In USGS-R/WQ-Review: Discrete water-quality data review and exploration toolbox

###Load libraries and setup options

require(WQReview)
require(knitr)
opts_chunk$set(dev = 'png',out.width='1024px',out.height='750px',dpi=60)

###Load up the data
load(paste(outputDir,"/data.rda",sep=""))
###Subset to site
qw.data$PlotTable <- subset(qw.data$PlotTable,SITE_NO == site)
if(!is.null(reports$chemFlagTable))
{
reports$chemFlagTable <- subset(reports$chemFlagTable, SITE_NO == site)
}
if(!is.null(reports$pestFlagTable))
{
reports$pestFlagTable <- subset(reports$pestFlagTable, SITE_NO == site) 
}
if(!is.null(reports$resultFlagTable))
{
reports$resultFlagTable <- subset(reports$resultFlagTable, SITE_NO == site) 
}

```r require(gridExtra)

    ###Run charge balance checks
    if(all(!is.na(reports$chemFlagTable$BadCB_30.21[which(reports$chemFlagTable$SITE_NO == site)])))
    {
    cat("# Chargbalance flag plots","\n")
    try({
            cbPlot <- qwcbPlot(qw.data,
                       site.selection = site,
                       highlightrecords = unique(reports$chemFlagTable$RECORD_NO[which(!is.na(reports$chemFlagTable$BadCB_30.21))]),
                       print=FALSE)
    scSumPlot <- qwscSumPlot(qw.data,
                       site.selection = site,
                       highlightrecords = unique(reports$chemFlagTable$RECORD_NO[which(!is.na(reports$chemFlagTable$BadCB_30.21))]),
                       print=FALSE)
    grid.arrange(cbPlot,scSumPlot,nrow=1,ncol=2)
    cat("\n\n")

}) }else{}

    ###Run result checks
    cat("#Result plots","\n")
    siteData <- subset(qw.data$PlotTable,SITE_NO == site &
                               RESULT_CR > Sys.time() - 60*60*24*365*3)
    allParms <- unique(siteData[c("PARM_CD","PARM_NM","PARM_SEQ_GRP_CD")])

    ###Run field
    parms <- subset(allParms, PARM_CD %in% c("00095","00061","00400","00010")
                    )
    cat("##Field","\n")
    for(j in 1:nrow(parms))
            {
           try({
                   if(length(unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]) > 0 )
                      ){
            cat("###*FLAG*",parms$PARM_CD[j],parms$PARM_NM[j],"*FLAG*\n")
                   } else (cat("###",parms$PARM_CD[j],parms$PARM_NM[j],"\n"))

            tsPlot <- qwtsPlot(qw.data = qw.data,
               site.selection = site,
               plotparm = parms$PARM_CD[j],
               highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
               wySymbol = TRUE,
               print = FALSE)

            seasonalPlot <- qwseasonalPlot(qw.data,
                           site.selection = site,
                           plotparm = parms$PARM_CD[j],
                           highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
                           wySymbol = TRUE,
                           print = FALSE)

            pqPlot <- qwparmParmPlot(qw.data,
                     site.selection = site,
                     yparm = parms$PARM_CD[j],
                     xparm = "00061",
                     highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
                     wySymbol = TRUE,
                     print = FALSE)

            pSCPlot <- qwparmParmPlot(qw.data,
                      site.selection = site,
                      yparm = parms$PARM_CD[j],
                      xparm = "00095",
                      highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
                      wySymbol = TRUE,
                      print = FALSE)

            grid.arrange(tsPlot,seasonalPlot,pqPlot,pSCPlot,nrow=2,ncol=2)
            cat("\n\n")
           })
    }

    ###Run major anions
    parms <- subset(allParms, PARM_SEQ_GRP_CD %in% c("INN") 
                    #| PARM_CD %in% c("00095","00061","00400","00010")
                    )
    cat("##Major anions","\n")
    for(j in 1:nrow(parms))
            {
           try({
                   if(length(unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]) > 0 )
                      ){
            cat("###*FLAG*",parms$PARM_CD[j],parms$PARM_NM[j],"*FLAG*\n")
                   } else (cat("###",parms$PARM_CD[j],parms$PARM_NM[j],"\n"))

            tsPlot <- qwtsPlot(qw.data = qw.data,
               site.selection = site,
               plotparm = parms$PARM_CD[j],
               highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
               wySymbol = TRUE,
               print = FALSE)

            seasonalPlot <- qwseasonalPlot(qw.data,
                           site.selection = site,
                           plotparm = parms$PARM_CD[j],
                           highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
                           wySymbol = TRUE,
                           print = FALSE)

            pqPlot <- qwparmParmPlot(qw.data,
                     site.selection = site,
                     yparm = parms$PARM_CD[j],
                     xparm = "00061",
                     highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
                     wySymbol = TRUE,
                     print = FALSE)

            pSCPlot <- qwparmParmPlot(qw.data,
                      site.selection = site,
                      yparm = parms$PARM_CD[j],
                      xparm = "00095",
                      highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
                      wySymbol = TRUE,
                      print = FALSE)

            grid.arrange(tsPlot,seasonalPlot,pqPlot,pSCPlot,nrow=2,ncol=2)
            cat("\n\n")
           })
    }




    ###Run major cations
    parms <- subset(allParms, PARM_SEQ_GRP_CD %in% c("INM") 
                    #| PARM_CD %in% c("00095","00061","00400","00010")
