Adding in modified vignette.

inst/doc/dataRetrieval.R

+## ----openLibrary, echo=FALSE------------------------------
+library(xtable)
+options(continue=" ")
+options(width=60)
+library(knitr)
+
+
+## ----include=TRUE ,echo=FALSE,eval=TRUE-------------------
+opts_chunk$set(highlight=TRUE, tidy=TRUE, keep.space=TRUE, keep.blank.space=FALSE, keep.comment=TRUE, tidy=FALSE,comment="")
+knit_hooks$set(inline = function(x) {
+   if (is.numeric(x)) round(x, 3)})
+knit_hooks$set(crop = hook_pdfcrop)
+
+bold.colHeaders <- function(x) {
+  x <- gsub("\\^(\\d)","$\\^\\1$",x)
+  x <- gsub("\\%","\\\\%",x)
+  x <- gsub("\\_"," ",x)
+  returnX <- paste("\\multicolumn{1}{c}{\\textbf{\\textsf{", x, "}}}", sep = "")
+}
+addSpace <- function(x) ifelse(x != "1", "[5pt]","")
+
+## ----workflow, echo=TRUE,eval=FALSE-----------------------
+#  library(dataRetrieval)
+#  # Choptank River near Greensboro, MD
+#  siteNumber <- "01491000"
+#  ChoptankInfo <- readNWISsite(siteNumber)
+#  parameterCd <- "00060"
+#  
+#  #Raw daily data:
+#  rawDailyData <- readNWISdv(siteNumber,parameterCd,
+#                        "1980-01-01","2010-01-01")
+#  
+#  # Sample data Nitrate:
+#  parameterCd <- "00618"
+#  qwData <- readNWISqw(siteNumber,parameterCd,
+#                        "1980-01-01","2010-01-01")
+#  
+
+## ----tableParameterCodes, echo=FALSE,results='asis'-------
+pCode <- c('00060', '00065', '00010','00045','00400')
+shortName <- c("Discharge [ft$^3$/s]","Gage height [ft]","Temperature [C]", "Precipitation [in]", "pH")
+
+data.df <- data.frame(pCode, shortName, stringsAsFactors=FALSE)
+
+print(xtable(data.df,
+       label="tab:params",
+       caption="Common USGS Parameter Codes"),
+       caption.placement="top",
+       size = "\\footnotesize",
+       latex.environment=NULL,
+       sanitize.text.function = function(x) {x},
+       sanitize.colnames.function =  bold.colHeaders,
+       sanitize.rownames.function = addSpace
+      )
+
+
+## ----tableParameterCodesDataRetrieval---------------------
+library(dataRetrieval)
+parameterCdFile <-  parameterCdFile
+names(parameterCdFile)
+
+## ----tableStatCodes, echo=FALSE,results='asis'------------
+StatCode <- c('00001', '00002', '00003','00008')
+shortName <- c("Maximum","Minimum","Mean", "Median")
+
+data.df <- data.frame(StatCode, shortName, stringsAsFactors=FALSE)
+
+print(xtable(data.df,label="tab:stat",
+           caption="Commonly used USGS Stat Codes"),
+       caption.placement="top",
+       size = "\\footnotesize",
+       latex.environment=NULL,
+       sanitize.colnames.function = bold.colHeaders,
+       sanitize.rownames.function = addSpace
+      )
+
+
+## ----getSite, echo=TRUE-----------------------------------
+siteNumbers <- c("01491000","01645000") 
+siteINFO <- readNWISsite(siteNumbers)
+
+## ----siteNames2, echo=TRUE--------------------------------
+siteINFO$station.nm
+
+## ----getSiteExtended, echo=TRUE---------------------------
+# Continuing from the previous example:
+# This pulls out just the daily data:
+
+dailyDataAvailable <- whatNWISData(siteNumbers,
+                    service="dv")
+
+
+## ----tablegda, echo=FALSE,results='asis'------------------
+tableData <- with(dailyDataAvailable, 
+      data.frame( 
