From 6964f0894ff976c5a49bd7427423260810bf7bf0 Mon Sep 17 00:00:00 2001
From: unknown <ldecicco@usgs.gov>
Date: Wed, 31 Dec 2014 13:16:59 -0600
Subject: [PATCH] Handling empty dates (full period of record)
---
R/readWQPdata.R | 37 +++++++++++++++++++++++++------------
R/readWQPqw.r | 14 ++++++++++----
R/whatWQPsites.R | 28 ++++++++++++++++++----------
man/readWQPdata.Rd | 8 +++-----
4 files changed, 56 insertions(+), 31 deletions(-)
diff --git a/R/readWQPdata.R b/R/readWQPdata.R
index 3aa5fbac..cc583184 100644
--- a/R/readWQPdata.R
+++ b/R/readWQPdata.R
@@ -91,9 +91,8 @@
#' pHData <- readWQPdata(siteid="USGS-04024315",characteristicName=nameToUse)
#' pHDataExpanded2 <- readWQPdata(bBox=c(-90.10,42.67,-88.64,43.35),characteristicName=nameToUse)
#' startDate <- as.Date("2013-01-01")
-#' nutrientPysical <- readWQPdata(statecode="US:55",siteType="Stream",
-#' sampleMedia="Water",startDate=startDate,
-#' characteristicType=c("Nutrient","Physical"))
+#' nutrientDaneCounty <- readWQPdata(countycode="US:55:025",startDate=startDate,
+#' characteristicType="Nutrient")
#' }
readWQPdata <- function(...){
@@ -113,17 +112,25 @@ readWQPdata <- function(...){
if(any(names(values) %in% dateNames)){
index <- which(names(values) %in% dateNames)
- # If a valid R date was put in, the format needs to be changed to mm-dd-yyyy for the WQP:
- if(all(is.Date(as.Date(values[index])))){
- dates <- as.Date(values[index])
- dates <- format(as.Date(dates), format="%m-%d-%Y")
- values[index] <- dates
- } else if (!all(is.Date(as.Date(values[index],format="%m-%d-%Y")))){
- warning("Please check the date format for the arguments: ", paste(names(values)[index], collapse=", "))
+
+ if("" %in% values[index]){
+ values <- values[-index[values[index] == ""]]
+ index <- which(names(values) %in% dateNames)
}
- names(values)[names(values) == 'startDate'] <- 'startDateLo'
- names(values)[names(values) == 'endDate'] <- 'startDateHi'
+ if(length(index) > 0){
+ # If a valid R date was put in, the format needs to be changed to mm-dd-yyyy for the WQP:
+ if(any(!is.na(as.Date(values[index], format="%Y-%m-%d")))){
+ dates <- as.Date(values[index[!is.na(as.Date(values[index], format="%Y-%m-%d"))]])
+ dates <- format(as.Date(dates), format="%m-%d-%Y")
+ values[index] <- dates
+ } else if (any(is.na(as.Date(values[index], format="%m-%d-%Y")))){
+ warning("Please check the date format for the arguments: ", paste(names(values)[index], collapse=", "))
+ }
+
+ names(values)[names(values) == 'startDate'] <- 'startDateLo'
+ names(values)[names(values) == 'endDate'] <- 'startDateHi'
+ }
}
@@ -161,10 +168,16 @@ readWQPdata <- function(...){
stringsAsFactors=FALSE)
if(any(!is.na(variableInfo$parameterCd))){
+ pcodes <- unique(variableInfo$parameterCd[!is.na(variableInfo$parameterCd)])
+ pcodes <- pcodes["" != pcodes]
+ paramINFO <- readNWISpCode(pcodes)
+ names(paramINFO)["parameter_cd" == names(paramINFO)] <- "parameterCd"
+
pCodeToName <- pCodeToName
varExtras <- pCodeToName[pCodeToName$parm_cd %in% unique(variableInfo$parameterCd[!is.na(variableInfo$parameterCd)]),]
names(varExtras)[names(varExtras) == "parm_cd"] <- "parameterCd"
variableInfo <- merge(variableInfo, varExtras, by="parameterCd", all = TRUE)
+ variableInfo <- merge(variableInfo, paramINFO, by="parameterCd", all = TRUE)
variableInfo <- unique(variableInfo)
}
diff --git a/R/readWQPqw.r b/R/readWQPqw.r
index 195fcbe8..17d34ae8 100644
--- a/R/readWQPqw.r
+++ b/R/readWQPqw.r
@@ -102,7 +102,7 @@
#' rawPcode <- readWQPqw('USGS-01594440','01075', '', '')
#' rawCharacteristicName <- readWQPqw('WIDNR_WQX-10032762','Specific conductance', '', '')
#' rawPHsites <- readWQPqw(c('USGS-05406450', 'USGS-05427949','WIDNR_WQX-133040'), 'pH','','')
-#' nwisEx <- readWQPqw('USGS-04024000',c('34247','30234','32104','34220'),'','')
