_name=station_nm&inventory_output=0&rdb_inventory_output=file&TZoutput=0&pm_cd_compare=Greater%20than&radio_parm_cds=previous_parm_cds&qw_attributes=0&format=rdb&rdb_qw_attributes=expanded&date_format=YYYY-MM-DD&rdb_compression=value&qw_sample_wide=0&begin_date=1985-01-01")
url_qw <- constructNWISURL(siteNumber,c('01075','00029','00453'),
startDate,endDate,'qw')
expect_equal(url_qw, "https://nwis.waterdata.usgs.gov/nwis/qwdata?search_site_no=01594440&search_site_no_match_type=exact&multiple_parameter_cds=01075,00029,00453¶m_cd_operator=OR&list_of_search_criteria=search_site_no,multiple_parameter_cds&group_key=NONE&sitefile_output_format=html_table&column_name=agency_cd&column_name=site_no&column_name=station_nm&inventory_output=0&rdb_inventory_output=file&TZoutput=0&pm_cd_compare=Greater%20than&radio_parm_cds=previous_parm_cds&qw_attributes=0&format=rdb&rdb_qw_attributes=expanded&date_format=YYYY-MM-DD&rdb_compression=value&qw_sample_wide=0&begin_date=1985-01-01")
url_daily_tsv <- constructNWISURL(siteNumber,pCode,startDate,endDate,'dv',
statCd=c("00003","00001"),format="tsv")
expect_equal(url_daily_tsv, "https://waterservices.usgs.gov/nwis/dv/?site=01594440&format=rdb,1.0&ParameterCd=00060,00010&StatCd=00003,00001&startDT=1985-01-01")
setAccess("internal")
url_rating <- constructNWISURL(siteNumber,service="rating",ratingType="base")
expect_equal(url_rating, "https://waterdata.usgs.gov/nwisweb/get_ratings/?Access=3&site_no=01594440&file_type=base")
url_peak <- constructNWISURL(siteNumber, service="peak")
expect_equal(url_peak, "https://nwis.waterdata.usgs.gov/usa/nwis/peak/?Access=3&site_no=01594440&range_selection=date_range&format=rdb")
url_meas <- constructNWISURL(siteNumber, service="meas")
expect_equal(url_meas, "https://waterdata.usgs.gov/nwis/measurements/?Access=3&site_no=01594440&range_selection=date_range&format=rdb_expanded")
urlQW <- constructNWISURL("450456092225801","70300",startDate="",endDate="","qw",expanded=TRUE)
expect_equal(urlQW, "https://nwis.waterdata.usgs.gov/nwis/qwdata?Access=3&search_site_no=450456092225801&search_site_no_match_type=exact&multiple_parameter_cds=70300¶m_cd_operator=AND&list_of_search_criteria=search_site_no,multiple_parameter_cds&group_key=NONE&sitefile_output_format=html_table&column_name=agency_cd&column_name=site_no&column_name=station_nm&inventory_output=0&rdb_inventory_output=file&TZoutput=0&pm_cd_compare=Greater%20than&radio_parm_cds=previous_parm_cds&qw_attributes=0&format=rdb&rdb_qw_attributes=expanded&date_format=YYYY-MM-DD&rdb_compression=value&qw_sample_wide=0")
setAccess("cooperator")
urlQW <- constructNWISURL("450456092225801","70300",startDate="",endDate="","qw",expanded=TRUE)
expect_equal(urlQW, "https://nwis.waterdata.usgs.gov/nwis/qwdata?Access=1&search_site_no=450456092225801&search_site_no_match_type=exact&multiple_parameter_cds=70300¶m_cd_operator=AND&list_of_search_criteria=search_site_no,multiple_parameter_cds&group_key=NONE&sitefile_output_format=html_table&column_name=agency_cd&column_name=site_no&column_name=station_nm&inventory_output=0&rdb_inventory_output=file&TZoutput=0&pm_cd_compare=Greater%20than&radio_parm_cds=previous_parm_cds&qw_attributes=0&format=rdb&rdb_qw_attributes=expanded&date_format=YYYY-MM-DD&rdb_compression=value&qw_sample_wide=0")
setAccess("USGS")
urlQW <- constructNWISURL("450456092225801","70300",startDate="",endDate="","qw",expanded=TRUE)
expect_equal(urlQW, "https://nwis.waterdata.usgs.gov/nwis/qwdata?Access=2&search_site_no=450456092225801&search_site_no_match_type=exact&multiple_parameter_cds=70300¶m_cd_operator=AND&list_of_search_criteria=search_site_no,multiple_parameter_cds&group_key=NONE&sitefile_output_format=html_table&column_name=agency_cd&column_name=site_no&column_name=station_nm&inventory_output=0&rdb_inventory_output=file&TZoutput=0&pm_cd_compare=Greater%20than&radio_parm_cds=previous_parm_cds&qw_attributes=0&format=rdb&rdb_qw_attributes=expanded&date_format=YYYY-MM-DD&rdb_compression=value&qw_sample_wide=0")