+      siteNumber= site_no,
+      srsname=srsname, 
+      startDate=as.character(startDate), 
+      endDate=as.character(endDate), 
+      count=as.character(count),
+      units=parameter_units,
+      statCd = statCd,
+      stringsAsFactors=FALSE)
+      )
+
+tableData$units[which(tableData$units == "ft3/s")] <- "ft$^3$/s"
+tableData$units[which(tableData$units == "uS/cm @25C")] <- "$\\mu$S/cm @25C"
+
+
+print(xtable(tableData,label="tab:gda",
+    caption="Daily mean data availabile at the Choptank River near Greensboro, MD. [Some columns deleted for space considerations]"),
+       caption.placement="top",
+       size = "\\footnotesize",
+       latex.environment=NULL,
+       sanitize.text.function = function(x) {x},
+       sanitize.colnames.function =  bold.colHeaders,
+       sanitize.rownames.function = addSpace
+      )
+
+
+## ----label=getPCodeInfo, echo=TRUE------------------------
+# Using defaults:
+parameterCd <- "00618" 
+parameterINFO <- readNWISpCode(parameterCd)
+colnames(parameterINFO)
+
+## ----siteNames, echo=TRUE---------------------------------
+parameterINFO$parameter_nm
+
+## ----label=getNWISDaily, echo=TRUE, eval=TRUE-------------
+
+# Continuing with our Choptank River example
+siteNumber <- "01491000"
+parameterCd <- "00060"  # Discharge
+startDate <- ""  # Will request earliest date
+endDate <- "" # Will request latest date
+
+discharge <- readNWISdv(siteNumber, 
+                    parameterCd, startDate, endDate)
+names(discharge)
+
+## ----label=getNWIStemperature, echo=TRUE------------------
+
+parameterCd <- c("00010","00060")  # Temperature and discharge
+statCd <- c("00001","00003")  # Mean and maximum
+startDate <- "2012-01-01"
+endDate <- "2012-05-01"
+
+temperatureAndFlow <- readNWISdv(siteNumber, parameterCd, 
+        startDate, endDate, statCd=statCd)
+
+
+## ----label=renameColumns, echo=TRUE-----------------------
+names(temperatureAndFlow)
+
+temperatureAndFlow <- renameColumns(temperatureAndFlow)
+names(temperatureAndFlow)
+
+## ----getNWIStemperaturePlot, echo=TRUE, fig.cap="Temperature and discharge plot of Choptank River in 2012.",out.width='1\\linewidth',out.height='1\\linewidth',fig.show='hold'----
+par(mar=c(5,5,5,5)) #sets the size of the plot window
+
+with(temperatureAndFlow, plot(
+  datetime, Temperature_water_degrees_Celsius_Max_01,
+  xlab="Date",ylab="Max Temperature [C]"
+  ))
+par(new=TRUE)
+with(temperatureAndFlow, plot(
+  datetime, Discharge_cubic_feet_per_second,
+  col="red",type="l",xaxt="n",yaxt="n",xlab="",ylab="",axes=FALSE
+  ))
+axis(4,col="red",col.axis="red")
+mtext(expression(paste("Mean Discharge [ft"^"3","/s]",
+                       sep="")),side=4,line=3,col="red")
+title(paste(siteINFO$station.nm[1],"2012",sep=" "))
+legend("topleft", c("Max Temperature", "Mean Discharge"), 
+       col=c("black","red"),lty=c(NA,1),pch=c(1,NA))
+
+## ----label=getNWISUnit, echo=TRUE-------------------------
+
+parameterCd <- "00060"  # Discharge
+startDate <- "2012-05-12" 
+endDate <- "2012-05-13" 
+dischargeToday <- readNWISunit(siteNumber, parameterCd, 
+        startDate, endDate)
+
+## ----dischargeData, echo=FALSE----------------------------
+head(dischargeToday)
+
+## ----label=getQW, echo=TRUE-------------------------------