+#' nwisEx <- readWQPqw('USGS-04024000',c('34247','30234','32104','34220'),'','2012-12-20')
#' }
readWQPqw <- function(siteNumbers,parameterCd,startDate="",endDate=""){
@@ -148,11 +148,17 @@ readWQPqw <- function(siteNumbers,parameterCd,startDate="",endDate=""){
variableInfo <- unique(variableInfo)
if(any(variableInfo$parameterCd != "")){
+ pcodes <- unique(variableInfo$parameterCd[!is.na(variableInfo$parameterCd)])
+ pcodes <- pcodes["" != pcodes]
+ paramINFO <- readNWISpCode(pcodes)
+ names(paramINFO)["parameter_cd" == names(paramINFO)] <- "parameterCd"
+
pCodeToName <- pCodeToName
- varExtras <- pCodeToName[pCodeToName$parm_cd %in%
- unique(variableInfo$parameterCd[!is.na(variableInfo$parameterCd)]),]
+ varExtras <- pCodeToName[pCodeToName$parm_cd %in% unique(variableInfo$parameterCd[!is.na(variableInfo$parameterCd)]),]
names(varExtras)[names(varExtras) == "parm_cd"] <- "parameterCd"
- variableInfo <- merge(variableInfo, varExtras, by="parameterCd", all=TRUE)
+ variableInfo <- merge(variableInfo, varExtras, by="parameterCd", all = TRUE)
+ variableInfo <- merge(variableInfo, paramINFO, by="parameterCd", all = TRUE)
+ variableInfo <- unique(variableInfo)
}
attr(retval, "siteInfo") <- siteInfo
diff --git a/R/whatWQPsites.R b/R/whatWQPsites.R
index c9b15dbd..70f01708 100644
--- a/R/whatWQPsites.R
+++ b/R/whatWQPsites.R
@@ -73,20 +73,28 @@ whatWQPsites <- function(...){
if(any(names(values) %in% dateNames)){
index <- which(names(values) %in% dateNames)
- # If a valid R date was put in, the format needs to be changed to mm-dd-yyyy for the WQP:
- if(all(is.Date(as.Date(values[index])))){
- dates <- as.Date(values[index])
- dates <- format(as.Date(dates), format="%m-%d-%Y")
- values[index] <- dates
- } else if (!all(is.Date(as.Date(values[index],format="%m-%d-%Y")))){
- warning("Please check the date format for the arguments: ", paste(names(values)[index], collapse=", "))
+
+ if("" %in% values[index]){
+ values <- values[-index[values[index] == ""]]
+ index <- which(names(values) %in% dateNames)
}
- names(values)[names(values) == 'startDate'] <- 'startDateLo'
- names(values)[names(values) == 'endDate'] <- 'startDateHi'
+ if(length(index) > 0){
+ # If a valid R date was put in, the format needs to be changed to mm-dd-yyyy for the WQP:
+ if(any(!is.na(as.Date(values[index], format="%Y-%m-%d")))){
+ dates <- as.Date(values[index[!is.na(as.Date(values[index], format="%Y-%m-%d"))]])
+ dates <- format(as.Date(dates), format="%m-%d-%Y")
+ values[index] <- dates
+ } else if (any(is.na(as.Date(values[index], format="%m-%d-%Y")))){
+ warning("Please check the date format for the arguments: ", paste(names(values)[index], collapse=", "))
+ }
+
+ names(values)[names(values) == 'startDate'] <- 'startDateLo'
+ names(values)[names(values) == 'endDate'] <- 'startDateHi'
+ }
}
-
+
urlCall <- paste(paste(names(values),values,sep="="),collapse="&")
diff --git a/man/readWQPdata.Rd b/man/readWQPdata.Rd
index b02c7df1..3d71d35d 100644
--- a/man/readWQPdata.Rd
+++ b/man/readWQPdata.Rd
@@ -98,12 +98,10 @@ because it allows for other agencies rather than the USGS.
\dontrun{
nameToUse <- "pH"
pHData <- readWQPdata(siteid="USGS-04024315",characteristicName=nameToUse)
-pHDataExpanded <- readWQPdata(bBox="-90.10,42.67,-88.64,43.35",characteristicName=nameToUse)
pHDataExpanded2 <- readWQPdata(bBox=c(-90.10,42.67,-88.64,43.35),characteristicName=nameToUse)
-startDate <- as.Date("2008-01-01")
-nutrientPysical <- readWQPdata(statecode="US:55",siteType="Stream",
- samplMedia="Water",startDateLo=startDate,
- characteristicType=c("Nutrient","Physical))
+startDate <- as.Date("2013-01-01")
+nutrientDaneCounty <- readWQPdata(countycode="US:55:025",startDate=startDate,
+ characteristicType="Nutrient")
}
}
\keyword{WQP}
--
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