tests/testthat/tests_general.R
In usgs/dataRetrieval: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data
context("General functions")
test_that("General NWIS retrievals working", {
testthat::skip_on_cran()
multiSite <- readNWISdata(sites=c("04025500","040263491"), service="iv",
parameterCd="00060",
startDate = "2020-11-01", endDate = "2020-11-02")
expect_is(multiSite$dateTime, 'POSIXct')
recent_uv <- readNWISdata(siteNumber="04025500",parameterCd="00060",service="uv",
startDate=as.Date(Sys.Date()-10),endDate=Sys.Date())
expect_equal(grep(x = attr(recent_uv, "url"),pattern = "https://waterservices.usgs.gov/nwis/iv/"),1)
older_uv <- readNWISdata(siteNumber="04025500",parameterCd="00060",service="uv",
startDate="2016-01-01",endDate="2016-01-02")
expect_equal(grep(x = attr(older_uv, "url"),pattern = "https://nwis.waterservices.usgs.gov/nwis/iv/"),1)
expect_error(readNWISdata(), "No arguments supplied")
expect_error(readNWISdata(siteNumber = NA), "NA's are not allowed in query")
bBoxEx <- readNWISdata(bBox=c(-83,36.5,-81,38.5), parameterCd="00010")
expect_true(length(unique(bBoxEx$site_no)) > 1)
startDate <- as.Date("2013-10-01")
endDate <- as.Date("2014-09-30")
waterYear <- readNWISdata(bBox=c(-83,36.5,-81,38.5), parameterCd="00010",
service="dv", startDate=startDate, endDate=endDate)
expect_is(waterYear$dateTime, 'POSIXct')
siteInfo <- readNWISdata(stateCd="WI", parameterCd="00010",hasDataTypeCd="iv",
service="site")
expect_is(siteInfo$station_nm, "character")
qwData <- readNWISdata(bBox=c(-82.5,41.52,-81,41),startDate=as.Date("2000-01-01"),
drain_area_va_min=50, qw_count_nu=50,qw_attributes="expanded",
qw_sample_wide="wide",list_of_search_criteria=c("lat_long_bounding_box",
"drain_area_va","obs_count_nu"),service="qw")
expect_is(qwData$startDateTime, "POSIXct")
url <- "https://waterservices.usgs.gov/nwis/dv/?site=09037500&format=rdb&ParameterCd=00060&StatCd=00003&startDT=1985-10-02&endDT=2012-09-06"
dv <- importRDB1(url, asDateTime = FALSE)
urlEmpty <- "https://nwis.waterdata.usgs.gov/nwis/qwdata?multiple_site_no=413437087150601&sort_key=site_no&group_key=NONE&inventory_output=0&begin_date=&end_date=&TZoutput=0¶m_group=NUT,INN&qw_attributes=0&format=rdb&qw_sample_wide=0&rdb_qw_attributes=expanded&date_format=YYYY-MM-DD&rdb_compression=value&list_of_search_criteria=multiple_site_no"
dv <- importRDB1(urlEmpty, asDateTime = FALSE)
expect_true(nrow(dv) == 0)
dailyStat <- readNWISdata(site=c("03112500","03111520","02319394"),service="stat",statReportType="daily",
statType=c("p25","p50","p75","min","max"),
parameterCd="00065",convertType=FALSE)
expect_true(length(dailyStat$min_va) > 1)
expect_is(dailyStat$p25_va,"character")
waterYearStat <- readNWISdata(site=c("01646500"),service="stat",statReportType="annual",
statYearType="water", missingData="on")
expect_is(waterYearStat$mean_va,"numeric")
expect_is(waterYearStat$parameter_cd,"character")
#Empty data
urlTest <- "https://nwis.waterservices.usgs.gov/nwis/iv/?site=11447650&format=waterml,1.1&ParameterCd=63680&startDT=2016-12-13&endDT=2016-12-13"
x <- importWaterML1(urlTest)
expect_equal(names(x), c("agency_cd","site_no","dateTime","tz_cd"))
#Test list:
args <- list(sites="05114000", service="iv",
parameterCd="00060",
startDate="2014-05-01T00:00Z",
endDate="2014-05-01T12:00Z")
instData <- readNWISdata(args)
args <- list(sites="05114000", service="dv",
parameterCd="00060",
startDate="2014-05-01",
endDate="2014-05-01")
