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Fixes #720
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@ldecicco-USGS
ldecicco-USGS committed Jul 31, 2024
1 parent 8d426d2 commit d813ec2
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Showing 3 changed files with 83 additions and 87 deletions.
149 changes: 74 additions & 75 deletions R/readNWISdata.R
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Original file line number Diff line number Diff line change
Expand Up @@ -91,16 +91,11 @@
#' tz = "America/Chicago"
#' )
#'
#' # Empty:
#' multiSite <- readNWISdata(
#' sites = c("04025000", "04072150"), service = "iv",
#' parameterCd = "00010"
#' )
#' # Not empty:
#' multiSite <- readNWISdata(
#' sites = c("04025500", "040263491"),
#' service = "iv", parameterCd = "00060"
#' )
#'
#' bBoxEx <- readNWISdata(bBox = c(-83, 36.5, -81, 38.5), parameterCd = "00010")
#'
#' startDate <- as.Date("2013-10-01")
Expand All @@ -118,17 +113,19 @@
#' hasDataTypeCd = "iv", service = "site"
#' )
#' temp <- readNWISdata(
#' bBox = c(-83, 36.5, -82.5, 36.75), parameterCd = "00010",
#' service = "site",
#' bBox = c(-83, 36.5, -82.5, 36.75), parameterCd = "00010", service = "site",
#' seriesCatalogOutput = TRUE
#' )
#'
#' GWL <- readNWISdata(site_no = c("392725077582401",
#' "375907091432201"),
#' parameterCd = "62610",
#' service = "gwlevels")
#'
#' levels <- readNWISdata(stateCd = "WI",
#' service = "gwlevels",
#' startDate = "2024-05-01",
#' endDate = "2024-05-30")
#'
#'
#'
#' meas <- readNWISdata(
#' state_cd = "WI", service = "measurements",
#' format = "rdb_expanded"
Expand Down Expand Up @@ -202,15 +199,15 @@
#' }
readNWISdata <- function(..., asDateTime = TRUE, convertType = TRUE, tz = "UTC") {
tz <- match.arg(tz, OlsonNames())

valuesList <- readNWISdots(...)

service <- valuesList$service
if (length(service) > 1) {
warning("Only one service value is allowed. Service: ", service[1], " will be used.")
service <- service[1]
}

if (any(service %in% c("qw", "qwdata"))) {
.Deprecated(
old = "readNWISdata", package = "dataRetrieval",
Expand All @@ -221,12 +218,12 @@ for more information.
https://cran.r-project.org/web/packages/dataRetrieval/vignettes/qwdata_changes.html"
)
}

values <- sapply(valuesList$values, function(x)utils:: URLencode(x))

baseURL <- drURL(service, arg.list = values)

if (service %in% c("site", "dv", "iv", "gwlevels")) {
if (service %in% c("site", "dv", "iv")) {
baseURL <- appendDrURL(baseURL, Access = pkg.env$access)
}
# actually get the data
Expand All @@ -238,7 +235,7 @@ https://cran.r-project.org/web/packages/dataRetrieval/vignettes/qwdata_changes.h
} else {
retval <- importWaterML1(baseURL, tz = tz, asDateTime = asDateTime)
}

if ("dv" == service) {
tzLib <- stats::setNames(
c(
Expand All @@ -263,15 +260,17 @@ https://cran.r-project.org/web/packages/dataRetrieval/vignettes/qwdata_changes.h
retval$dateTime <- as.POSIXct(retval$dateTime, tzLib[tz = retval$tz_cd[1]])
}
}

if ("iv" == service || "iv_recent" == service) {
if (tz == "") {
retval$tz_cd <- rep("UTC", nrow(retval))
} else {
retval$tz_cd <- rep(tz, nrow(retval))
}
} else if("gwlevels" == service && "parameterCd" %in% names(values)){
retval <- retval[retval$parameter_cd %in% values[["parameterCd"]], ]
}

