Merge pull request #60 from ldecicco-USGS/master

Back to basics.

NAMESPACE

@@ -21,10 +21,8 @@ export(dataOverview)
 export(dateFormatCheck)
 export(estCrossVal)
 export(estDailyFromSurfaces)
-export(estFNsegs)
 export(estSurfaces)
 export(fixSampleFrame)
-export(flexFN)
 export(flowDuration)
 export(fluxBiasMulti)
 export(fluxBiasStat)

R/modelEstimation.R

@@ -125,151 +125,3 @@ setUpEstimation<-function(eList,
   return(eList)
 
 }
-
-#' Flexible Flow Normalization
-#' 
-#' @param eList named list with at least the Daily, Sample, and INFO dataframes
-#' @param nSegments integer number of flow normalized segments to create
-#' @param segStart integer vector of start years (water) for each FN conc/flux segment
-#' @param segEnd integer vector of end years (water) for each FN conc/flux segment
-#' @param dStart Date vector of start days for each flow segment
-#' @param dEnd Date vector of end days for each flow segment
-#' 
-#' @export
-#' @examples
-#' eList <- Choptank_eList
-#' eList <- setUpEstimation(eList)
-#' nSegments <- 2
-#' segStart <- c(1985,2000)
-#' segEnd <- c(2001,2010)
-#' dStart <- as.Date(c("1988-10-01","2002-05-15"))
-#' dEnd <- as.Date(c("1998-09-30","2009-09-30"))
-#' eList <- flexFN(eList,nSegments,segStart,segEnd,dStart,dEnd)
-#' plotFluxHist(eList)
-flexFN <- function(eList, nSegments, segStart, segEnd,dStart,dEnd){
-
-  dateInfo <- data.frame(segStart,segEnd,dStart,dEnd)
-
-  if(nrow(dateInfo) != nSegments){
-    stop("Length of segStart and segEnd must equal nSegments")
-  }
-
-  Daily <- eList$Daily
-  Sample <- eList$Sample
-
-  Sample$WaterYear <- as.integer(Sample$DecYear)
-  Sample$WaterYear[Sample$Month >= 10] <- Sample$WaterYear[Sample$Month >= 10] +1
-
-  Daily$WaterYear <- as.integer(Daily$DecYear)
-  Daily$WaterYear[Daily$Month >= 10] <- Daily$WaterYear[Daily$Month >= 10] +1
-
-  yStartSample <- min(Sample$WaterYear)
-  yEndSample <- max(Sample$WaterYear)
-
-  yStartDaily <- min(Daily$WaterYear)
-  yEndDaily <- max(Daily$WaterYear)
-
-  checkWY <- function(dates, yStart, yEnd){
-    segWY <- as.integer(format(dates,"%Y"))
-    segMonth <- as.integer(format(dates,"%m"))
-    segWY[segMonth > 9] <- segWY[segMonth > 9]+1
-
-    if(segWY[1] < yStart | segWY[length(segWY)] > yEnd){
-      stop("Flow segment dates outside range")
-    }
-    return(segWY)
-  }
-
-  if(segStart[1] < yStartSample | segEnd[length(segEnd)] > yEndSample){
-    stop("Sample segment years outside range")
-  }
-
-  if(nSegments>1){
-    for(i in (seq(nSegments-1)+1)){
-      if(segStart[i] != segEnd[i-1] -1){
-        stop("segStart and segEnd need to be continuous")
-      }
-    }
-  }
-
-  dStartWY <- checkWY(dStart, yStartDaily, yEndDaily)  
-  dEndWY <- checkWY(dEnd, yStartDaily, yEndDaily)
-
-  if(any(as.integer(dEnd - dStart) < 365)){
-    stop("Each flow normaliziation section must span at least 365 days")
-  }
-
-  DailyFN <- estDailyFromSurfaces(eList)
-  DailyFN$FNConc <- NULL
-  DailyFN$FNFlux <- NULL
-
-  newList <- as.egret(eList$INFO,DailyFN,Sample,eList$surfaces)
-
-  for(i in seq(nSegments)){
-    dailyReturn <- estFNsegs(newList,segStart[i],segEnd[i],dStart[i],dEnd[i])
-    DailyFN <- merge(DailyFN, dailyReturn[,c("Date","FNConc","FNFlux")],by=c("Date"),all.x=TRUE)
-  }
-  FNConcCols <- grep("FNConc",names(DailyFN))
-  FNConcCols <- names(DailyFN)[FNConcCols]
-
-  FNFluxCols <- grep("FNFlux",names(DailyFN))
-  FNFluxCols <- names(DailyFN)[FNFluxCols]
-
-  DailyFN$FNConc <- rowSums(DailyFN[,FNConcCols],na.rm = TRUE)
-  DailyFN$FNFlux <- rowSums(DailyFN[,FNFluxCols],na.rm = TRUE)
-
-  DailyFN[rowSums(is.na(DailyFN[,FNConcCols]))==length(FNConcCols),"FNConc"] <- NA
-  DailyFN[rowSums(is.na(DailyFN[,FNFluxCols]))==length(FNFluxCols),"FNFlux"] <- NA
-
-  DailyFN <- DailyFN[,!(names(DailyFN) %in% c(FNConcCols,FNFluxCols))]
-
-  INFO <- eList$INFO
-  INFO$shortName <- paste0(INFO$shortName,"*")
-  INFO$nSegments <- nSegments
-
-  attr(INFO,"segmentInfo") <- dateInfo
-
-  newList <- as.egret(INFO,DailyFN,Sample,eList$surfaces)
-
-  return(newList)
-
-}
-
-
-#' Segment estimates
-#' 
-#' @param eList named list with at least the Daily, Sample, and INFO dataframes
-#' @param segStart_i integer vector of start years (water) for each FN conc/flux segment
-#' @param segEnd_i integer vector of end years (water) for each FN conc/flux segment
-#' @param dStart_i Date vector of start days for each flow segment
-#' @param dEnd_i Date vector of end days for each flow segment
-#' 
-#' @export
-#' @examples
-#' eList <- Choptank_eList
-#' eList <- setUpEstimation(eList)
-#' nSegments <- 2
-#' segStart <- c(1985,2000)
-#' segEnd <- c(2001,2010)
-#' dStart <- as.Date(c("1988-10-01","2002-05-15"))
-#' dEnd <- as.Date(c("1998-09-30","2009-09-30"))
-#' eList <- estFNsegs(eList,segStart[1],segEnd[1],dStart[1],dEnd[1])
-estFNsegs <- function(eList, segStart_i,segEnd_i,dStart_i,dEnd_i){
-
-  Daily <- eList$Daily
-  Sample <- eList$Sample
-
-  Daily <- Daily[Daily$Date >= dStart_i & Daily$Date <= dEnd_i,]
-
-  Sample$WaterYear <- as.integer(Sample$DecYear)
-  Sample$WaterYear[Sample$Month >= 10] <- Sample$WaterYear[Sample$Month >= 10] +1
-  Sample <- Sample[Sample$WaterYear >= segStart_i & Sample$WaterYear <= segEnd_i,]
-
-  newList <- as.egret(eList$INFO,Daily,Sample,eList$surfaces)
-
-  newDaily <- estDailyFromSurfaces(newList)
-  return(newDaily)
-}
-
-
-