put readNWISSample back in, but send to WQP

NAMESPACE

@@ -106,6 +106,7 @@ export(randomSubset)
 export(readDataFromFile)
 export(readNWISDaily)
 export(readNWISInfo)
+export(readNWISSample)
 export(readUserDaily)
 export(readUserInfo)
 export(readUserSample)

NEWS

@@ -1,7 +1,8 @@
 EGRET 3.0.10
 ===========
-* Removed readNWISSample because the underlying data from NWIS is retired.
+* Fix bug with 0 concentration values in readWQPSample.
 * Style updates.
+* Port readNWISSample to Water Quality Portal. NWIS services are retired.
 
 
 EGRET 3.0.9

R/EGRET.R

@@ -62,10 +62,10 @@ NULL
 
 #' Constants included with EGRET
 #' 
-#'\itemize{
-#'  \item{fluxConst}{Flux conversion object}
-#'  \item{qConst}{Flow conversion object}
-#'  \item{monthInfo}{Month object}
+#'\tabular{ll}{
+#' fluxConst \tab Flux conversion object\cr
+#' qConst \tab Flow conversion object\cr
+#' monthInfo \tab Month object\cr
 #'}
 #'
 #'@aliases fluxConst qConst monthInfo concConst

R/boxConcMonth.R

@@ -17,7 +17,7 @@
 #' @param tinyPlot logical variable, if TRUE plot is designed to be plotted small as part of a multi-plot figure, default is FALSE.
 #' @param logScale logical if TRUE y plotted in log axis
 #' @param customPar logical defaults to FALSE. If TRUE, par() should be set by user before calling this function 
-#' @param las numeric in {0,1,2,3}; the style of axis labels, see ?par
+#' @param las numeric in c(0,1,2,3); the style of axis labels, see ?par
 #' @param showXLabels logical defaults to TRUE. If FALSE, the x axis label is not plotted
 #' @param showYLabels logical defaults to TRUE. If FALSE, the y axis label is not plotted
 #' @param showXAxis logical defaults to TRUE. If FALSE, the x axis is not plotted

R/boxQTwice.R

@@ -27,7 +27,7 @@
 #' @param logScale logical if TRUE y plotted in log axis. Defaults to TRUE.
 #' @param tinyPlot logical variable, if TRUE plot is designed to be plotted small as part of a multi-plot figure, default is FALSE.
 #' @param customPar logical defaults to FALSE. If TRUE, par() should be set by user before calling this function 
-#' @param las numeric in {0,1,2,3}; the style of axis labels, see ?par
+#' @param las numeric in c(0,1,2,3); the style of axis labels, see ?par
 #' @param usgsStyle logical option to use USGS style guidelines. Setting this option
 #' to TRUE does NOT guarantee USGS compliance. It will only change automatically
 #' generated labels. 

R/boxResidMonth.R

@@ -21,7 +21,7 @@
 #' @param cex.main magnification to be used for main titles relative to the current setting of cex
 #' @param font.main font to be used for plot main titles
 #' @param customPar logical defaults to FALSE. If TRUE, par() should be set by user before calling this function 
-#' @param las numeric in {0,1,2,3}; the style of axis labels
+#' @param las numeric in c(0,1,2,3); the style of axis labels
 #' @param randomCensored logical. Show censored residuals as randomized. Default = FALSE.
 #' @param monthLab object of monthLabel class, or numeric represented the short code, 
 #' or character representing the descriptive name.

R/readNWISSample.R

@@ -0,0 +1,61 @@
+#' Import NWIS Sample Data for EGRET analysis
+#'
+#' Imports data from NWIS web service. 
+#' A list of parameter and statistic codes can be found here: \url{https://help.waterdata.usgs.gov/codes-and-parameters}
+#' For raw data, use \code{\link[dataRetrieval]{readNWISqw}} from the dataRetrieval package.
+#' This function will retrieve the raw data, and compress it (summing constituents) if 
+#' more than 1 parameter code is supplied. See
+#' section 3.2.4 of the vignette for more details.
+#'
+#' @param siteNumber character USGS site number.  This is usually an 8 digit number
+#' @param parameterCd character USGS parameter code.  This is usually an 5 digit number.
+#' @param startDate character starting date for data retrieval in the form YYYY-MM-DD.
+#' Default is empty quotes "" which will retrieve the full period of record.
+#' @param endDate character ending date for data retrieval in the form YYYY-MM-DD.
+#' Default is empty quotes "" which will retrieve the full period of record.
+#' @param verbose logical specifying whether or not to display progress message
+#' @keywords data import USGS WRTDS
+#' @export
+#' @return A data frame 'Sample' with the following columns:
+#' \tabular{lll}{
+#' Name \tab Type \tab Description \cr
+#' Date \tab Date \tab Date \cr
+#' ConcLow \tab numeric \tab Lower limit of concentration \cr
+#' ConcHigh \tab numeric \tab Upper limit of concentration \cr
+#' Uncen \tab integer \tab Uncensored data (1=TRUE, 0=FALSE) \cr
+#' ConcAve \tab numeric \tab Average concentration \cr
+#' Julian \tab integer \tab Number of days since Jan. 1, 1850\cr
+#' Month \tab integer \tab Month of the year [1-12] \cr 
+#' Day \tab integer \tab Day of the year [1-366] \cr
+#' DecYear \tab numeric \tab Decimal year \cr
+#' MonthSeq \tab integer \tab Number of months since January 1, 1850 \cr
+#' SinDY \tab numeric \tab Sine of the DecYear \cr
+#' CosDY \tab numeric \tab Cosine of the DecYear
+#' }
+#' @seealso \code{\link{compressData}}, \code{\link{populateSampleColumns}},
+#' \code{\link[dataRetrieval]{readNWISqw}}
+#' @examples
+#' \donttest{
+#' # These examples require an internet connection to run
+#' 
+#' Sample_01075 <- readNWISSample('01594440','01075', '1985-01-01', '1985-03-31')
+#' }
+readNWISSample <- function(siteNumber,
+                           parameterCd,
+                           startDate = "",
+                           endDate = "",
+                           verbose = TRUE){
+
+
+  siteNumber <- paste0("USGS-", siteNumber)
+
+  Sample <- readWQPSample(siteNumber = siteNumber,
+                          characteristicName = parameterCd,
+                          startDate = startDate,
+                          endDate = endDate,
+                          verbose = verbose)
+
+  return(Sample)
+
+}
+