setAccess("public")
urlQW <- constructNWISURL("450456092225801","70300",startDate="",endDate="","qw",expanded=TRUE)
expect_equal(urlQW, "https://nwis.waterdata.usgs.gov/nwis/qwdata?search_site_no=450456092225801&search_site_no_match_type=exact&multiple_parameter_cds=70300¶m_cd_operator=AND&list_of_search_criteria=search_site_no,multiple_parameter_cds&group_key=NONE&sitefile_output_format=html_table&column_name=agency_cd&column_name=site_no&column_name=station_nm&inventory_output=0&rdb_inventory_output=file&TZoutput=0&pm_cd_compare=Greater%20than&radio_parm_cds=previous_parm_cds&qw_attributes=0&format=rdb&rdb_qw_attributes=expanded&date_format=YYYY-MM-DD&rdb_compression=value&qw_sample_wide=0")
url_use <- constructUseURL(years=c(1990,1995),stateCd="Ohio",countyCd = c(1,3), categories = "ALL")
expect_equal(url_use, "https://waterdata.usgs.gov/OH/nwis/water_use?format=rdb&rdb_compression=value&wu_area=county&wu_county=1%2C3&wu_year=1990%2C1995&wu_category=ALL")
})
context("Construct WQP urls")
test_that("Construct WQP urls", {
testthat::skip_on_cran()
site_id <- '01594440'
startDate <- '1985-01-01'
endDate <- ''
pCode <- c("00060","00010")
url_wqp <- constructWQPURL(paste("USGS",site_id,sep="-"),
c('01075','00029','00453'),
startDate,endDate)
expect_equal(url_wqp, "https://www.waterqualitydata.us/data/Result/search?siteid=USGS-01594440&pCode=01075;00029;00453&startDateLo=01-01-1985&mimeType=tsv&zip=yes")
#Multiple characteristicNames
charNames <- c("Temperature","Temperature, sample","Temperature, water",
"Temperature, water, deg F")
obs_url_orig <- constructWQPURL(siteNumbers = c("IIDFG-41WSSPAHS", "USGS-02352560"),
parameterCd = c("Temperature","Temperature, sample","Temperature, water", "Temperature, water, deg F"),
"","")
expect_equal(obs_url_orig, "https://www.waterqualitydata.us/data/Result/search?siteid=IIDFG-41WSSPAHS;USGS-02352560&characteristicName=Temperature;Temperature%2C%20sample;Temperature%2C%20water;Temperature%2C%20water%2C%20deg%20F&mimeType=tsv&zip=yes")
})
context("checkWQPdates")
test_that("checkWQPdates", {
values <- list(startDateLo="01-01-2002", characteristicName="Phosphorous",
endDate=as.Date("2014-01-01"))
values1 <- checkWQPdates(values)
expect_equal(values1$startDateHi, "01-01-2014")
expect_equal(values1$startDateLo, "01-01-2002")
})
context("Construct WQP urls")
test_that("Construct WQP urls", {
siteNumber <- '01594440'
startDate <- '1985-01-01'
endDate <- ''
pCode <- c("00060","00010")
url_wqp <- constructWQPURL(paste("USGS",siteNumber,sep="-"),
c('01075','00029','00453'),
startDate,endDate)
expect_equal(url_wqp, "https://www.waterqualitydata.us/data/Result/search?siteid=USGS-01594440&pCode=01075;00029;00453&startDateLo=01-01-1985&mimeType=tsv&zip=yes")
rawSampleURL_Zip <- constructWQPURL('USGS-01594440','01075', '', '', TRUE)
expect_equal(rawSampleURL_Zip, "https://www.waterqualitydata.us/data/Result/search?siteid=USGS-01594440&pCode=01075&mimeType=tsv&zip=yes")
})
context("pCode Stuff")
test_that("pCode Stuff", {
testthat::skip_on_cran()
paramINFO <- readNWISpCode(c('01075','00060','00931', NA))
expect_equal(nrow(paramINFO), 4)
paramINFO <- readNWISpCode("all")
expect_equal(attr(paramINFO, "url"),"https://nwis.waterdata.usgs.gov/nwis/pmcodes/pmcodes?radio_pm_search=param_group&pm_group=All+--+include+all+parameter+groups&show=parameter_group_nm&show=parameter_nm&show=casrn&show=srsname&show=parameter_units&format=rdb")
})
usgs/dataRetrieval documentation built on Feb. 27, 2021, 12:40 a.m.