return(retval)
}

Expand All @@ -293,7 +292,7 @@ https://cran.r-project.org/web/packages/dataRetrieval/vignettes/qwdata_changes.h
#' stateCdLookup(c("West Virginia", "Wisconsin", 200, 55, "MN"))
stateCdLookup <- function(input, outputType = "postal") {
outputType <- match.arg(outputType, c("postal", "fullName", "tableIndex", "id"))

retVal <- rep(NA, length(input))
index <- 1
for (i in input) {
Expand All @@ -304,24 +303,24 @@ stateCdLookup <- function(input, outputType = "postal") {
} else {
i <- which(tolower(i) == tolower(stateCd$STATE_NAME))
}

if (length(i) > 0) {
output <- switch(outputType,
postal = stateCd$STUSAB[i],
fullName = stateCd$STATE_NAME[i],
tableIndex = i,
id = as.integer(stateCd$STATE[i])
postal = stateCd$STUSAB[i],
fullName = stateCd$STATE_NAME[i],
tableIndex = i,
id = as.integer(stateCd$STATE[i])
)
retVal[index] <- output
}

index <- index + 1
}

if (length(retVal[-1]) == 0) {
paste("Could not find", input, "in the state lookup table. See `stateCd` for complete list.")
}

return(retVal)
}

Expand All @@ -342,31 +341,31 @@ stateCdLookup <- function(input, outputType = "postal") {
#' already_correct <- countyCdLookup(county = "51001")
countyCdLookup <- function(state, county, outputType = "id") {
outputType <- match.arg(outputType, c("fullName", "tableIndex", "id", "fullEntry"))

if (missing(state)) {
return(county)
}

if (missing(county)) {
stop("No county code provided")
}

if (length(state) > 1) {
stop("Only one state allowed in countyCdLookup.")
}

# first turn state into stateCd postal name
stateCd <- stateCdLookup(state, outputType = "postal")
state_counties <- countyCd[countyCd$STUSAB == stateCd, ]

if (is.numeric(county) || !is.na(suppressWarnings(as.numeric(county)))) {
county_i <- which(as.numeric(county) == as.numeric(countyCd$COUNTY) & stateCd == countyCd$STUSAB)
} else {
county_in_state <- grep(tolower(county), tolower(state_counties$COUNTY_NAME))

county_i <- which(countyCd$STUSAB == stateCd &
countyCd$COUNTY_NAME == state_counties$COUNTY_NAME[county_in_state])

countyCd$COUNTY_NAME == state_counties$COUNTY_NAME[county_in_state])
if (length(county_i) == 0) {
stop(paste(
"Could not find", county, "(county), ", stateCd,
Expand All @@ -379,14 +378,14 @@ countyCdLookup <- function(state, county, outputType = "id") {
))
}
}

retVal <- switch(outputType,
fullName = countyCd$COUNTY_NAME[county_i],
tableIndex = county_i,
id = countyCd$COUNTY[county_i],
fullEntry = countyCd[county_i, ]
fullName = countyCd$COUNTY_NAME[county_i],
tableIndex = county_i,
id = countyCd$COUNTY[county_i],
fullEntry = countyCd[county_i, ]
)

return(retVal)
}

Expand All @@ -398,51 +397,51 @@ readNWISdots <- function(...) {
if (length(list(...)) == 0) {
stop("No arguments supplied")
}

matchReturn <- convertLists(...)

if (anyNA(unlist(matchReturn))) {
stop("NA's are not allowed in query")
}

if ("service" %in% names(matchReturn)) {
service <- matchReturn$service
matchReturn$service <- NULL
} else {
service <- "dv"
}

match.arg(service, c(
"dv", "iv", "iv_recent", "gwlevels",
"site", "uv", "qw", "measurements",
"qwdata", "stat", "rating", "peak"
))

if (service == "uv") {
service <- "iv"
} else if (service == "qw") {
service <- "qwdata"
}

if (length(service) > 1) {
stop("Only one service call allowed.")
}

values <- sapply(matchReturn, function(x) as.character(paste0(eval(x), collapse = ",")))

names(values)[names(values) == "startDate"] <- "startDT"
names(values)[names(values) == "endDate"] <- "endDT"
names(values)[names(values) == "siteNumber"] <- "sites"
names(values)[names(values) == "siteNumbers"] <- "sites"

format.default <- "waterml,1.1"

if (service == "iv" && "startDT" %in% names(values)) {
if (as.Date(values[["startDT"]]) >= Sys.Date() - 120) {
service <- "iv_recent"
}
}

names(values)[names(values) == "statecode"] <- "stateCd"
if ("stateCd" %in% names(values)) {