dailyData <- readNWISdata(args)
expect_lt(nrow(dailyData), nrow(instData))
args <- list(stateCd="OH",parameterCd="00665")
sites <- whatNWISsites(args)
expect_type(sites, "list")
#Test counties:
dailyStaffordVA <- readNWISdata(stateCd = "Virginia",
countyCd="Stafford",
parameterCd = "00060",
startDate = "2015-01-01",
endDate = "2015-01-30")
expect_gt(nrow(dailyStaffordVA),1)
AS <- readNWISdata(stateCd = "AS", service="site")
expect_gt(nrow(AS),0)
site_id <- '01594440'
rating_curve <- readNWISdata(service = "rating", site_no = site_id, file_type="base")
rating_curve2 <- readNWISrating(siteNumber = site_id, type = "base")
expect_equal(attr(rating_curve,"url"), "https://waterdata.usgs.gov/nwisweb/get_ratings/?site_no=01594440&file_type=base")
expect_equal(rating_curve$INDEP, rating_curve2$INDEP)
state_rating_list <- readNWISdata(service = "rating", file_type="base", period = 24)
expect_true(all(names(state_rating_list) %in% c("agency_cd",
"site_no",
"type",
"update_time",
"url")))
})
test_that("whatNWISdata",{
#no service specified:
availableData <- whatNWISdata(siteNumber = '05114000')
expect_equal(ncol(availableData), 24)
uvData <- whatNWISdata(siteNumber = '05114000',service="uv")
expect_equal(unique(uvData$data_type_cd), "uv")
#multiple services
uvDataMulti <- whatNWISdata(siteNumber = c('05114000','09423350'),service=c("uv","dv"))
expect_true(all(unique(uvDataMulti$data_type_cd) %in% c("uv","dv")))
#state codes:
flowAndTemp <- whatNWISdata(stateCd = "WI", service = c("uv","dv"),
parameterCd = c("00060","00010"),
statCd = "00003")
expect_true(all(unique(flowAndTemp$data_type_cd) %in% c("uv","dv")))
expect_true(all(unique(flowAndTemp$parm_cd) %in% c("00060","00010")))
expect_true(all(unique(flowAndTemp$stat_cd) %in% c("00003",NA)))
})
test_that("General WQP retrievals working", {
testthat::skip_on_cran()
nameToUse <- "pH"
pHData <- readWQPdata(siteid="USGS-04024315",characteristicName=nameToUse)
expect_is(pHData$ActivityStartDateTime, 'POSIXct')
#testing lists:
startDate <- as.Date("2013-01-01")
secchi.names = c("Depth, Secchi disk depth",
"Depth, Secchi disk depth (choice list)",
"Secchi Reading Condition (choice list)",
"Water transparency, Secchi disc")
args_2 <- list('startDateLo' = startDate,
'startDateHi' = "2013-12-31",
statecode="WI",
characteristicName=secchi.names)
wqp.summary <- readWQPdata(args_2, querySummary = TRUE)
expect_true("list" %in% class(wqp.summary))
#pretty sloooow:
# wqp.data <- readWQPdata(args_2, querySummary = FALSE)
# expect_false("list" %in% class(wqp.data))
# Testing multiple lists:
arg_3 <- list('startDateLo' = startDate,
'startDateHi' = "2013-12-31")
arg_4 <- list(statecode="WI",
characteristicName=secchi.names)
wqp.summary <- readWQPdata(arg_3, arg_4, querySummary=TRUE)
expect_true("list" %in% class(wqp.summary))
lakeSites <- whatWQPsites(args_2)
expect_type(lakeSites, "list")
# Test county code:
# dailyLexingtonVA <- readWQPdata(statecode = "Virginia",
# countycode="Lexington",
# parameterCd = "00010")
#
# expect_equal(ncol(dailyLexingtonVA),65)
site1 <- readWQPsummary(siteid="USGS-07144100",
summaryYears=5,
dataProfile="periodOfRecord")
expect_type(site1$ActivityCount, "double")
expect_type(site1$MonitoringLocationIdentifier, "character")
expect_equal(attr(site1, "url"), "https://www.waterqualitydata.us/data/summary/monitoringLocation/search?siteid=USGS-07144100&summaryYears=5&dataProfile=periodOfRecord&zip=yes&mimeType=csv")
