Reduce direct imports

.gitignore

@@ -7,7 +7,6 @@ Meta/
 Newstuff/
 *.docx
 vignettes/*.html
-vignettes/*.R
 vignettes/EGRET.R
 vignettes/Enhancements.R
 vignettes/TrendsByMonth.R

DESCRIPTION

@@ -58,6 +58,6 @@ Copyright: This software is in the public domain because it contains materials
     the United States Department of Interior. For more information, see the
     official USGS copyright policy at
     https://www.usgs.gov/information-policies-and-instructions/copyrights-and-credits
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(old_usage = TRUE)
 Encoding: UTF-8

NAMESPACE

@@ -140,35 +140,12 @@ exportClasses(fluxUnit)
 exportClasses(monthLabel)
 exportClasses(qUnit)
 import(methods)
-importFrom(grDevices,colorRampPalette)
-importFrom(graphics,abline)
 importFrom(graphics,axis)
-importFrom(graphics,box)
-importFrom(graphics,boxplot)
-importFrom(graphics,contour)
-importFrom(graphics,filled.contour)
-importFrom(graphics,grconvertX)
-importFrom(graphics,grconvertY)
-importFrom(graphics,legend)
 importFrom(graphics,lines)
 importFrom(graphics,mtext)
 importFrom(graphics,par)
 importFrom(graphics,plot)
 importFrom(graphics,points)
 importFrom(graphics,segments)
 importFrom(graphics,title)
-importFrom(stats,aggregate)
-importFrom(stats,filter)
-importFrom(stats,lm)
-importFrom(stats,median)
-importFrom(stats,na.omit)
-importFrom(stats,predict)
-importFrom(stats,quantile)
-importFrom(stats,reshape)
-importFrom(stats,rnorm)
-importFrom(stats,sd)
 importFrom(stats,var)
-importFrom(utils,URLencode)
-importFrom(utils,read.delim)
-importFrom(utils,tail)
-importFrom(utils,write.table)

R/EGRET.R

@@ -26,43 +26,20 @@ Extended Documentation: https://rconnect.usgs.gov/EGRET")
 #'
 #' @name EGRET-package
 #' @docType package
-#' @importFrom utils write.table
-#' @importFrom utils read.delim
-#' @importFrom utils URLencode
-#' @importFrom utils tail
-#' @importFrom stats aggregate
-#' @importFrom stats lm
-#' @importFrom stats median
-#' @importFrom stats sd
-#' @importFrom stats reshape
-#' @importFrom stats filter
-#' @importFrom stats rnorm
-#' @importFrom stats na.omit
 #' 
-#' @importFrom graphics abline
 #' @importFrom graphics axis
-#' @importFrom graphics box
-#' @importFrom graphics boxplot
-#' @importFrom graphics contour
-#' @importFrom graphics filled.contour
-#' @importFrom graphics grconvertX
-#' @importFrom graphics grconvertY
-#' @importFrom graphics legend
 #' @importFrom graphics lines
 #' @importFrom graphics mtext
 #' @importFrom graphics par
 #' @importFrom graphics points
 #' @importFrom graphics segments
 #' @importFrom graphics title
-#' @importFrom stats predict
-#' @importFrom stats quantile
-#' @importFrom grDevices colorRampPalette
 #' @author Robert M. Hirsch \email{rhirsch@@usgs.gov}, Laura De Cicco \email{ldecicco@@usgs.gov}
 #' @references Hirsch, R.M., and De Cicco, L.A., 2014, User guide to Exploration and Graphics for RivEr Trends 
 #' (EGRET) and dataRetrieval: R packages for hydrologic data: U.S. Geological Survey Techniques and Methods book 4, 
 #' chap. A10, 94 p., \doi{10.3133/tm4A10}
-#' @keywords water-quality graphics streamflow statistics 
-NULL
+#' @keywords internal  
+"_PACKAGE"
 
 #' Example eList
 #'

R/boxConcMonth.R

@@ -124,7 +124,7 @@ boxConcMonth <- function(eList, printTitle = TRUE,
                        units = localINFO$param.units)
   yTicksLab <- prettyNum(yInfo$ticks)
 
-  boxplot(tempDF$conc ~ tempDF$month,
+  graphics::boxplot(tempDF$conc ~ tempDF$month,
           ylim = c(yInfo$bottom,yInfo$top),
           yaxs = "i",
           yTicks = yInfo$ticks,

R/boxConcThree.R

@@ -107,7 +107,7 @@ boxConcThree<-function (eList, tinyPlot=FALSE,
   yTicks <- yPretty(yMax)
   yTop <- yTicks[length(yTicks)]
 