Expand All @@ -458,15 +457,15 @@ readNWISdots <- function(...) {
stop("NWIS does not include U.S. Minor Outlying Islands")
}
}

if ("parameterCd" %in% names(matchReturn)) {
pcodeCheck <- (nchar(matchReturn$parameterCd) == 5) & !is.na(suppressWarnings(as.numeric(matchReturn$parameterCd)))
if (!all(pcodeCheck)) {
badPcode <- matchReturn$parameterCd[which(!pcodeCheck)]
stop("The following pCodes appear mistyped:", paste(badPcode, collapse = ", "))
}
}

names(values)[names(values) == "countycode"] <- "countyCd"
if ("countyCd" %in% names(values)) {
if ("stateCd" %in% names(values)) {
Expand All @@ -477,14 +476,14 @@ readNWISdots <- function(...) {
values <- values[names(values) != "stateCd"]
}
}

if (service %in% c("peak", "qwdata", "measurements", "gwlevels")) {
format.default <- "rdb"

names(values)[names(values) == "startDT"] <- "begin_date"
names(values)[names(values) == "endDT"] <- "end_date"
names(values)[names(values) == "sites"] <- "site_no"

if ("bBox" %in% names(values)) {
values["nw_longitude_va"] <- as.character(matchReturn$bBox[1])
values["nw_latitude_va"] <- as.character(matchReturn$bBox[2])
Expand All @@ -493,49 +492,49 @@ readNWISdots <- function(...) {
values["coordinate_format"] <- "decimal_degrees"
values <- values[-which("bBox" %in% names(values))]
}

values["date_format"] <- "YYYY-MM-DD"
values["rdb_inventory_output"] <- "file"
values["TZoutput"] <- "0"

if (all(c("begin_date", "end_date") %in% names(values))) {
values["range_selection"] <- "date_range"
}

if (service == "qwdata" && !("qw_sample_wide" %in% names(values))) {
values["qw_sample_wide"] <- "wide"
}
}

if (service %in% c("peak", "gwlevels") && "state_cd" %in% names(values)) {
values["list_of_search_criteria"] <- "state_cd"
}

if (service%in% c("peak", "gwlevels") && "huc2_cd" %in% names(values)) {
if (service %in% c("peak", "gwlevels") && "huc2_cd" %in% names(values)) {
values["list_of_search_criteria"] <- "huc2_cd"
}


if(service == "gwlevels" && "aquiferCd" %in% names(values)){
values["aquiferCd"] <- "nat_aqfr_cd"
}

if (service %in% c("peak", "gwlevels") && "bBox" %in% names(values)) {
values["list_of_search_criteria"] <- "lat_long_bounding_box"
}

if (service == "gwlevels" && "aquiferCd" %in% names(values)) {
values["aquiferCd"] <- "nat_aqfr_cd"
}

if (service %in% c("site", "gwlevels", "stat", "rating", "peak")) {
format.default <- "rdb"
}

if (service == "stat") {
message("Please be aware the NWIS data service feeding this function is in BETA.\n
Data formatting could be changed at any time, and is not guaranteed")
}

if (!("format" %in% names(values))) {
values["format"] <- format.default
}

return(list(values = values, service = service))
}

Expand All @@ -548,4 +547,4 @@ convertLists <- function(...) {
list(...)[sapply(list(...), class) != "list"]
) # get the non-list parts
return(matchReturn)
}
}
2 changes: 1 addition & 1 deletion R/readNWISunit.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -521,7 +521,7 @@ readNWISgwl <- function(siteNumbers,
tz = tz
)

if(!is.na(parameterCd)){
if(!all(is.na(parameterCd))){
data <- data[data$parameter_cd %in% parameterCd, ]
}

Expand Down
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