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ldecicco-USGS merged 2 commits into from
Apr 30, 2026
Merged

Switch to samples in vignette #886

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6d6a8f0
Switch to samples in vignette
ldecicco-USGS Apr 30, 2026
2ee9add
Merge branch 'main' of github.com:DOI-USGS/dataRetrieval
ldecicco-USGS Apr 30, 2026
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166 changes: 83 additions & 83 deletions tests/testthat/tests_general.R
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Original file line number Diff line number Diff line change
Expand Up @@ -295,16 +295,16 @@ test_that("read_waterdata_ts_meta", {
test_that("General WQP retrievals working", {
testthat::skip_on_cran()
testthat::skip_on_ci()
nameToUse <- "pH"
pHData <- readWQPdata(
siteid = "USGS-04024315",
characteristicName = nameToUse,
service = "ResultWQX3"
)
expect_is(pHData$Activity_StartDateTime, "POSIXct")
expect_type(pHData$USGSpcode, "character")
expect_type(pHData$Result_Measure, "double")
expect_type(pHData$SampleCollectionMethod_Identifier, "character")
# nameToUse <- "pH"
# pHData <- readWQPdata(
# siteid = "USGS-04024315",
# characteristicName = nameToUse,
# service = "ResultWQX3"
# )
# expect_is(pHData$Activity_StartDateTime, "POSIXct")
# expect_type(pHData$USGSpcode, "character")
# expect_type(pHData$Result_Measure, "double")
# expect_type(pHData$SampleCollectionMethod_Identifier, "character")
#
# # testing lists:
startDate <- as.Date("2022-01-01")
Expand Down Expand Up @@ -335,80 +335,80 @@ test_that("General WQP retrievals working", {
characteristicName = secchi.names
)

wqp.summary_no_atts <- readWQPdata(
siteid = "USGS-04024315",
characteristicName = nameToUse,
ignore_attributes = TRUE,
service = "ResultWQX3"
)
expect_true(
!all(
c("siteInfo", "variableInfo") %in% names(attributes(wqp.summary_no_atts))
)
)

rawPcode <- readWQPqw("USGS-01594440", "01075", "", "", legacy = FALSE)
expect_true(all(
c("url", "queryTime", "siteInfo") %in%
names(attributes(rawPcode))
))

# This means wqp_check_status was called:
expect_true("dataProviders" %in% names(attr(rawPcode, "headerInfo")))

rawPcode2 <- readWQPqw(
"USGS-01594440",
"01075",
"",
"",
ignore_attributes = TRUE
)
expect_true(all(
!c("queryTime", "siteInfo") %in%
names(attributes(rawPcode2))
))

# This means wqp_check_status wasn't called:
expect_false("dataProviders" %in% names(attr(rawPcode2, "headerInfo")))

pHData <- readWQPdata(
siteid = "USGS-04024315",
characteristicName = "pH",
service = "ResultWQX3"
)
expect_true(all(
c("url", "queryTime", "siteInfo", "headerInfo") %in%
names(attributes(pHData))
))

# # This means wqp_check_status was called:
expect_true("dataProviders" %in% names(attr(pHData, "headerInfo")))

pHData2 <- readWQPdata(
siteid = "USGS-04024315",
characteristicName = "pH",
ignore_attributes = TRUE,
service = "ResultWQX3"
)
expect_true(all(
!c("queryTime", "siteInfo") %in%
names(attributes(pHData2))
))

# wqp.summary_no_atts <- readWQPdata(
# siteid = "USGS-04024315",
# characteristicName = nameToUse,
# ignore_attributes = TRUE,
# service = "ResultWQX3"
# )
# expect_true(
# !all(
# c("siteInfo", "variableInfo") %in% names(attributes(wqp.summary_no_atts))
# )
# )
#
# rawPcode <- readWQPqw("USGS-01594440", "01075", "", "", legacy = FALSE)
# expect_true(all(
# c("url", "queryTime", "siteInfo") %in%
# names(attributes(rawPcode))
# ))
#
# # This means wqp_check_status was called:
expect_false("dataProviders" %in% names(attr(pHData2, "headerInfo")))

rawPcode <- readWQPqw(
"USGS-01594440",
"01075",
ignore_attributes = TRUE,
legacy = FALSE
)
headerInfo <- attr(rawPcode, "headerInfo")
wqp_request_id <- headerInfo$`wqp-request-id`
count_info <- wqp_check_status(wqp_request_id)

