###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") }) }
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$PARM_CD[j])]), wySymbol = TRUE, print = FALSE) grid.arrange(tsPlot,seasonalPlot,pqPlot,pSCPlot,nrow=2,ncol=2) cat("\n\n") }) }
parms <- subset(allParms, PARM_SEQ_GRP_CD %in% c("SED") #| PARM_CD %in% c("00095","00061","00400","00010") ) cat("##Sediment","\n") for(j in 1:nrow(parms)) { try({ if(length(unique(reports$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") }) }
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