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context("Unit values")
test_that("Unit value data returns correct types", {
testthat::skip_on_cran()
siteNumber <- '05114000'
parameterCd <- '00060'
startDate <- "2014-10-10"
endDate <- "2014-10-10"
rawData <- readNWISuv(siteNumber,parameterCd,startDate,endDate)
rawData <- renameNWISColumns(rawData)
spreadOver120 <- readNWISuv(siteNumber,parameterCd,
as.Date(Sys.Date()-200),
Sys.Date())
expect_true(min(spreadOver120$dateTime) < as.POSIXct(Sys.Date(), tz="UTC"))
recent_uv <- readNWISuv(siteNumber,parameterCd,
as.Date(Sys.Date()-10),
Sys.Date())
expect_equal(grep(x = attr(recent_uv, "url"), pattern = "https://waterservices.usgs.gov/nwis/iv/"),1)
expect_equal(grep(x = attr(spreadOver120, "url"),pattern = "https://nwis.waterservices.usgs.gov/nwis/iv/"),1)
expect_equal(attr(rawData, "url"),"https://nwis.waterservices.usgs.gov/nwis/iv/?site=05114000&format=waterml,1.1&ParameterCd=00060&startDT=2014-10-10&endDT=2014-10-10")
timeZoneChange <- readNWISuv(c('04024430','04024000'),parameterCd,
"2013-11-03","2013-11-03",
tz="America/Chicago")
timeZoneChange <- renameNWISColumns(timeZoneChange)
expect_is(rawData$dateTime, 'POSIXct')
expect_is(rawData$Flow_Inst, 'numeric')
expect_equal(attr(rawData, "url"), "https://nwis.waterservices.usgs.gov/nwis/iv/?site=05114000&format=waterml,1.1&ParameterCd=00060&startDT=2014-10-10&endDT=2014-10-10")
# #First switchover to standard time:
# expect_that(as.numeric(timeZoneChange[which(timeZoneChange$tz_cd == "America/Chicago")[1],"dateTime"]),
# equals(as.numeric(as.POSIXct("2013-11-03 01:00:00", tz="UTC")+60*60*6)))
site <- "04087170"
pCode <- "63680"
startDate <- "2012-07-10"
endDate <- "2012-07-17"
dd_2 <- readNWISuv(site, pCode, startDate, endDate)
expect_true(any(names(dd_2) %in% c("agency_cd","site_no",
"dateTime",
"X_63680_00000","X_63680_00000_cd",
"X_.YSI.6136.UP._63680_00000",
"X_.YSI.6136.UP._63680_00000_cd",
"tz_cd")))
noData <- readNWISuv("01196500","00010", "2016-06-15", "2016-06-15")
# expect_equal(noData$X_00010_00000[1], as.numeric(NA))
})
context("Peak, rating, meas, site")
test_that("peak, rating curves, surface-water measurements", {
testthat::skip_on_cran()
siteNumbers <- c('01594440','040851325')
data <- readNWISpeak(siteNumbers)
expect_is(data$agency_cd, 'character')
#Rating curvs:
siteNumber <- '01594440'
data <- readNWISrating(siteNumber, "base")
expect_that(length(attr(data, "RATING")),equals(7))
#Surface meas:
siteNumbers <- c('01594440','040851325')
data <- readNWISmeas(siteNumbers)
expect_is(data$agency_cd, 'character')
siteINFO <- readNWISsite('05114000')
expect_is(siteINFO$agency_cd, 'character')
siteINFOMulti <- readNWISsite(c('05114000','09423350'))
expect_true(nrow(siteINFOMulti) == 2)
Meas07227500.ex <- readNWISmeas("07227500",expanded=TRUE)
expect_is(Meas07227500.ex$measurement_dt, 'Date')
expect_is(Meas07227500.ex$measurement_dateTime, 'POSIXct')
expect_error(whatNWISdata(siteNumber = "10312000",parameterCd = "50286"))
url <- "https://waterservices.usgs.gov/nwis/site/?format=rdb&seriesCatalogOutput=true&sites=05114000"
x <- importRDB1(url)
})
context("qw")
test_that("NWIS qw tests", {
testthat::skip_on_cran()
siteNumbers <- c('04024430','04024000')