R/readWQPSample.R

@@ -52,7 +52,7 @@ readWQPSample <- function(siteNumber,
                   "ResultStatusIdentifier",
                   "ResultValueTypeName")
 
-  if(packageVersion("dataRetrieval") >= "2.7.17"){
+  if(utils::packageVersion("dataRetrieval") >= "2.7.17"){
     data <- suppressMessages(dataRetrieval::readWQPqw(siteNumbers = siteNumber,
                                      parameterCd = characteristicName,
                                      startDate = startDate,

tests/testthat/tests_imports.R

@@ -27,25 +27,25 @@ test_that("External NWIS Sample tests", {
   SampleNames <- c("Date","ConcLow","ConcHigh","Uncen","ConcAve","Julian","Month",   
                    "Day","DecYear","MonthSeq","waterYear","SinDY","CosDY")
 
-  expect_warning(Sample_01075 <- readNWISSample('01594440',
+  Sample_01075 <- readNWISSample('01594440',
                                  '01075', 
                                  '1985-01-01', 
-                                 '1985-03-31'))
+                                 '1985-03-31')
 
   expect_true(all(SampleNames %in% names(Sample_01075)))
 
-  expect_warning(Sample_All2 <- readNWISSample('05114000',
+  Sample_All2 <- readNWISSample('05114000',
                                 c('00915','00931'), 
                                 '1985-01-01', 
-                                '1985-03-31'))
+                                '1985-03-31')
 
   expect_true(all(SampleNames %in% names(Sample_All2)))
 
-  Sample_Select <- expect_warning(readNWISSample('05114000',
+  Sample_Select <- readNWISSample('05114000',
                                   c('00915','00931'), 
-                                  '', ''))
+                                  '', '')
 
-  expect_true(all(names(Sample_Select) %in% SampleNames))
+  expect_true(all(SampleNames %in% names(Sample_Select)))
 
   expect_is(Sample_Select$Date, 'Date')
   expect_is(Sample_Select$ConcAve, 'numeric')
@@ -73,16 +73,15 @@ test_that("External INFO tests", {
   INFO <- readNWISInfo('05114000','00010',interactive=FALSE)
   expect_true(all(requiredColumns %in% names(INFO)))
 
-  # nameToUse <- 'Specific conductance'
-  # pcodeToUse <- '00095'
-  # 
-  # INFO_WQP <- readWQPInfo('USGS-04024315',pcodeToUse,interactive=FALSE)
-  # expect_true(all(requiredColumns %in% names(INFO_WQP)))
-  # 
-  # INFO2 <- readWQPInfo('WIDNR_WQX-10032762',nameToUse,interactive=FALSE)
-  # expect_true(all(requiredColumns %in% names(INFO2)))
-  # 
-  # 
+  nameToUse <- 'Specific conductance'
+  pcodeToUse <- '00095'
+
+  INFO_WQP <- readWQPInfo('USGS-04024315',pcodeToUse,interactive=FALSE)
+  expect_true(all(requiredColumns %in% names(INFO_WQP)))
+
+  INFO2 <- readWQPInfo('WIDNR_WQX-10032762',nameToUse,interactive=FALSE)
+  expect_true(all(requiredColumns %in% names(INFO2)))
+
 })
 
 test_that("User tests", {

tests/testthat/tests_utils.R

@@ -69,15 +69,15 @@ test_that("data functions work", {
   compressed <- compressData(dataInput)
   expect_is(compressed, "data.frame")
   expect_gt(nrow(compressed), 1)
-  expect_equal(names(compressed), c("dateTime", "ConcLow", "ConcHigh",
-                                    "Uncen"))
+  expect_true(all(c("dateTime", "ConcLow", "ConcHigh", "Uncen") %in% 
+                 names(compressed)))
 
   #mergeReport
 
   siteNumber <- '01594440'
   pCode <- '01075'
   Daily <- readNWISDaily(siteNumber,'00060', '1985-01-01', '1990-03-31')
-  expect_warning(Sample <- readNWISSample(siteNumber,pCode, '1985-01-01', '1990-03-31'))
+  Sample <- readNWISSample(siteNumber,pCode, '1985-01-01', '1990-03-31')
   INFO <- readNWISInfo(siteNumber,pCode,interactive=FALSE)
   eList <- mergeReport(INFO, Daily, Sample)
   expect_equal(names(eList), c("INFO", "Daily", "Sample", "surfaces"))