wqp.summary_no_atts <- readWQPdata(siteid="USGS-04024315",
characteristicName=nameToUse,
ignore_attributes = TRUE)
expect_true(!all(c("siteInfo","variableInfo") %in% names(attributes(wqp.summary_no_atts))))
})
test_that("WQP head query retrievals working", {
testthat::skip_on_cran()
nameToUse <- "pH"
pHDataQueryResults <- readWQPdata(siteid="USGS-04024315",
characteristicName=nameToUse,
querySummary=TRUE)
expect_false(is.null(pHDataQueryResults$date))
expect_is(pHDataQueryResults$date, 'Date')
expect_false(is.null(pHDataQueryResults$`total-site-count`))
expect_is(pHDataQueryResults$`total-site-count`, 'numeric')
expect_false(is.null(pHDataQueryResults$`total-result-count`))
expect_is(pHDataQueryResults$`total-result-count`, 'numeric')
pHDataQueryResults <- readWQPqw(siteNumbers="USGS-04024315",
parameterCd=nameToUse,
querySummary=TRUE)
expect_false(is.null(pHDataQueryResults$date))
expect_is(pHDataQueryResults$date, 'Date')
expect_false(is.null(pHDataQueryResults$`total-site-count`))
expect_is(pHDataQueryResults$`total-site-count`, 'numeric')
expect_false(is.null(pHDataQueryResults$`total-result-count`))
expect_is(pHDataQueryResults$`total-result-count`, 'numeric')
})
test_that("zeroPad handles NAs", {
toPad <- c(1,5,55,NA)
padded <- zeroPad(toPad,3)
expect_true(identical(c("001","005","055",NA),padded))
})
test_that("Dates with no days can be handled", {
testthat::skip_on_cran()
empty_df <- readNWISgwl("425957088141001", startDate = "1980-01-01")
expect_true(nrow(empty_df) > 0)
})
context("whatWQPsamples")
test_that("whatWQPsamples working", {
testthat::skip_on_cran()
# The warning is caused by a confirmed bug in WQP
siteInfo <- suppressWarnings(whatWQPsamples(siteid="USGS-01594440"))
expect_true(nrow(siteInfo) > 0)
})
context("whatWQPmetrics")
test_that("whatWQPmetrics working", {
testthat::skip_on_cran()
type <- "Stream"
siteInfo <- whatWQPmetrics(countycode="US:55:025",siteType=type)
expect_true(ncol(siteInfo) >= 21)
})
context("whatWQPdata")
test_that("whatWQPdata working", {
testthat::skip_on_cran()
site1 <- whatWQPdata(siteid="USGS-01594440")
expect_is(site1, "data.frame")
expect_equal(1, nrow(site1))
type <- "Stream"
sites <- whatWQPdata(countycode="US:55:025",siteType=type)
expect_gt(nrow(sites), 1)
lakeSites <- whatWQPdata(siteType = "Lake, Reservoir, Impoundment", statecode = "US:55")
expect_is(lakeSites$activityCount, "numeric")
})
context("whatNWISsites")
test_that("whatNWISsites working", {
testthat::skip_on_cran()
siteListPhos <- whatNWISsites(stateCd="OH",parameterCd="00665")
expect_true(nrow(siteListPhos) > 0)
expect_true(is.numeric(siteListPhos$dec_lat_va))
bboxSites <- whatNWISsites(bbox = c(-92.5, 45.4, -87, 47), parameterCd="00060")
expect_true(nrow(bboxSites) > 0)
expect_true(is.numeric(bboxSites$dec_lat_va))
})
context("readWQPdots")
test_that("readWQPdots working", {
testthat::skip_on_cran()
# bbox vector turned into single string with coords separated by semicolons
formArgs_bbox <- dataRetrieval:::readWQPdots(bbox = c(-92.5, 45.4, -87, 47))
expect_true(length(formArgs_bbox) == 2)
expect_true(length(gregexpr(";", formArgs_bbox)[[1]]) == 3)
# NWIS names (siteNumber) converted to WQP expected names (siteid)
formArgs_site <- dataRetrieval:::readWQPdots(siteNumber="04010301")
expect_true(length(formArgs_site) == 2)
expect_true("siteid" %in% names(formArgs_site))
expect_false("siteNumber" %in% names(formArgs_site))