-  boxplot(concV ~ index,varwidth=TRUE,
+  graphics::boxplot(concV ~ index,varwidth=TRUE,
           names = groupNames,xlab = "", ylab = yLab,
           ylim = c(0,yTop), axes = FALSE,
           main = plotTitle, font.main = font.main, cex = cex,
@@ -119,7 +119,7 @@ boxConcThree<-function (eList, tinyPlot=FALSE,
   axis(2,tcl=0.5,las=1,at=yTicks,cex.axis=cex.axis)
   axis(3,tcl=0.5,at=c(1,2,3),labels=FALSE)
   axis(4,tcl=0.5,at=yTicks,labels=FALSE)
-  box()
+  graphics::box()
   if (!tinyPlot) mtext(title2,side=3,line=-1.5)
   invisible(eList)
 }

R/boxQTwice.R

@@ -111,7 +111,7 @@ boxQTwice<-function(eList,
     logScaleText <- ""
   }
 
-  boxplot(bigQ~index,varwidth=TRUE,
+  graphics::boxplot(bigQ~index,varwidth=TRUE,
           names=groupNames,xlab="",
           ylim=c(yInfo$bottom,yInfo$top),
           main=plotTitle,cex=cex,ylab=yLabel,

R/boxResidMonth.R

@@ -104,7 +104,7 @@ boxResidMonth <- function(eList,
   monthList <- singleMonthList[localSample$Month]
   monthList <- factor(monthList, namesListFactor)
 
-  boxplot(resid ~ monthList,
+  graphics::boxplot(resid ~ monthList,
           varwidth = TRUE,
           xlab = "Month", ylab = yLab,
           main = plotTitle,
@@ -114,7 +114,7 @@ boxResidMonth <- function(eList,
           cex.axis = cex.axis,
           las = las,
           ...)
-  abline(h = 0)  
+  graphics::abline(h = 0)  
   if (!tinyPlot) mtext(title2, side = 3, line = -1.5)
   invisible(eList)
 }

R/calculateMonthlyResults.R

@@ -16,22 +16,22 @@ calculateMonthlyResults <- function(eList){
 
   localDaily <- getDaily(eList)
 
-  nDays <- aggregate(localDaily$ConcDay, by=list(localDaily$MonthSeq), function(x) sum(!is.na(x)))$x
+  nDays <- stats::aggregate(localDaily$ConcDay, by=list(localDaily$MonthSeq), function(x) sum(!is.na(x)))$x
 
-  Q <- aggregate(localDaily$Q, by=list(localDaily$MonthSeq), mean)$x
-  DecYear <- aggregate(localDaily$DecYear, by=list(localDaily$MonthSeq), mean)$x
+  Q <- stats::aggregate(localDaily$Q, by=list(localDaily$MonthSeq), mean)$x
+  DecYear <- stats::aggregate(localDaily$DecYear, by=list(localDaily$MonthSeq), mean)$x
   Year <- trunc(DecYear)
-  Month <- aggregate(localDaily$Month, by=list(localDaily$MonthSeq), mean)$x
-  Conc <- aggregate(localDaily$ConcDay, by=list(localDaily$MonthSeq), mean)$x
-  Flux <- aggregate(localDaily$FluxDay, by=list(localDaily$MonthSeq), mean)$x
-  FNConc <- aggregate(localDaily$FNConc, by=list(localDaily$MonthSeq), mean)$x
-  FNFlux <- aggregate(localDaily$FNFlux, by=list(localDaily$MonthSeq), mean)$x
+  Month <- stats::aggregate(localDaily$Month, by=list(localDaily$MonthSeq), mean)$x
+  Conc <- stats::aggregate(localDaily$ConcDay, by=list(localDaily$MonthSeq), mean)$x
+  Flux <- stats::aggregate(localDaily$FluxDay, by=list(localDaily$MonthSeq), mean)$x
+  FNConc <- stats::aggregate(localDaily$FNConc, by=list(localDaily$MonthSeq), mean)$x
+  FNFlux <- stats::aggregate(localDaily$FNFlux, by=list(localDaily$MonthSeq), mean)$x
 
   kalman <- all(c("GenConc","GenFlux") %in% names(localDaily))
 
   if(kalman){
-    GenConc <- aggregate(localDaily$GenConc, by=list(localDaily$MonthSeq), mean)$x
-    GenFlux <- aggregate(localDaily$GenFlux, by=list(localDaily$MonthSeq), mean)$x
+    GenConc <- stats::aggregate(localDaily$GenConc, by=list(localDaily$MonthSeq), mean)$x
+    GenFlux <- stats::aggregate(localDaily$GenFlux, by=list(localDaily$MonthSeq), mean)$x
 