startDate <- '2010-01-01'
endDate <- ''
parameterCd <- c('34247','30234','32104','34220')
rawNWISqwData <- readNWISqw(siteNumbers,parameterCd,startDate,endDate)
expect_is(rawNWISqwData$startDateTime, 'POSIXct')
rawNWISqwDataReshaped <- readNWISqw(siteNumbers,parameterCd,
startDate,endDate,reshape=TRUE)
expect_is(rawNWISqwDataReshaped$startDateTime, 'POSIXct')
expect_gt(ncol(rawNWISqwDataReshaped), ncol(rawNWISqwData))
expect_lt(nrow(rawNWISqwDataReshaped), nrow(rawNWISqwData))
parameterCd <- "all"
rawNWISall <- readNWISqw(siteNumbers,parameterCd,
startDate,"2011-01-01",reshape=TRUE)
expect_is(rawNWISall$startDateTime, 'POSIXct')
pgroup <- c("NUT")
rawNWISNutrients <- readNWISqw(siteNumbers,pgroup,
startDate,endDate)
expect_is(rawNWISNutrients$startDateTime, 'POSIXct')
qwret <- readNWISqw("413437087150601", parameterCd = c("NUT","INN"),startDate = "",endDate = "")
expect_true(nrow(qwret) == 0)
siteNumber <- '455638089034501'
wy_start <- paste0(2014, "-10-01")
wy_end <- paste0(2015, "-09-30")
#No data test:
no.data <- readNWISqw(siteNumbers = siteNumber,
parameterCd = '00060',
startDate = wy_start,
endDat = wy_end)
expect_true(nrow(no.data) == 0)
})
context("dv")
test_that("NWIS dv tests", {
testthat::skip_on_cran()
siteNumber <- '04085427'
startDate <- '2012-01-01'
endDate <- '2012-06-30'
pCode <- '00060'
rawDailyQ <- readNWISdv(siteNumber,pCode, startDate, endDate)
expect_is(rawDailyQ$Date, 'Date')
rawDailyQAndTempMeanMax <- readNWISdv(siteNumber,c('00010','00060'),
startDate, endDate, statCd=c('00001','00003'))
expect_true(length(grep("00060", names(rawDailyQAndTempMeanMax))) >= 2 &
length(grep("00010", names(rawDailyQAndTempMeanMax))) >= 2)
rawDailyMultiSites<- readNWISdv(c("01491000","01645000"),c('00010','00060'),
startDate, endDate, statCd=c('00001','00003'))
expect_true(length(unique(rawDailyMultiSites$site_no)) > 1)
# # Site with no data:
# x <- readNWISdv("10258500","00060", "2015-02-08", "2015-02-14")
# expect_true(sum(is.na(x$X_00060_00003)) > 0)
site <- "05212700"
notActive <- readNWISdv(site, "00060", "2014-01-01","2014-01-07")
expect_true(nrow(notActive) == 0)
})
test_that("WQP qw tests", {
testthat::skip_on_cran()
nameToUse <- 'Specific conductance'
pcodeToUse <- '00095'
INFO_WQP <- readWQPqw('USGS-04024315',pcodeToUse, startDate = "", endDate = "")
expect_is(INFO_WQP$ActivityStartDateTime, 'POSIXct')
INFO2 <- readWQPqw('WIDNR_WQX-10032762',nameToUse, startDate = "", endDate = "")
expect_is(INFO2$ActivityStartDateTime, 'POSIXct')
})
context("readNWISstat tests")
test_that("readNWISstat tests", {
testthat::skip_on_cran()
data <- readNWISstat(siteNumbers=c("02171500"),parameterCd=c("00010","00060"),
statReportType="daily",statType=c("mean","p75","p25"),startDate="2000",endDate="2010")
expect_is(data$begin_yr, 'numeric')
expect_true(length(data) > 3)
monthData <- readNWISstat(siteNumbers=c("02171500"),parameterCd=c("00010","00060"),
statReportType="monthly",startDate="2000",endDate="2010")
expect_is(monthData$mean_va, 'numeric')
annualData <- readNWISstat(siteNumbers=c("02171500"),parameterCd=c("00010","00060"),statReportType="annual",
startDate="2000",endDate="2010")
expect_gt(nrow(annualData),2)
})
context("readNWISuse tests")
test_that("readNWISuse tests", {