# NWIS names (stateCd) converted to WQP expected names (statecode)
formArgs <- dataRetrieval:::readWQPdots(stateCd="OH",parameterCd="00665")
expect_true(length(formArgs) == 3)
expect_true("statecode" %in% names(formArgs))
expect_false("stateCd" %in% names(formArgs))
})
# context("NGWMN")
# test_that("NGWMN functions working", {
# testthat::skip_on_cran()
# # noDataSite <- "UTGS.401544112060301"
# # noDataSite <- readNGWMNlevels(siteNumbers = noDataSite)
# # expect_true(is.data.frame(noDataSite))
# #
# # #bounding box and multi-site getFeatureOfInterest request
# # bboxSites <- readNGWMNdata(service = "featureOfInterest",
# # bbox = c(30, -99, 31, 102))
# # expect_gt(nrow(bboxSites), 0)
# # siteInfo <- readNGWMNsites(bboxSites$site[1:3])
# # expect_equal(nrow(siteInfo), 3)
#
# #one site
# # site <- "USGS.430427089284901"
# # oneSite <- readNGWMNlevels(siteNumbers = site)
# # siteInfo <- readNGWMNsites(site)
# # expect_true(is.numeric(oneSite$value))
# # expect_true(is.character(oneSite$site))
# # expect_true(is.data.frame(siteInfo))
# # expect_true(nrow(siteInfo) > 0)
# # expect_true(nrow(oneSite) > 0)
#
# #non-USGS site
# # data <- readNGWMNlevels(siteNumbers = "MBMG.103306")
# # expect_true(nrow(data) > 1)
# # expect_true(is.numeric(oneSite$value))
#
# #sites with colons and NAs work
#
# # na_colons <- c(NA, bboxSites$site[200:212], NA, NA)
# # returnDF <- readNGWMNdata(service = "observation",
# # siteNumbers = na_colons, asDateTime = FALSE)
# # expect_is(returnDF, "data.frame")
# # expect_true(nrow(returnDF) > 1)
# # #expect_true(!is.null(attributes(returnDF)$siteInfo))
# #
# # sites <- c("USGS:424427089494701", NA)
# # siteInfo <- readNGWMNsites(sites)
# # expect_is(siteInfo, "data.frame")
# # expect_true(nrow(siteInfo) == 1)
#
# #time zones
# # tzSite <- "USGS.385111104214403"
# # tzDataUTC <- readNGWMNlevels(tzSite, asDateTime = TRUE)
# # tzDataMT <- readNGWMNlevels(tzSite, asDateTime = TRUE,
# # tz = "US/Mountain")
# # expect_gt(nrow(tzDataMT), 1)
# # expect_gt(nrow(tzDataUTC), 1)
# # expect_is(tzDataUTC$dateTime, "POSIXct")
# # expect_is(tzDataMT$dateTime, "POSIXct")
# # expect_equal(attr(tzDataMT$dateTime, 'tzone'), "US/Mountain")
# # expect_equal(attr(tzDataUTC$dateTime, 'tzone'), "UTC")
# })
context("getWebServiceData")
test_that("long urls use POST", {
testthat::skip_on_cran()
url <- paste0(rep("reallylongurl", 200), collapse = '')
with_mock(
RETRY = function(method, ...) {
return(method == "POST")
},
status_code = function(resp) 200,
headers = function(resp) list(`content-type` = "logical"),
content = function(resp, encoding) resp,
expect_true(getWebServiceData(url)),
.env = "httr"
)
})
test_that("ngwmn urls don't use post", {
testthat::skip_on_cran()
url <- paste0(rep("urlwithngwmn", 200), collapse = '')
with_mock(
RETRY = function(method, ...) {
return(method == "POST")
},
status_code = function(resp) 200,
headers = function(resp) list(`content-type` = "logical"),
content = function(resp, encoding) resp,
expect_false(getWebServiceData(url)),
.env = "httr"
)
})
test_that("400 errors return a verbose error", {
testthat::skip_on_cran()
url <- "https://waterservices.usgs.gov/nwis/site/?stateCd=IA&bBox=-92.821445,42.303044,-92.167168,42.646524&format=mapper"
expect_error(getWebServiceData(url))
expect_equal(tryCatch(getWebServiceData(url), error = function(e) e$message), "HTTP Status 400 - syntactic error: Only one Major filter can be supplied. Found [bbox] and [stateCd]. Please remove the extra major filter[s].")