     MonthlyResults <- data.frame(Month, Year, nDays,
                                  DecYear, Q,

R/cumQdate.R

@@ -27,7 +27,7 @@
 #' annualFlow <- cumQdate(eList)
 #' head(annualFlow)
 #' plot(annualFlow)
-#' mod1 <- lm(annualFlow[,2] ~ annualFlow[,1])
+#' mod1 <- stats::lm(annualFlow[,2] ~ annualFlow[,1])
 #' summary(mod1)
 cumQdate <- function(eList, 
                      paStart = 10, paLong = 12, 
@@ -65,6 +65,6 @@ cumQdate <- function(eList,
     }  
   }
 
-  annualSeries <- na.omit(annualSeries)
+  annualSeries <- stats::na.omit(annualSeries)
   return(annualSeries)
 }

R/estSurfaces.R

@@ -92,7 +92,7 @@ estSurfaces<-function(eList, surfaceStart=NA, surfaceEnd=NA, localSample=NA,
 
     sliceIndex <- which(vectorYear >= decimalDate(as.Date(surfaceStart)) & vectorYear <= 
                           decimalDate(as.Date(surfaceEnd)))
-    Year <- vectorYear[c(sliceIndex[1]-1, sliceIndex, tail(sliceIndex, n = 1)+1)]
+    Year <- vectorYear[c(sliceIndex[1]-1, sliceIndex, utils::tail(sliceIndex, n = 1)+1)]
 
     nVectorYear <- length(Year)
     estPtYear <- rep(Year,each=14)

R/genericEGRETplot.R

@@ -84,9 +84,9 @@ genericEGRETDotPlot <- function(x,y, xlim, ylim,
        ylim=ylim,yaxs=yaxs,ylab=if(showYLabels) ylab else "", main=plotTitle,col=col,lwd=lwd,
        pch=pch,cex=cex,cex.main=cex.main,font.main=font.main,cex.lab=cex.lab,...)
 
-  box()
-  if (hLine) abline(h = 0)
-  if (oneToOneLine) abline(a=0,b=1)
+  graphics::box()
+  if (hLine) graphics::abline(h = 0)
+  if (oneToOneLine) graphics::abline(a=0,b=1)
 
   if(rmSciX){
     xTicksLab <- prettyNum(xTicks)

R/kalman_functions.R

@@ -106,7 +106,7 @@ WRTDSKalman <- function(eList, rho = 0.90, niter = 200,
       endFill <- zends[iGap]+1
       nFill <- zz$length[iGap]+2
       if(i == 1 | i == numGap) {
-        z <- rnorm(nFill - 2)
+        z <- stats::rnorm(nFill - 2)
         xfill <- c(xxP[startFill], z, xxP[endFill])
       } else {
         xfill <- genmissing(xxP[startFill], xxP[endFill], rho, nFill)
@@ -385,7 +385,7 @@ plotWRTDSKalman <- function(eList, sideBySide = FALSE,
                       ylab = ylab, 
                       cex.main = 0.9, 
                       plotTitle = title2)
-  abline(a = 0, b = 1)
+  graphics::abline(a = 0, b = 1)
 
   if(sideBySide){
     mtext(mainTitle, line = -1, side = 3, outer = TRUE, cex= 1)

R/makeAnnualSeries.R

@@ -97,7 +97,7 @@ makeAnnualSeries<-function(eList, edgeAdjust = TRUE) {
     if (goodDay > 26 * paLong) {
       annualSeries[1, 4:8, i] <- mean(yearDaily$DecYear, 
                                       na.rm = TRUE)
-      annualSeries[2, 4, i] <- median(yearDaily$Q, na.rm = TRUE)
+      annualSeries[2, 4, i] <- stats::median(yearDaily$Q, na.rm = TRUE)
       annualSeries[2, 5, i] <- mean(yearDaily$Q, na.rm = TRUE)
       annualSeries[2, 6, i] <- max(yearDaily$Q30, na.rm = TRUE)
       annualSeries[2, 7, i] <- max(yearDaily$Q7, na.rm = TRUE)
@@ -111,7 +111,7 @@ makeAnnualSeries<-function(eList, edgeAdjust = TRUE) {
     numYears <- length(x)
     xVec <- seq(1,numYears)
     xy <- data.frame(x,y,xVec)
-    xy <- na.omit(xy)
+    xy <- stats::na.omit(xy)
     goodYears <- length(xy$x)
     x <- xy$x
     x1 <- x[1]
@@ -126,9 +126,9 @@ makeAnnualSeries<-function(eList, edgeAdjust = TRUE) {
         window
       }
       w <- triCube(x - xi, thisWindow)
-      mod <- lm(xy$y ~ x, weights = w)
+      mod <- stats::lm(xy$y ~ x, weights = w)
       new <- data.frame(x = x[i])
-      z <- exp(predict(mod, new))
+      z <- exp(stats::predict(mod, new))
       iYear <- xy$xVec[i]
       annualSeries[3, istat, iYear] <- z
     }