                    )
    cat("##Major cations","\n")
    for(j in 1:nrow(parms))
            {
            try({
                    if(length(unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]) > 0 )
                      ){
            cat("###*FLAG*",parms$PARM_CD[j],parms$PARM_NM[j],"*FLAG*\n")
                    } else(cat("###",parms$PARM_CD[j],parms$PARM_NM[j],"\n"))
            tsPlot <- qwtsPlot(qw.data = qw.data,
               site.selection = site,
               plotparm = parms$PARM_CD[j],
               highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
               wySymbol = TRUE,
               print = FALSE)

            seasonalPlot <- qwseasonalPlot(qw.data,
                           site.selection = site,
                           plotparm = parms$PARM_CD[j],
                           highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
                           wySymbol = TRUE,
                           print = FALSE)

            pqPlot <- qwparmParmPlot(qw.data,
                     site.selection = site,
                     yparm = parms$PARM_CD[j],
                     xparm = "00061",
                     highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
                     wySymbol = TRUE,
                     print = FALSE)

            pSCPlot <- qwparmParmPlot(qw.data,
                      site.selection = site,
                      yparm = parms$PARM_CD[j],
                      xparm = "00095",
                      highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
                      wySymbol = TRUE,
                      print = FALSE)

            grid.arrange(tsPlot,seasonalPlot,pqPlot,pSCPlot,nrow=2,ncol=2)
            cat("\n\n")
            })
    }

Run nutrients

    parms <- subset(allParms, PARM_SEQ_GRP_CD %in% c("NUT") 
                    #| PARM_CD %in% c("00095","00061","00400","00010")
                    )
    cat("##Nutrients","\n")
    for(j in 1:nrow(parms))
            {
            try({
                    if(length(unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]) > 0 )
                      ){
            cat("###*FLAG*",parms$PARM_CD[j],parms$PARM_NM[j],"*FLAG*\n")
                    }else (cat("###",parms$PARM_CD[j],parms$PARM_NM[j],"\n"))
            tsPlot <- qwtsPlot(qw.data = qw.data,
               site.selection = site,
               plotparm = parms$PARM_CD[j],
               highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
               wySymbol = TRUE,
               print = FALSE)

            seasonalPlot <- qwseasonalPlot(qw.data,
                           site.selection = site,
                           plotparm = parms$PARM_CD[j],
                           highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
                           wySymbol = TRUE,
                           print = FALSE)

            pqPlot <- qwparmParmPlot(qw.data,
                     site.selection = site,
                     yparm = parms$PARM_CD[j],
                     xparm = "00061",
                     highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
                     wySymbol = TRUE,
                     print = FALSE)

            pSCPlot <- qwparmParmPlot(qw.data,
                      site.selection = site,
                      yparm = parms$PARM_CD[j],
                      xparm = "00095",
                      highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
                      wySymbol = TRUE,
                      print = FALSE)

            grid.arrange(tsPlot,seasonalPlot,pqPlot,pSCPlot,nrow=2,ncol=2)
            cat("\n\n")
            })
    }

Run sediment

    parms <- subset(allParms, PARM_SEQ_GRP_CD %in% c("SED") 
                    #| PARM_CD %in% c("00095","00061","00400","00010")
                    )
    cat("##Sediment","\n")
    for(j in 1:nrow(parms))
            {
            try({
                    if(length(unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]) > 0 )
                      ){
            cat("###*FLAG*",parms$PARM_CD[j],parms$PARM_NM[j],"*FLAG*\n")
                    }else (cat("###",parms$PARM_CD[j],parms$PARM_NM[j],"\n"))

            tsPlot <- qwtsPlot(qw.data = qw.data,
               site.selection = site,
               plotparm = parms$PARM_CD[j],
               highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
               wySymbol = TRUE,
               print = FALSE)

            seasonalPlot <- qwseasonalPlot(qw.data,
                           site.selection = site,
                           plotparm = parms$PARM_CD[j],
                           highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
                           wySymbol = TRUE,
                           print = FALSE)

            pqPlot <- qwparmParmPlot(qw.data,
                     site.selection = site,
                     yparm = parms$PARM_CD[j],
                     xparm = "00061",
                     highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
                     wySymbol = TRUE,
                     print = FALSE)

            pSCPlot <- qwparmParmPlot(qw.data,
                      site.selection = site,
                      yparm = parms$PARM_CD[j],
                      xparm = "00095",
                      highlightrecords = unique(reports$resultFlagTable$RECORD_NO[which(reports$resultFlagTable$PARM_CD == parms$PARM_CD[j])]),
                      wySymbol = TRUE,
                      print = FALSE)

            grid.arrange(tsPlot,seasonalPlot,pqPlot,pSCPlot,nrow=2,ncol=2)
            cat("\n\n")
            })
    }