testthat::skip_on_cran()
dc <- readNWISuse(years=c(2000,2005,2010),stateCd = "DC", countyCd = NULL)
expect_true(nrow(dc)==3)
expect_is(dc$state_cd, 'character')
ohio <- readNWISuse(years=2005,stateCd="OH",countyCd="ALL")
expect_true(nrow(ohio)==88)
twoCounties <- readNWISuse(years=2010,stateCd="PA",countyCd=c("Cambria","Indiana"))
expect_true(nrow(twoCounties)==2)
})
context("state tests")
test_that("state county tests",{
testthat::skip_on_cran()
fullName <- stateCdLookup("wi", "fullName")
expect_equal(fullName, "Wisconsin")
abbriev <- stateCdLookup("Wisconsin", "postal")
expect_equal(abbriev, "WI")
id <- stateCdLookup("WI", "id")
expect_equal(id, 55)
name <- stateCdLookup(55, "fullName")
expect_equal(name, "Wisconsin")
multipleStates <- stateCdLookup(c("West Virginia", "Wisconsin", 55, "MN"))
expect_equal(multipleStates, c("WV","WI","WI","MN"))
id <- countyCdLookup(state = "WI", county = "Dane")
expect_equal(id, "025")
name <- countyCdLookup(state = "OH", county = 13, output = "fullName")
expect_equal(name, "Belmont County")
index <- countyCdLookup(state = "Pennsylvania", county = "ALLEGHENY COUNTY", output = "tableIndex")
expect_equal(index, 2246)
fromIDs <- countyCdLookup(state = 13, county = 5, output = "fullName")
expect_equal(fromIDs, "Bacon County")
counties <- c("51001","51003")
already_ready <- countyCdLookup(county = counties)
expect_equal(counties, already_ready)
})
context("water year column")
df_test <- data.frame(site_no = as.character(1:13),
dateTime = seq(as.Date("2010-01-01"),as.Date("2011-01-31"),
by="months"),
result_va = 1:13, stringsAsFactors = FALSE)
test_that("addWaterYear works with Date, POSIXct, character, but breaks with numeric", {
testthat::skip_on_cran()
df_date <- df_test
df_date_wy <- addWaterYear(df_date)
expect_equal(ncol(df_date_wy), ncol(df_date) + 1)
df_posixct <- df_test
df_posixct$dateTime <- as.POSIXct(df_posixct$dateTime)
df_posixct_wy <- addWaterYear(df_posixct)
expect_equal(ncol(df_posixct_wy), ncol(df_posixct) + 1)
df_char <- df_test
df_char$dateTime <- as.character(df_char$dateTime)
df_char_wy <- addWaterYear(df_char)
expect_equal(ncol(df_char_wy), ncol(df_char) + 1)
df_num <- df_test
df_num$dateTime <- as.numeric(df_num$dateTime)
dfnum2 <- addWaterYear(df_num)
expect_equal(dfnum2$waterYear, rep(NA, 13))
})
test_that("addWaterYear works for each column name", {
testthat::skip_on_cran()
nwisqw_style <- df_test
nwisqw_style_wy <- addWaterYear(nwisqw_style)
expect_equal(ncol(nwisqw_style_wy), ncol(nwisqw_style) + 1)
nwisdata_style <- df_test
names(nwisdata_style)[2] <- "Date"
nwisdata_style_wy <- addWaterYear(nwisdata_style)
expect_equal(ncol(nwisdata_style_wy), ncol(nwisdata_style) + 1)
wqp_style <- df_test
names(wqp_style)[2] <- "ActivityStartDate"
wqp_style[['ActivityEndDate']] <- wqp_style[["ActivityStartDate"]]
wqp_style_wy <- addWaterYear(wqp_style)
expect_equal(ncol(wqp_style_wy), ncol(wqp_style) + 2)
userspecified_style <- df_test
names(userspecified_style)[2] <- "MyDateCol"
expect_error(addWaterYear(userspecified_style),
"specified date column does not exist in supplied data frame")
})
test_that("addWaterYear correctly calculates the WY and is numeric", {
testthat::skip_on_cran()
df_test_wy <- addWaterYear(df_test)
