From 2d03d1567e0ee376d89db934e20613f804edfbac Mon Sep 17 00:00:00 2001
From: Laura DeCicco <ldecicco@usgs.gov>
Date: Mon, 8 Apr 2013 10:13:26 -0500
Subject: [PATCH] Added some easy checks to the water quality data to assure
that the number of samples returned matched what the water quality portal
said should return.
---
DESCRIPTION | 3 ++-
R/getRawQWData.r | 7 ++++++-
R/getWQPData.r | 24 ++++++++++--------------
man/getWaterML1Data.Rd | 8 ++++----
4 files changed, 22 insertions(+), 20 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index b980422e..f566b42c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -56,7 +56,8 @@ Collate:
'padVariable.r'
Depends:
R (>= 2.15.0),
- XML
+ XML,
+ RCurl
Imports:
zoo
Suggests:
diff --git a/R/getRawQWData.r b/R/getRawQWData.r
index 57ae17a7..3ab00903 100644
--- a/R/getRawQWData.r
+++ b/R/getRawQWData.r
@@ -21,8 +21,13 @@
getRawQWData <- function(siteNumber,ParameterCd,StartDate,EndDate,interactive=TRUE){
url <- constructNWISURL(siteNumber,ParameterCd,StartDate,EndDate,"wqp")
-
+ h <- basicHeaderGatherer()
+ doc <- getURI(url, headerfunction = h$update)
+ numToBeReturned <- as.numeric(h$value()["Total-Result-Count"])
suppressWarnings(retval <- read.delim(url, header = TRUE, quote="\"", dec=".", sep='\t', colClasses=c('character'), fill = TRUE))
+ actualNumReturned <- nrow(retval)
+
+ if(actualNumReturned != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", actualNumReturned, " were returned")
return(retval)
}
\ No newline at end of file
diff --git a/R/getWQPData.r b/R/getWQPData.r
index 488279bd..9f8cae0e 100644
--- a/R/getWQPData.r
+++ b/R/getWQPData.r
@@ -45,23 +45,15 @@ getWQPData <- function(siteNumber,characteristicName,StartDate,EndDate,interacti
"&startDateHi=",
EndDate,
"&countrycode=US&mimeType=tsv",sep = "")
+ h <- basicHeaderGatherer()
+ doc <- getURI(url, headerfunction = h$update)
+ numToBeReturned <- as.numeric(h$value()["Total-Result-Count"])
suppressWarnings(retval <- read.delim(url, header = TRUE, quote="\"", dec=".", sep='\t', colClasses=c('character'), fill = TRUE))
- qualifier <- ifelse((
- (
- retval$ResultDetectionConditionText == "Not Detected"
- & length(grep("Lower", retval$DetectionQuantitationLimitTypeName)) > 0
- )
- |
- (
- retval$ResultMeasureValue < retval$DetectionQuantitationLimitMeasure.MeasureValue
- & retval$ResultValueTypeName == "Actual"
- )
- ),
- "<",
- ""
- )
+ qualifier <- ifelse((retval$ResultDetectionConditionText == "Not Detected" |
+ retval$ResultDetectionConditionText == "Detected Not Quantified" |
+ retval$ResultMeasureValue < retval$DetectionQuantitationLimitMeasure.MeasureValue),"<","")
correctedData<-ifelse((nchar(qualifier)==0),retval$ResultMeasureValue,retval$DetectionQuantitationLimitMeasure.MeasureValue)
test <- data.frame(retval$CharacteristicName)
@@ -70,6 +62,9 @@ getWQPData <- function(siteNumber,characteristicName,StartDate,EndDate,interacti
test$dateTime <- as.Date(retval$ActivityStartDate, "%Y-%m-%d")
originalLength <- nrow(test)
+
+ if(originalLength != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", originalLength, " were returned")
+
test$qualifier <- qualifier
test$value <- as.numeric(correctedData)
@@ -85,5 +80,6 @@ getWQPData <- function(siteNumber,characteristicName,StartDate,EndDate,interacti
data <- reshape(test, idvar="dateTime", timevar = "CharacteristicName", direction="wide")
data$dateTime <- format(data$dateTime, "%Y-%m-%d")
data$dateTime <- as.Date(data$dateTime)
+
return(data)
}
\ No newline at end of file
diff --git a/man/getWaterML1Data.Rd b/man/getWaterML1Data.Rd
index c8cc08e7..eb259185 100644
--- a/man/getWaterML1Data.Rd
+++ b/man/getWaterML1Data.Rd
@@ -9,14 +9,14 @@
retrieval}
}
\value{
- Daily a data frame containing columns 'Date' and
- 'Discharge'
+ mergedDF a data frame containing columns agency, site,
+ dateTime, values, and remark codes for all requested
+ combinations
}
\description{
This function accepts a url parameter that already
contains the desired NWIS site, parameter code,
- statistic, startdate and enddate. It returns a data frame
- containing "Date" and "Discharge"
+ statistic, startdate and enddate.
}
\examples{
url <- "http://waterservices.usgs.gov/nwis/dv/?format=waterml,1.1&sites="
--
GitLab