})
test_that("internal functions",{
# get empty_col type
expect_equal(dataRetrieval:::empty_col("numeric"), numeric())
expect_equal(dataRetrieval:::empty_col("character"), character())
expect_equal(dataRetrieval:::empty_col("Date"), as.Date(numeric(),origin = "1970-01-01"))
# add empty columns
df1 <- data.frame(a = 1:2,
b = c("a","b"),
c = as.Date(c("2010-01-01","2010-01-02")),
stringsAsFactors = FALSE)
df2 <- data.frame(d = 1:2,
b = c("a","b"),
e = factor(c("c","d")),
stringsAsFactors = FALSE)
df2_ret <- dataRetrieval:::add_empty_col(df2, df1, c("a","c"))
df1_ret <- dataRetrieval:::add_empty_col(df1, df2, c("d","e"))
expect_true(ncol(df2_ret) == 5)
expect_true(ncol(df1_ret) == 5)
expect_true(all(is.na(df2_ret[,c("a","c")])))
expect_true(all(is.na(df1_ret[,c("d","e")])))
bound_df <- dataRetrieval:::r_bind_dr(df1, df2)
expect_true(nrow(bound_df) == 4)
expect_true(class(bound_df$c) == "Date")
expect_true(class(bound_df$a) == "integer")
expect_true(class(bound_df$b) == "character")
})
usgs/dataRetrieval documentation built on Feb. 27, 2021, 12:40 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("General functions")
test_that("General NWIS retrievals working", {
testthat::skip_on_cran()
multiSite <- readNWISdata(sites=c("04025500","040263491"), service="iv",
parameterCd="00060",
startDate = "2020-11-01", endDate = "2020-11-02")
expect_is(multiSite$dateTime, 'POSIXct')
recent_uv <- readNWISdata(siteNumber="04025500",parameterCd="00060",service="uv",
startDate=as.Date(Sys.Date()-10),endDate=Sys.Date())
expect_equal(grep(x = attr(recent_uv, "url"),pattern = "https://waterservices.usgs.gov/nwis/iv/"),1)
older_uv <- readNWISdata(siteNumber="04025500",parameterCd="00060",service="uv",
startDate="2016-01-01",endDate="2016-01-02")
expect_equal(grep(x = attr(older_uv, "url"),pattern = "https://nwis.waterservices.usgs.gov/nwis/iv/"),1)
expect_error(readNWISdata(), "No arguments supplied")
expect_error(readNWISdata(siteNumber = NA), "NA's are not allowed in query")
bBoxEx <- readNWISdata(bBox=c(-83,36.5,-81,38.5), parameterCd="00010")
expect_true(length(unique(bBoxEx$site_no)) > 1)
startDate <- as.Date("2013-10-01")
endDate <- as.Date("2014-09-30")
waterYear <- readNWISdata(bBox=c(-83,36.5,-81,38.5), parameterCd="00010",
service="dv", startDate=startDate, endDate=endDate)
expect_is(waterYear$dateTime, 'POSIXct')
siteInfo <- readNWISdata(stateCd="WI", parameterCd="00010",hasDataTypeCd="iv",
service="site")
expect_is(siteInfo$station_nm, "character")
qwData <- readNWISdata(bBox=c(-82.5,41.52,-81,41),startDate=as.Date("2000-01-01"),
drain_area_va_min=50, qw_count_nu=50,qw_attributes="expanded",
qw_sample_wide="wide",list_of_search_criteria=c("lat_long_bounding_box",
"drain_area_va","obs_count_nu"),service="qw")
expect_is(qwData$startDateTime, "POSIXct")
url <- "https://waterservices.usgs.gov/nwis/dv/?site=09037500&format=rdb&ParameterCd=00060&StatCd=00003&startDT=1985-10-02&endDT=2012-09-06"
dv <- importRDB1(url, asDateTime = FALSE)
urlEmpty <- "https://nwis.waterdata.usgs.gov/nwis/qwdata?multiple_site_no=413437087150601&sort_key=site_no&group_key=NONE&inventory_output=0&begin_date=&end_date=&TZoutput=0¶m_group=NUT,INN&qw_attributes=0&format=rdb&qw_sample_wide=0&rdb_qw_attributes=expanded&date_format=YYYY-MM-DD&rdb_compression=value&list_of_search_criteria=multiple_site_no"
dv <- importRDB1(urlEmpty, asDateTime = FALSE)
expect_true(nrow(dv) == 0)
dailyStat <- readNWISdata(site=c("03112500","03111520","02319394"),service="stat",statReportType="daily",
statType=c("p25","p50","p75","min","max"),
parameterCd="00065",convertType=FALSE)
expect_true(length(dailyStat$min_va) > 1)
expect_is(dailyStat$p25_va,"character")
waterYearStat <- readNWISdata(site=c("01646500"),service="stat",statReportType="annual",
statYearType="water", missingData="on")
expect_is(waterYearStat$mean_va,"numeric")
expect_is(waterYearStat$parameter_cd,"character")
#Empty data