expect_is(df_test_wy[['waterYear']], "numeric")
expect_true(all(df_test_wy[['waterYear']][1:9] == 2010))
expect_true(all(df_test_wy[['waterYear']][10:13] == 2011))
})
test_that("addWaterYear adds column next to dateTime", {
testthat::skip_on_cran()
df_test_wy <- addWaterYear(df_test)
dateTime_col <- which(names(df_test_wy) == "dateTime")
expect_equal(names(df_test_wy)[dateTime_col + 1], "waterYear")
})
test_that("addWaterYear can be used with pipes", {
testthat::skip_on_cran()
df_test_wy <- df_test
df_test_wy <- addWaterYear(df_test_wy)
expect_equal(ncol(df_test_wy), ncol(df_test) + 1)
})
test_that("addWaterYear doesn't add another WY column if it exists", {
testthat::skip_on_cran()
df_test_wy <- addWaterYear(df_test)
expect_equal(ncol(df_test_wy), ncol(df_test) + 1)
df_test_wy2 <- addWaterYear(df_test_wy)
expect_equal(ncol(df_test_wy2), ncol(df_test_wy))
})
test_that("calcWaterYear can handle missing values", {
dateVec <- seq(as.Date("2010-01-01"),as.Date("2011-01-31"), by="months")
dateVec[c(3,7,12)] <- NA
wyVec <- dataRetrieval:::calcWaterYear(dateVec)
expect_is(wyVec, "numeric")
expect_true(all(is.na(wyVec[c(3,7,12)])))
})
context("Construct NWIS urls")
test_that("Construct NWIS urls", {
testthat::skip_on_cran()
siteNumber <- '01594440'
startDate <- '1985-01-01'
endDate <- ''
pCode <- c("00060","00010")
url_daily <- constructNWISURL(siteNumber,pCode,
startDate,endDate,'dv',statCd=c("00003","00001"))
expect_equal(url_daily, "https://waterservices.usgs.gov/nwis/dv/?site=01594440&format=waterml,1.1&ParameterCd=00060,00010&StatCd=00003,00001&startDT=1985-01-01")
url_unit <- constructNWISURL(siteNumber,pCode,"2012-06-28","2012-06-30",'iv')
expect_equal(url_unit, "https://nwis.waterservices.usgs.gov/nwis/iv/?site=01594440&format=waterml,1.1&ParameterCd=00060,00010&startDT=2012-06-28&endDT=2012-06-30")
url_qw_single <- constructNWISURL(siteNumber,"01075",startDate,endDate,'qw')
expect_equal(url_qw_single, "https://nwis.waterdata.usgs.gov/nwis/qwdata?search_site_no=01594440&search_site_no_match_type=exact&multiple_parameter_cds=01075¶m_cd_operator=AND&list_of_search_criteria=search_site_no,multiple_parameter_cds&group_key=NONE&sitefile_output_format=html_table&column_name=agency_cd&column_name=site_no&column_name=station_nm&inventory_output=0&rdb_inventory_output=file&TZoutput=0&pm_cd_compare=Greater%20than&radio_parm_cds=previous_parm_cds&qw_attributes=0&format=rdb&rdb_qw_attributes=expanded&date_format=YYYY-MM-DD&rdb_compression=value&qw_sample_wide=0&begin_date=1985-01-01")
url_qw <- constructNWISURL(siteNumber,c('01075','00029','00453'),
startDate,endDate,'qw')
expect_equal(url_qw, "https://nwis.waterdata.usgs.gov/nwis/qwdata?search_site_no=01594440&search_site_no_match_type=exact&multiple_parameter_cds=01075,00029,00453¶m_cd_operator=OR&list_of_search_criteria=search_site_no,multiple_parameter_cds&group_key=NONE&sitefile_output_format=html_table&column_name=agency_cd&column_name=site_no&column_name=station_nm&inventory_output=0&rdb_inventory_output=file&TZoutput=0&pm_cd_compare=Greater%20than&radio_parm_cds=previous_parm_cds&qw_attributes=0&format=rdb&rdb_qw_attributes=expanded&date_format=YYYY-MM-DD&rdb_compression=value&qw_sample_wide=0&begin_date=1985-01-01")