expect_true("dataProviders" %in% names(count_info))
# expect_true("dataProviders" %in% names(attr(rawPcode, "headerInfo")))
#
# rawPcode2 <- readWQPqw(
# "USGS-01594440",
# "01075",
# "",
# "",
# ignore_attributes = TRUE
# )
# expect_true(all(
# !c("queryTime", "siteInfo") %in%
# names(attributes(rawPcode2))
# ))
#
# # This means wqp_check_status wasn't called:
# expect_false("dataProviders" %in% names(attr(rawPcode2, "headerInfo")))
#
# pHData <- readWQPdata(
# siteid = "USGS-04024315",
# characteristicName = "pH",
# service = "ResultWQX3"
# )
# expect_true(all(
# c("url", "queryTime", "siteInfo", "headerInfo") %in%
# names(attributes(pHData))
# ))
#
# # # This means wqp_check_status was called:
# expect_true("dataProviders" %in% names(attr(pHData, "headerInfo")))
#
# pHData2 <- readWQPdata(
# siteid = "USGS-04024315",
# characteristicName = "pH",
# ignore_attributes = TRUE,
# service = "ResultWQX3"
# )
# expect_true(all(
# !c("queryTime", "siteInfo") %in%
# names(attributes(pHData2))
# ))
#
# # # This means wqp_check_status was called:
# expect_false("dataProviders" %in% names(attr(pHData2, "headerInfo")))
#
# rawPcode <- readWQPqw(
# "USGS-01594440",
# "01075",
# ignore_attributes = TRUE,
# legacy = FALSE
# )
# headerInfo <- attr(rawPcode, "headerInfo")
# wqp_request_id <- headerInfo$`wqp-request-id`
# count_info <- wqp_check_status(wqp_request_id)
#
# expect_true("dataProviders" %in% names(count_info))
})


Expand Down
68 changes: 34 additions & 34 deletions tests/testthat/tests_userFriendly_fxns.R
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Original file line number Diff line number Diff line change
Expand Up @@ -233,40 +233,40 @@ test_that("read_waterdata_daily", {
test_that("WQP qw tests", {
testthat::skip_on_cran()
skip_on_ci()
nameToUse <- "Specific conductance"
pcodeToUse <- "00095"

INFO_WQP <- readWQPqw(
"USGS-04024315",
pcodeToUse,
startDate = "",
endDate = "",
legacy = FALSE
)
expect_is(INFO_WQP$Activity_StartDateTime, "POSIXct")

INFO2 <- readWQPqw(
"WIDNR_WQX-10032762",
nameToUse,
startDate = "",
endDate = "",
legacy = FALSE
)
expect_is(INFO2$Activity_StartDateTime, "POSIXct")

df <- readWQPqw("USGS-04193500", parameterCd = "00665", legacy = FALSE)
expect_true(nrow(df) > 0)

df2 <- readWQPqw("USGS-05427718", parameterCd = "all")
expect_true(nrow(df2) > 0)

#Empty legacy:
df3 <- readWQPqw(
siteNumbers = "USGS-385032115220501",
parameterCd = "all",
legacy = TRUE
)
expect_true(nrow(df3) == 0)
# nameToUse <- "Specific conductance"
# pcodeToUse <- "00095"
#
# INFO_WQP <- readWQPqw(
# "USGS-04024315",
# pcodeToUse,
# startDate = "",
# endDate = "",
# legacy = FALSE
# )
# expect_is(INFO_WQP$Activity_StartDateTime, "POSIXct")
#
# INFO2 <- readWQPqw(
# "WIDNR_WQX-10032762",
# nameToUse,
# startDate = "",
# endDate = "",
# legacy = FALSE
# )
# expect_is(INFO2$Activity_StartDateTime, "POSIXct")
#
# df <- readWQPqw("USGS-04193500", parameterCd = "00665", legacy = FALSE)
# expect_true(nrow(df) > 0)
#
# df2 <- readWQPqw("USGS-05427718", parameterCd = "all")
# expect_true(nrow(df2) > 0)
#
# #Empty legacy:
# df3 <- readWQPqw(
# siteNumbers = "USGS-385032115220501",
# parameterCd = "all",
# legacy = TRUE
# )
# expect_true(nrow(df3) == 0)
})


Expand Down
20 changes: 12 additions & 8 deletions vignettes/join_by_closest.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -46,9 +46,13 @@ pcode_uv <- "99133"
pcode_samples <- "00631"
start_date <- as.Date("2018-01-01")
end_date <- as.Date("2020-01-01")
samples_data <- readWQPqw(site_samples, pcode_samples,
startDate = start_date,
endDate = end_date)

samples_data <- read_waterdata_samples(
monitoringLocationIdentifier = site_samples,
usgsPCode = pcode_samples,
activityStartDateUpper = end_date,
activityStartDateLower = start_date,
dataProfile = "fullphyschem")

uv_data <- read_waterdata_continuous(monitoring_location_id = site_uv,
parameter_code = c(pcode_uv),
Expand All @@ -60,11 +64,11 @@ Next we'll clean up the discrete water quality data to make it easy to follow in

```{r trimsamplesdata}
samples_trim <- samples_data |>
filter(ActivityTypeCode == "Sample-Routine",
!is.na(ActivityStartDateTime)) |>
select(samples_date = ActivityStartDateTime,
val_samples = ResultMeasureValue,
det_txt = ResultDetectionConditionText)
filter(Activity_TypeCode == "Sample-Routine",
!is.na(Activity_StartDateTime)) |>
select(samples_date = Activity_StartDateTime,
val_samples = Result_Measure,
det_txt = Result_ResultDetectionCondition)
```

```{r showsamplestrim, echo=FALSE}
Expand Down
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