urlTest <- "https://nwis.waterservices.usgs.gov/nwis/iv/?site=11447650&format=waterml,1.1&ParameterCd=63680&startDT=2016-12-13&endDT=2016-12-13"
x <- importWaterML1(urlTest)
expect_equal(names(x), c("agency_cd","site_no","dateTime","tz_cd"))
#Test list:
args <- list(sites="05114000", service="iv",
parameterCd="00060",
startDate="2014-05-01T00:00Z",
endDate="2014-05-01T12:00Z")
instData <- readNWISdata(args)
args <- list(sites="05114000", service="dv",
parameterCd="00060",
startDate="2014-05-01",
endDate="2014-05-01")
dailyData <- readNWISdata(args)
expect_lt(nrow(dailyData), nrow(instData))
args <- list(stateCd="OH",parameterCd="00665")
sites <- whatNWISsites(args)
expect_type(sites, "list")
#Test counties:
dailyStaffordVA <- readNWISdata(stateCd = "Virginia",
countyCd="Stafford",
parameterCd = "00060",
startDate = "2015-01-01",
endDate = "2015-01-30")
expect_gt(nrow(dailyStaffordVA),1)
AS <- readNWISdata(stateCd = "AS", service="site")
expect_gt(nrow(AS),0)
site_id <- '01594440'
rating_curve <- readNWISdata(service = "rating", site_no = site_id, file_type="base")
rating_curve2 <- readNWISrating(siteNumber = site_id, type = "base")
expect_equal(attr(rating_curve,"url"), "https://waterdata.usgs.gov/nwisweb/get_ratings/?site_no=01594440&file_type=base")
expect_equal(rating_curve$INDEP, rating_curve2$INDEP)
state_rating_list <- readNWISdata(service = "rating", file_type="base", period = 24)
expect_true(all(names(state_rating_list) %in% c("agency_cd",
"site_no",
"type",
"update_time",
"url")))
})
test_that("whatNWISdata",{
#no service specified:
availableData <- whatNWISdata(siteNumber = '05114000')
expect_equal(ncol(availableData), 24)
uvData <- whatNWISdata(siteNumber = '05114000',service="uv")
expect_equal(unique(uvData$data_type_cd), "uv")
#multiple services
uvDataMulti <- whatNWISdata(siteNumber = c('05114000','09423350'),service=c("uv","dv"))
expect_true(all(unique(uvDataMulti$data_type_cd) %in% c("uv","dv")))
#state codes:
flowAndTemp <- whatNWISdata(stateCd = "WI", service = c("uv","dv"),
parameterCd = c("00060","00010"),
statCd = "00003")
expect_true(all(unique(flowAndTemp$data_type_cd) %in% c("uv","dv")))
expect_true(all(unique(flowAndTemp$parm_cd) %in% c("00060","00010")))
expect_true(all(unique(flowAndTemp$stat_cd) %in% c("00003",NA)))
})
test_that("General WQP retrievals working", {
testthat::skip_on_cran()
nameToUse <- "pH"
pHData <- readWQPdata(siteid="USGS-04024315",characteristicName=nameToUse)
expect_is(pHData$ActivityStartDateTime, 'POSIXct')
#testing lists:
startDate <- as.Date("2013-01-01")
secchi.names = c("Depth, Secchi disk depth",
"Depth, Secchi disk depth (choice list)",
"Secchi Reading Condition (choice list)",
"Water transparency, Secchi disc")
args_2 <- list('startDateLo' = startDate,
'startDateHi' = "2013-12-31",
statecode="WI",
characteristicName=secchi.names)
wqp.summary <- readWQPdata(args_2, querySummary = TRUE)
expect_true("list" %in% class(wqp.summary))
#pretty sloooow:
# wqp.data <- readWQPdata(args_2, querySummary = FALSE)
# expect_false("list" %in% class(wqp.data))
# Testing multiple lists:
arg_3 <- list('startDateLo' = startDate,
'startDateHi' = "2013-12-31")
arg_4 <- list(statecode="WI",
characteristicName=secchi.names)
wqp.summary <- readWQPdata(arg_3, arg_4, querySummary=TRUE)
expect_true("list" %in% class(wqp.summary))
lakeSites <- whatWQPsites(args_2)
expect_type(lakeSites, "list")
# Test county code:
# dailyLexingtonVA <- readWQPdata(statecode = "Virginia",
# countycode="Lexington",
# parameterCd = "00010")
#
# expect_equal(ncol(dailyLexingtonVA),65)
site1 <- readWQPsummary(siteid="USGS-07144100",
summaryYears=5,
dataProfile="periodOfRecord")
expect_type(site1$ActivityCount, "double")
expect_type(site1$MonitoringLocationIdentifier, "character")
expect_equal(attr(site1, "url"), "https://www.waterqualitydata.us/data/summary/monitoringLocation/search?siteid=USGS-07144100&summaryYears=5&dataProfile=periodOfRecord&zip=yes&mimeType=csv")
wqp.summary_no_atts <- readWQPdata(siteid="USGS-04024315",
