Merge pull request #374 from ldecicco-USGS/main

Fixes #373

.github/workflows/R-CMD-check.yaml

@@ -31,19 +31,19 @@ jobs:
     steps:
       - uses: actions/checkout@c0a81a463886bb75afe234e07a9fd5bb79219196
 
-      - uses: r-lib/actions/setup-pandoc@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/setup-pandoc@4a9a68ffb70ac0fc90d9683fae64a0d779f7d0fe
 
-      - uses: r-lib/actions/setup-r@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/setup-r@3e80f8fe880a36a9f35bf3e832f1bef8af687b69
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/setup-r-dependencies@e93f9af25505a6e249a7ae3bbaaa9413db8a0de4
         with:
           extra-packages: any::rcmdcheck
           needs: check
 
-      - uses: r-lib/actions/check-r-package@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/check-r-package@d26c5f95c4f10c7444cec87a1effe7d8af8897b8
         with:
           upload-snapshots: true

.github/workflows/test-coverage.yaml

@@ -14,9 +14,9 @@ jobs:
     steps:
       - uses: actions/checkout@c0a81a463886bb75afe234e07a9fd5bb79219196
 
-      - uses: r-lib/actions/setup-r@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/setup-r@3e80f8fe880a36a9f35bf3e832f1bef8af687b69
 
-      - uses: r-lib/actions/setup-pandoc@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/setup-pandoc@4a9a68ffb70ac0fc90d9683fae64a0d779f7d0fe
 
       - name: Query dependencies
         run: |

NEWS

@@ -1,3 +1,8 @@
+EGRET 3.0.9
+===========
+* Bug fix for the monthly concentration trend results in runPairs.
+* Formatting and style updates in plotMonthTrend
+
 EGRET 3.0.8
 ===========
 * Added GenConc to tableResult function

R/blankTime.R

@@ -10,6 +10,16 @@
 #' @param eList named list with at least the Daily dataframe
 #' @keywords water-quality statistics
 #' @return eList named list with modified Daily data frame.
+#' @details
+#' The startBlank and endBlank arguments should generally coincide with the starting and
+#' ending date of the period of analysis that is being used.  startBlank should be
+#' placed fairly close to the start of the period of no data and endBlank should
+#' be placed fairly close to the end of the period of no data.  They do not eliminate
+#' any water quality data from the set of data being used to estimate the model,
+#' they only eliminate results computed for the specified blank period.  If the data
+#' set has more than one large data gap the \code{blankTime()} function can be used
+#' multiple times to blank out multiple sets of results.
+#' 
 #' @export
 #' @examples
 #' startBlank = "2004-10-01"
@@ -20,15 +30,22 @@ blankTime<-function(eList, startBlank, endBlank) {
 
   localDaily <- getDaily(eList)
 
-  startBlank<-as.Date(startBlank)
-  endBlank<-as.Date(endBlank)
-  startJulian<-as.numeric(julian(startBlank,origin=as.Date("1850-01-01")))
-  endJulian<-as.numeric(julian(endBlank,origin=as.Date("1850-01-01")))
-  bad<-ifelse(localDaily$Julian>=startJulian&localDaily$Julian<=endJulian,TRUE,FALSE)
-  localDaily$ConcDay<-ifelse(bad,NA,localDaily$ConcDay)
-  localDaily$FluxDay<-ifelse(bad,NA,localDaily$FluxDay)
-  localDaily$FNConc<-ifelse(bad,NA,localDaily$FNConc)
-  localDaily$FNFlux<-ifelse(bad,NA,localDaily$FNFlux)
+  startBlank <- as.Date(startBlank)
+  endBlank <- as.Date(endBlank)
+  startJulian <- as.numeric(julian(startBlank,origin=as.Date("1850-01-01")))
+  endJulian <- as.numeric(julian(endBlank,origin=as.Date("1850-01-01")))
+  bad <- localDaily$Julian >= startJulian & 
+                localDaily$Julian <= endJulian
+  localDaily$ConcDay <- ifelse(bad,NA,localDaily$ConcDay)
+  localDaily$FluxDay <- ifelse(bad,NA,localDaily$FluxDay)
+  localDaily$FNConc <- ifelse(bad,NA,localDaily$FNConc)
+  localDaily$FNFlux <- ifelse(bad,NA,localDaily$FNFlux)
+
+  wrtdsK <- all(c("GenConc", "GenFlux") %in% names(localDaily))
+  if(wrtdsK){
+    localDaily$GenConc <- ifelse(bad,NA,localDaily$GenConc)
+    localDaily$GenFlux <- ifelse(bad,NA,localDaily$GenFlux)
+  }
 
   eList$Daily <- localDaily
 

R/errorStats.R

@@ -22,7 +22,7 @@ errorStats <- function(eList) {
 
   eListR <- makeAugmentedSample(eList)
   Sample <- eListR$Sample
-  n <- length(Sample$Dates)
+  # n <- length(Sample$Date)
   Sample$Pred <- log(Sample$rObserved) - Sample$rResid
   Sample$trueFlux <- Sample$rObserved * Sample$Q * 86.4
   Sample$trueLogF <- log(Sample$trueFlux)

R/readNWISSample.r

@@ -67,7 +67,7 @@ readNWISSample <- function(siteNumber,
                                            expanded = TRUE)
     totalColumns <- c("sample_dt",  "remark_cd",  "result_va")
 
-    extras <- rawSample[, c("medium_cd", "hyd_cond_cd", "samp_type_cd", 
+    extras <- rawSample[, c("sample_dt", "medium_cd", "hyd_cond_cd", "samp_type_cd", 
                             "hyd_event_cd", "dqi_cd", "rpt_lev_cd")]
 
     if(length(unique(rawSample$medium_cd)) > 1){
@@ -80,9 +80,13 @@ readNWISSample <- function(siteNumber,
   if(nrow(rawSample) > 0){
     compressedData <- compressData(rawSample[,totalColumns],
                                    verbose = verbose)
+
     Sample <- populateSampleColumns(compressedData)
     if(!multi_pcodes){
-      Sample <- cbind(Sample, extras)
+      Sample <- merge(x = Sample, y = extras, 
+                      by.x = "Date",
+                      by.y = "sample_dt", 
+                      all.x = TRUE)
     }
 
   } else {

R/setupYears.R

@@ -70,7 +70,7 @@ setupYears <- function(localDaily, paLong = 12, paStart = 10) {
 
   numYears <- nrow(StartEndSeq)
 
-  DecYear<-rep(NA,numYears)
+  DecYear <- rep(NA,numYears)
   Q <- rep(NA,numYears)
   Conc <- rep(NA,numYears)
   Flux <- rep(NA,numYears)
@@ -158,7 +158,7 @@ setupYears <- function(localDaily, paLong = 12, paStart = 10) {
 
   AnnualResults <- AnnualResults[!is.na(AnnualResults$DecYear),]
 
-  AnnualResults <- na.omit(AnnualResults)
+  # AnnualResults <- na.omit(AnnualResults)
 
   return(AnnualResults)		
 }