R/plot1of15.R

@@ -50,5 +50,5 @@ plot1of15<-function(eList, yearStart, yearEnd, qf, istat,
   axis(2,tcl=0.5,at=yTicks,labels=FALSE)
   axis(3,tcl=0.5,at=xTicks,labels=FALSE)
   axis(4,tcl=0.5,at=yTicks,labels=FALSE)
-  box()
+  graphics::box()
 }

R/plotConcQSmooth.R

@@ -217,18 +217,18 @@ plotConcQSmooth<-function(eList,
   cols<-colorVal[index]
 
   legendLeft <- if(legendLeft == 0) {
-    grconvertX(0.05, from="npc", to="user")
+    graphics::grconvertX(0.05, from="npc", to="user")
   } else {
     legendLeft
   }
 
   legendTop <- if(legendTop == 0) {
-    grconvertY(0.3, from="npc", to="user") 
+    graphics::grconvertY(0.3, from="npc", to="user") 
   } else {
     legendTop
   }
 
-  if (printLegend) legend(legendLeft,legendTop ,legend=words,lty=ltys,col=cols,lwd=lwd,cex=cex.legend)
+  if (printLegend) graphics::legend(legendLeft,legendTop ,legend=words,lty=ltys,col=cols,lwd=lwd,cex=cex.legend)
 
   printResults<-rep(NA,48*4)
   dim(printResults)<-c(48,4)

R/plotConcTimeSmooth.R

@@ -222,16 +222,16 @@ plotConcTimeSmooth<-function (eList, q1, q2, q3,
   cols <- colorVal[index]
 
   legendLeft <- if(legendLeft == 0) {
-    grconvertX(0.05, from="npc", to="user")
+    graphics::grconvertX(0.05, from="npc", to="user")
   } else {
     legendLeft
   }
 
   if(legendTop == 0) {
-    legendTop <- grconvertY(0.3, from="npc", to="user") 
+    legendTop <- graphics::grconvertY(0.3, from="npc", to="user") 
   } 
 
-  if (printLegend) legend(legendLeft,legendTop,legend=words,lty=ltys,col=cols,lwd=lwd,cex=cex.legend)
+  if (printLegend) graphics::legend(legendLeft,legendTop,legend=words,lty=ltys,col=cols,lwd=lwd,cex=cex.legend)
 
   printResults <- rep(NA, numX * 4)
   dim(printResults) <- c(numX, 4)

R/plotContours.R

@@ -61,7 +61,7 @@
 #'              contourLevels = clevel)  
 #' plotContours(eList, yearStart, yearEnd, qBottom, qTop = 50, 
 #'              contourLevels = clevel, flowDuration = FALSE) 
-#' colors <- colorRampPalette(c("white","black"))
+#' colors <- grDevices::colorRampPalette(c("white","black"))
 #' plotContours(eList, yearStart, yearEnd, qBottom, qTop = 50, 
 #'              contourLevels = clevel, color.palette = colors, 
 #'              flowDuration = FALSE)
@@ -75,7 +75,7 @@ plotContours <- function(eList, yearStart, yearEnd,
                          yTicks = NA, tick.lwd = 1, usgsStyle = FALSE,
                          lwd = 2, cex.main = 1, cex.axis = 1,
                          concLab = 1,
-                         color.palette = colorRampPalette(c("white","gray","blue","red")), ...) {
+                         color.palette = grDevices::colorRampPalette(c("white","gray","blue","red")), ...) {
 
   localINFO <- getInfo(eList)
   localDaily <- getDaily(eList)
@@ -129,9 +129,9 @@ plotContours <- function(eList, yearStart, yearEnd,
   numX<-length(x)
   numY<-length(y)
 
-  qBottomT <- ifelse(is.na(qBottom), quantile(localDaily$Q, probs = 0.05)*qFactor, qBottom)
+  qBottomT <- ifelse(is.na(qBottom), stats::quantile(localDaily$Q, probs = 0.05)*qFactor, qBottom)
 