url_daily_tsv <- constructNWISURL(siteNumber,pCode,startDate,endDate,'dv',
statCd=c("00003","00001"),format="tsv")
expect_equal(url_daily_tsv, "https://waterservices.usgs.gov/nwis/dv/?site=01594440&format=rdb,1.0&ParameterCd=00060,00010&StatCd=00003,00001&startDT=1985-01-01")
setAccess("internal")
url_rating <- constructNWISURL(siteNumber,service="rating",ratingType="base")
expect_equal(url_rating, "https://waterdata.usgs.gov/nwisweb/get_ratings/?Access=3&site_no=01594440&file_type=base")
url_peak <- constructNWISURL(siteNumber, service="peak")
expect_equal(url_peak, "https://nwis.waterdata.usgs.gov/usa/nwis/peak/?Access=3&site_no=01594440&range_selection=date_range&format=rdb")
url_meas <- constructNWISURL(siteNumber, service="meas")
expect_equal(url_meas, "https://waterdata.usgs.gov/nwis/measurements/?Access=3&site_no=01594440&range_selection=date_range&format=rdb_expanded")
urlQW <- constructNWISURL("450456092225801","70300",startDate="",endDate="","qw",expanded=TRUE)
expect_equal(urlQW, "https://nwis.waterdata.usgs.gov/nwis/qwdata?Access=3&search_site_no=450456092225801&search_site_no_match_type=exact&multiple_parameter_cds=70300¶m_cd_operator=AND&list_of_search_criteria=search_site_no,multiple_parameter_cds&group_key=NONE&sitefile_output_format=html_table&column_name=agency_cd&column_name=site_no&column_name=station_nm&inventory_output=0&rdb_inventory_output=file&TZoutput=0&pm_cd_compare=Greater%20than&radio_parm_cds=previous_parm_cds&qw_attributes=0&format=rdb&rdb_qw_attributes=expanded&date_format=YYYY-MM-DD&rdb_compression=value&qw_sample_wide=0")
setAccess("cooperator")
urlQW <- constructNWISURL("450456092225801","70300",startDate="",endDate="","qw",expanded=TRUE)
expect_equal(urlQW, "https://nwis.waterdata.usgs.gov/nwis/qwdata?Access=1&search_site_no=450456092225801&search_site_no_match_type=exact&multiple_parameter_cds=70300¶m_cd_operator=AND&list_of_search_criteria=search_site_no,multiple_parameter_cds&group_key=NONE&sitefile_output_format=html_table&column_name=agency_cd&column_name=site_no&column_name=station_nm&inventory_output=0&rdb_inventory_output=file&TZoutput=0&pm_cd_compare=Greater%20than&radio_parm_cds=previous_parm_cds&qw_attributes=0&format=rdb&rdb_qw_attributes=expanded&date_format=YYYY-MM-DD&rdb_compression=value&qw_sample_wide=0")
setAccess("USGS")
urlQW <- constructNWISURL("450456092225801","70300",startDate="",endDate="","qw",expanded=TRUE)
expect_equal(urlQW, "https://nwis.waterdata.usgs.gov/nwis/qwdata?Access=2&search_site_no=450456092225801&search_site_no_match_type=exact&multiple_parameter_cds=70300¶m_cd_operator=AND&list_of_search_criteria=search_site_no,multiple_parameter_cds&group_key=NONE&sitefile_output_format=html_table&column_name=agency_cd&column_name=site_no&column_name=station_nm&inventory_output=0&rdb_inventory_output=file&TZoutput=0&pm_cd_compare=Greater%20than&radio_parm_cds=previous_parm_cds&qw_attributes=0&format=rdb&rdb_qw_attributes=expanded&date_format=YYYY-MM-DD&rdb_compression=value&qw_sample_wide=0")
setAccess("public")
urlQW <- constructNWISURL("450456092225801","70300",startDate="",endDate="","qw",expanded=TRUE)