+ 
+# Dissolved Nitrate parameter codes:
+parameterCd <- c("00618","71851")
+startDate <- "1985-10-01"
+endDate <- "2012-09-30"
+
+dissolvedNitrate <- readNWISqw(siteNumber, parameterCd, 
+      startDate, endDate, expanded=TRUE)
+names(dissolvedNitrate)
+
+
+
+## ----getQWtemperaturePlot, echo=TRUE, fig.cap=paste(parameterINFO$parameter_nm, "at", siteINFO$station.nm[1])----
+with(dissolvedNitrate, plot(
+  startDateTime, result_va_00618,
+  xlab="Date",ylab = paste(parameterINFO$srsname,
+      "[",parameterINFO$parameter_units,"]")
+  ))
+title(siteINFO$station.nm[1])
+
+## ----label=geturl, echo=TRUE, eval=FALSE------------------
+#  # Dissolved Nitrate parameter codes:
+#  pCode <- c("00618","71851")
+#  startDate <- "1964-06-11"
+#  endDate <- "2012-12-18"
+#  url_qw <- constructNWISURL(siteNumber,pCode,startDate,endDate,'qw')
+#  url_dv <- constructNWISURL(siteNumber,"00060",startDate,endDate,
+#                             'dv',statCd="00003")
+#  url_uv <- constructNWISURL(siteNumber,"00060",startDate,endDate,'uv')
+
+## ----label=getQWData, echo=TRUE, eval=FALSE---------------
+#  specificCond <- readWQPqw('WIDNR_WQX-10032762',
+#                  'Specific conductance','2011-05-01','2011-09-30')
+
+## ----siteSearch-------------------------------------------
+sites <- whatNWISsites(bBox="-83.0,36.5,-81.0,38.5", 
+                      parameterCd="00010,00060",
+                      hasDataTypeCd="dv")
+
+names(sites)
+nrow(sites)
+
+## ----dataExample------------------------------------------
+dischargeWI <- readNWISdata(stateCd="WI",
+                           parameterCd="00060",
+                           drainAreaMin="50",
+                           statCd="00003")
+names(dischargeWI)
+nrow(dischargeWI)
+
+## ----NJChloride, eval=FALSE-------------------------------
+#  
+#  sitesNJ <- whatWQPsites(statecode="US:34",
+#                         characteristicName="Chloride")
+#  
+
+## ----phData, eval=FALSE-----------------------------------
+#  
+#  dataPH <- readWQPdata(statecode="US:55",
+#                   characteristicName="pH")
+#  
+
+## ----helpFunc,eval = FALSE--------------------------------
+#  ?readNWISpCode
+
+## ----rawFunc,eval = TRUE----------------------------------
+readNWISpCode
+
+## ----seeVignette,eval = FALSE-----------------------------
+#  vignette(dataRetrieval)
+
+## ----installFromCran,eval = FALSE-------------------------
+#  install.packages("dataRetrieval",
+#  repos=c("http://usgs-r.github.com","http://cran.us.r-project.org"),
+#  dependencies=TRUE,
+#  type="both")
+
+## ----openLibraryTest, eval=FALSE--------------------------
+#  library(dataRetrieval)
+
+## ----label=getSiteApp, echo=TRUE--------------------------
+availableData <- whatNWISData(siteNumber, "dv")
+dailyData <- availableData["00003" == availableData$statCd,]
+
+tableData <- with(dailyData, 
+      data.frame(
+        shortName=srsname, 
+        Start=startDate, 
+        End=endDate, 
+        Count=count,
+        Units=parameter_units)
+      )
+tableData
+
+## ----label=saveData, echo=TRUE, eval=FALSE----------------
+#  write.table(tableData, file="tableData.tsv",sep="\t",
+#              row.names = FALSE,quote=FALSE)
+