-  qTopT <- ifelse(is.na(qTop), quantile(localDaily$Q, probs = 0.95)*qFactor, qTop)
+  qTopT <- ifelse(is.na(qTop), stats::quantile(localDaily$Q, probs = 0.95)*qFactor, qTop)
 
   if(any(is.na(yTicks))){
 
@@ -212,28 +212,28 @@ plotContours <- function(eList, yearStart, yearEnd,
   yLab<-ifelse(usgsStyle,qUnit@unitUSGS,qUnit@qUnitExpress)
 
   logY <- log(y,10)
-  filled.contour(x,log(y,10),surft,levels=contourLevels,xlim=c(yearStart,yearEnd),
+  graphics::filled.contour(x,log(y,10),surft,levels=contourLevels,xlim=c(yearStart,yearEnd),
                  ylim=c(log(yTicks[1],10),log(yTicks[nYTicks],10)),
                  xaxs="i",yaxs="i",
                  color.palette=color.palette, # ...,
                  plot.axes={
 
-                   width <- grconvertX(par("usr")[2],from="user",to="inches") - grconvertX(par("usr")[1],from="user",to="inches")
-                   height <- grconvertY(par("usr")[4],from="user",to="inches") - grconvertY(par("usr")[3],from="user",to="inches")
+                   width <- graphics::grconvertX(par("usr")[2],from="user",to="inches") - graphics::grconvertX(par("usr")[1],from="user",to="inches")
+                   height <- graphics::grconvertY(par("usr")[4],from="user",to="inches") - graphics::grconvertY(par("usr")[3],from="user",to="inches")
 
                    axis(1,tcl=0,at=xTicks,labels=xlabels,cex.axis=cex.axis)
                    axis(2,tcl=0,las=1,at=log(yTicks,10),labels=yTicks,cex.axis=cex.axis)
                    axis(3, tcl = 0, at = xTicks, labels =FALSE,cex.axis=cex.axis)
                    axis(4, tcl = 0, at = log(yTicks, 10), labels=FALSE,cex.axis=cex.axis)
-                   if(flowDuration) contour(x,log(y,10),durSurf,add=TRUE,drawlabels=FALSE,levels=plevels,lwd=lwd)
+                   if(flowDuration) graphics::contour(x,log(y,10),durSurf,add=TRUE,drawlabels=FALSE,levels=plevels,lwd=lwd)
                    segments(v1[1],v1[2],v1[3],v1[4])
                    segments(v2[1],v2[2],v2[3],v2[4])
                    segments(h1[1],h1[2],h1[3],h1[4])
 
-                   segments(xTicks, rep(log(yTicks[1],10),length(xTicks)), xTicks, rep(grconvertY(grconvertY(par("usr")[3],from="user",to="inches")+tcl,from="inches",to="user"),length(xTicks)), lwd = tick.lwd)
-                   segments(xTicks, rep(log(yTicks[nYTicks],10),length(xTicks)), xTicks, rep(grconvertY(grconvertY(par("usr")[4],from="user",to="inches")-tcl,from="inches",to="user"),length(xTicks)), lwd = tick.lwd)
-                   segments(rep(yearStart,length(yTicks)), log(yTicks,10), rep(grconvertX(grconvertX(par("usr")[1],from="user",to="inches")+tcl,from="inches",to="user"),length(yTicks)),log(yTicks,10), lwd = tick.lwd)
-                   segments(rep(grconvertX(grconvertX(par("usr")[2],from="user",to="inches")-tcl,from="inches",to="user"),length(yTicks)), log(yTicks,10), rep(yearEnd,length(yTicks)),log(yTicks,10), lwd = tick.lwd)
+                   segments(xTicks, rep(log(yTicks[1],10),length(xTicks)), xTicks, rep(graphics::grconvertY(graphics::grconvertY(par("usr")[3],from="user",to="inches")+tcl,from="inches",to="user"),length(xTicks)), lwd = tick.lwd)
+                   segments(xTicks, rep(log(yTicks[nYTicks],10),length(xTicks)), xTicks, rep(graphics::grconvertY(graphics::grconvertY(par("usr")[4],from="user",to="inches")-tcl,from="inches",to="user"),length(xTicks)), lwd = tick.lwd)
+                   segments(rep(yearStart,length(yTicks)), log(yTicks,10), rep(graphics::grconvertX(graphics::grconvertX(par("usr")[1],from="user",to="inches")+tcl,from="inches",to="user"),length(yTicks)),log(yTicks,10), lwd = tick.lwd)
+                   segments(rep(graphics::grconvertX(graphics::grconvertX(par("usr")[2],from="user",to="inches")-tcl,from="inches",to="user"),length(yTicks)), log(yTicks,10), rep(yearEnd,length(yTicks)),log(yTicks,10), lwd = tick.lwd)
                  },
                   plot.title = {
                     if(printTitle) {