characteristicName=nameToUse,
ignore_attributes = TRUE)
expect_true(!all(c("siteInfo","variableInfo") %in% names(attributes(wqp.summary_no_atts))))
})
test_that("WQP head query retrievals working", {
testthat::skip_on_cran()
nameToUse <- "pH"
pHDataQueryResults <- readWQPdata(siteid="USGS-04024315",
characteristicName=nameToUse,
querySummary=TRUE)
expect_false(is.null(pHDataQueryResults$date))
expect_is(pHDataQueryResults$date, 'Date')
expect_false(is.null(pHDataQueryResults$`total-site-count`))
expect_is(pHDataQueryResults$`total-site-count`, 'numeric')
expect_false(is.null(pHDataQueryResults$`total-result-count`))
expect_is(pHDataQueryResults$`total-result-count`, 'numeric')
pHDataQueryResults <- readWQPqw(siteNumbers="USGS-04024315",
parameterCd=nameToUse,
querySummary=TRUE)
expect_false(is.null(pHDataQueryResults$date))
expect_is(pHDataQueryResults$date, 'Date')
expect_false(is.null(pHDataQueryResults$`total-site-count`))
expect_is(pHDataQueryResults$`total-site-count`, 'numeric')
expect_false(is.null(pHDataQueryResults$`total-result-count`))
expect_is(pHDataQueryResults$`total-result-count`, 'numeric')
})
test_that("zeroPad handles NAs", {
toPad <- c(1,5,55,NA)
padded <- zeroPad(toPad,3)
expect_true(identical(c("001","005","055",NA),padded))
})
test_that("Dates with no days can be handled", {
testthat::skip_on_cran()
empty_df <- readNWISgwl("425957088141001", startDate = "1980-01-01")
expect_true(nrow(empty_df) > 0)
})
context("whatWQPsamples")
test_that("whatWQPsamples working", {
testthat::skip_on_cran()
# The warning is caused by a confirmed bug in WQP
siteInfo <- suppressWarnings(whatWQPsamples(siteid="USGS-01594440"))
expect_true(nrow(siteInfo) > 0)
})
context("whatWQPmetrics")
test_that("whatWQPmetrics working", {
testthat::skip_on_cran()
type <- "Stream"
siteInfo <- whatWQPmetrics(countycode="US:55:025",siteType=type)
expect_true(ncol(siteInfo) >= 21)
})
context("whatWQPdata")
test_that("whatWQPdata working", {
testthat::skip_on_cran()
site1 <- whatWQPdata(siteid="USGS-01594440")
expect_is(site1, "data.frame")
expect_equal(1, nrow(site1))
type <- "Stream"
sites <- whatWQPdata(countycode="US:55:025",siteType=type)
expect_gt(nrow(sites), 1)
lakeSites <- whatWQPdata(siteType = "Lake, Reservoir, Impoundment", statecode = "US:55")
expect_is(lakeSites$activityCount, "numeric")
})
context("whatNWISsites")
test_that("whatNWISsites working", {
testthat::skip_on_cran()
siteListPhos <- whatNWISsites(stateCd="OH",parameterCd="00665")
expect_true(nrow(siteListPhos) > 0)
expect_true(is.numeric(siteListPhos$dec_lat_va))
bboxSites <- whatNWISsites(bbox = c(-92.5, 45.4, -87, 47), parameterCd="00060")
expect_true(nrow(bboxSites) > 0)
expect_true(is.numeric(bboxSites$dec_lat_va))
})
context("readWQPdots")
test_that("readWQPdots working", {
testthat::skip_on_cran()
# bbox vector turned into single string with coords separated by semicolons
formArgs_bbox <- dataRetrieval:::readWQPdots(bbox = c(-92.5, 45.4, -87, 47))
expect_true(length(formArgs_bbox) == 2)
expect_true(length(gregexpr(";", formArgs_bbox)[[1]]) == 3)
# NWIS names (siteNumber) converted to WQP expected names (siteid)
formArgs_site <- dataRetrieval:::readWQPdots(siteNumber="04010301")
expect_true(length(formArgs_site) == 2)
expect_true("siteid" %in% names(formArgs_site))
expect_false("siteNumber" %in% names(formArgs_site))
# NWIS names (stateCd) converted to WQP expected names (statecode)
formArgs <- dataRetrieval:::readWQPdots(stateCd="OH",parameterCd="00665")
expect_true(length(formArgs) == 3)
expect_true("statecode" %in% names(formArgs))
expect_false("stateCd" %in% names(formArgs))
})