expect_equal(urlQW, "https://nwis.waterdata.usgs.gov/nwis/qwdata?search_site_no=450456092225801&search_site_no_match_type=exact&multiple_parameter_cds=70300¶m_cd_operator=AND&list_of_search_criteria=search_site_no,multiple_parameter_cds&group_key=NONE&sitefile_output_format=html_table&column_name=agency_cd&column_name=site_no&column_name=station_nm&inventory_output=0&rdb_inventory_output=file&TZoutput=0&pm_cd_compare=Greater%20than&radio_parm_cds=previous_parm_cds&qw_attributes=0&format=rdb&rdb_qw_attributes=expanded&date_format=YYYY-MM-DD&rdb_compression=value&qw_sample_wide=0")
url_use <- constructUseURL(years=c(1990,1995),stateCd="Ohio",countyCd = c(1,3), categories = "ALL")
expect_equal(url_use, "https://waterdata.usgs.gov/OH/nwis/water_use?format=rdb&rdb_compression=value&wu_area=county&wu_county=1%2C3&wu_year=1990%2C1995&wu_category=ALL")
})
context("Construct WQP urls")
test_that("Construct WQP urls", {
testthat::skip_on_cran()
site_id <- '01594440'
startDate <- '1985-01-01'
endDate <- ''
pCode <- c("00060","00010")
url_wqp <- constructWQPURL(paste("USGS",site_id,sep="-"),
c('01075','00029','00453'),
startDate,endDate)
expect_equal(url_wqp, "https://www.waterqualitydata.us/data/Result/search?siteid=USGS-01594440&pCode=01075;00029;00453&startDateLo=01-01-1985&mimeType=tsv&zip=yes")
#Multiple characteristicNames
charNames <- c("Temperature","Temperature, sample","Temperature, water",
"Temperature, water, deg F")
obs_url_orig <- constructWQPURL(siteNumbers = c("IIDFG-41WSSPAHS", "USGS-02352560"),
parameterCd = c("Temperature","Temperature, sample","Temperature, water", "Temperature, water, deg F"),
"","")
expect_equal(obs_url_orig, "https://www.waterqualitydata.us/data/Result/search?siteid=IIDFG-41WSSPAHS;USGS-02352560&characteristicName=Temperature;Temperature%2C%20sample;Temperature%2C%20water;Temperature%2C%20water%2C%20deg%20F&mimeType=tsv&zip=yes")
})
context("checkWQPdates")
test_that("checkWQPdates", {
values <- list(startDateLo="01-01-2002", characteristicName="Phosphorous",
endDate=as.Date("2014-01-01"))
values1 <- checkWQPdates(values)
expect_equal(values1$startDateHi, "01-01-2014")
expect_equal(values1$startDateLo, "01-01-2002")
})
context("Construct WQP urls")
test_that("Construct WQP urls", {
siteNumber <- '01594440'
startDate <- '1985-01-01'
endDate <- ''
pCode <- c("00060","00010")
url_wqp <- constructWQPURL(paste("USGS",siteNumber,sep="-"),
c('01075','00029','00453'),
startDate,endDate)
expect_equal(url_wqp, "https://www.waterqualitydata.us/data/Result/search?siteid=USGS-01594440&pCode=01075;00029;00453&startDateLo=01-01-1985&mimeType=tsv&zip=yes")
rawSampleURL_Zip <- constructWQPURL('USGS-01594440','01075', '', '', TRUE)
expect_equal(rawSampleURL_Zip, "https://www.waterqualitydata.us/data/Result/search?siteid=USGS-01594440&pCode=01075&mimeType=tsv&zip=yes")
})
context("pCode Stuff")
test_that("pCode Stuff", {
testthat::skip_on_cran()
paramINFO <- readNWISpCode(c('01075','00060','00931', NA))
expect_equal(nrow(paramINFO), 4)
paramINFO <- readNWISpCode("all")
expect_equal(attr(paramINFO, "url"),"https://nwis.waterdata.usgs.gov/nwis/pmcodes/pmcodes?radio_pm_search=param_group&pm_group=All+--+include+all+parameter+groups&show=parameter_group_nm&show=parameter_nm&show=casrn&show=srsname&show=parameter_units&format=rdb")
})
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