# context("NGWMN")
# test_that("NGWMN functions working", {
# testthat::skip_on_cran()
# # noDataSite <- "UTGS.401544112060301"
# # noDataSite <- readNGWMNlevels(siteNumbers = noDataSite)
# # expect_true(is.data.frame(noDataSite))
# #
# # #bounding box and multi-site getFeatureOfInterest request
# # bboxSites <- readNGWMNdata(service = "featureOfInterest",
# # bbox = c(30, -99, 31, 102))
# # expect_gt(nrow(bboxSites), 0)
# # siteInfo <- readNGWMNsites(bboxSites$site[1:3])
# # expect_equal(nrow(siteInfo), 3)
#
# #one site
# # site <- "USGS.430427089284901"
# # oneSite <- readNGWMNlevels(siteNumbers = site)
# # siteInfo <- readNGWMNsites(site)
# # expect_true(is.numeric(oneSite$value))
# # expect_true(is.character(oneSite$site))
# # expect_true(is.data.frame(siteInfo))
# # expect_true(nrow(siteInfo) > 0)
# # expect_true(nrow(oneSite) > 0)
#
# #non-USGS site
# # data <- readNGWMNlevels(siteNumbers = "MBMG.103306")
# # expect_true(nrow(data) > 1)
# # expect_true(is.numeric(oneSite$value))
#
# #sites with colons and NAs work
#
# # na_colons <- c(NA, bboxSites$site[200:212], NA, NA)
# # returnDF <- readNGWMNdata(service = "observation",
# # siteNumbers = na_colons, asDateTime = FALSE)
# # expect_is(returnDF, "data.frame")
# # expect_true(nrow(returnDF) > 1)
# # #expect_true(!is.null(attributes(returnDF)$siteInfo))
# #
# # sites <- c("USGS:424427089494701", NA)
# # siteInfo <- readNGWMNsites(sites)
# # expect_is(siteInfo, "data.frame")
# # expect_true(nrow(siteInfo) == 1)
#
# #time zones
# # tzSite <- "USGS.385111104214403"
# # tzDataUTC <- readNGWMNlevels(tzSite, asDateTime = TRUE)
# # tzDataMT <- readNGWMNlevels(tzSite, asDateTime = TRUE,
# # tz = "US/Mountain")
# # expect_gt(nrow(tzDataMT), 1)
# # expect_gt(nrow(tzDataUTC), 1)
# # expect_is(tzDataUTC$dateTime, "POSIXct")
# # expect_is(tzDataMT$dateTime, "POSIXct")
# # expect_equal(attr(tzDataMT$dateTime, 'tzone'), "US/Mountain")
# # expect_equal(attr(tzDataUTC$dateTime, 'tzone'), "UTC")
# })
context("getWebServiceData")
test_that("long urls use POST", {
testthat::skip_on_cran()
url <- paste0(rep("reallylongurl", 200), collapse = '')
with_mock(
RETRY = function(method, ...) {
return(method == "POST")
},
status_code = function(resp) 200,
headers = function(resp) list(`content-type` = "logical"),
content = function(resp, encoding) resp,
expect_true(getWebServiceData(url)),
.env = "httr"
)
})
test_that("ngwmn urls don't use post", {
testthat::skip_on_cran()
url <- paste0(rep("urlwithngwmn", 200), collapse = '')
with_mock(
RETRY = function(method, ...) {
return(method == "POST")
},
status_code = function(resp) 200,
headers = function(resp) list(`content-type` = "logical"),
content = function(resp, encoding) resp,
expect_false(getWebServiceData(url)),
.env = "httr"
)
})
test_that("400 errors return a verbose error", {
testthat::skip_on_cran()
url <- "https://waterservices.usgs.gov/nwis/site/?stateCd=IA&bBox=-92.821445,42.303044,-92.167168,42.646524&format=mapper"
expect_error(getWebServiceData(url))
expect_equal(tryCatch(getWebServiceData(url), error = function(e) e$message), "HTTP Status 400 - syntactic error: Only one Major filter can be supplied. Found [bbox] and [stateCd]. Please remove the extra major filter[s].")
})
test_that("internal functions",{
# get empty_col type
expect_equal(dataRetrieval:::empty_col("numeric"), numeric())
expect_equal(dataRetrieval:::empty_col("character"), character())
expect_equal(dataRetrieval:::empty_col("Date"), as.Date(numeric(),origin = "1970-01-01"))
# add empty columns
df1 <- data.frame(a = 1:2,
b = c("a","b"),
c = as.Date(c("2010-01-01","2010-01-02")),
stringsAsFactors = FALSE)
df2 <- data.frame(d = 1:2,
b = c("a","b"),
e = factor(c("c","d")),
stringsAsFactors = FALSE)
df2_ret <- dataRetrieval:::add_empty_col(df2, df1, c("a","c"))
df1_ret <- dataRetrieval:::add_empty_col(df1, df2, c("d","e"))
expect_true(ncol(df2_ret) == 5)
expect_true(ncol(df1_ret) == 5)
expect_true(all(is.na(df2_ret[,c("a","c")])))
expect_true(all(is.na(df1_ret[,c("d","e")])))
bound_df <- dataRetrieval:::r_bind_dr(df1, df2)
expect_true(nrow(bound_df) == 4)
expect_true(class(bound_df$c) == "Date")
expect_true(class(bound_df$a) == "integer")
expect_true(class(bound_df$b) == "character")
})
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.