Merge pull request #210 from ldecicco-USGS/master

Adding a few columns to runPairs output

.Rbuildignore

@@ -19,3 +19,4 @@ DISCLAIMER.md
 code.json
 hexSticker.R
 ^docs$
+EGRET.Rcheck

.travis.yml

@@ -6,7 +6,6 @@
 
 language: r
 cache: packages
-dist: trusty
 
 matrix:
   include:
@@ -27,20 +26,20 @@ repos:
 
 env:
    global:
-     - R_BUILD_ARGS="--no-vignettes --no-manual"
-     - R_CHECK_ARGS="--no-vignettes --no-manual --as-cran"
      - NOT_CRAN="true"
      - _R_CHECK_FORCE_SUGGESTS_=false
-
+
+r_build_args: --no-build-vignettes --no-manual --no-resave-data
+r_check_args: --no-build-vignettes --no-manual --as-cran    
 warnings_are_errors: true
 
 r_github_packages:
   - jimhester/covr
 
 script: 
   - |
-    R CMD build .
-    travis_wait 20 R CMD check EGRET*tar.gz
+    R CMD build . --no-build-vignettes --no-manual --no-resave-data
+    travis_wait 20 R CMD check EGRET*tar.gz --no-build-vignettes --no-manual --as-cran
 
 after_success:
   - if [[ "${R_CODECOV}" ]]; then travis_wait 20 R -e 'covr::coveralls()'; fi

R/egret_objects.R

@@ -55,11 +55,11 @@ as.egret <- function(INFO, Daily, Sample=NA, surfaces=NA) {
                 Sample=Sample, 
                 surfaces=surfaces)
 
-  if(!is.na(Daily) && !("Q" %in% names(Daily))){
+  if(!all(is.na(Daily)) && !("Q" %in% names(Daily))){
     stop("Missing column 'Q' in Daily dataframe.")
   }
 
-  if(!is.na(Sample) && !all((c("ConcLow","ConcHigh","Uncen","ConcAve") %in% names(Sample)))){
+  if(!all(is.na(Sample)) && !all((c("ConcLow","ConcHigh","Uncen","ConcAve") %in% names(Sample)))){
     message("\nPlease double check that the Sample dataframe is correctly defined.")
     message("\nMissing columns:", c("ConcLow","ConcHigh","Uncen","ConcAve")[!(c("ConcLow","ConcHigh","Uncen","ConcAve") %in% names(Sample))])
   }
@@ -68,7 +68,7 @@ as.egret <- function(INFO, Daily, Sample=NA, surfaces=NA) {
     message("\nPlease double check that the INFO dataframe is correctly defined.")
   }
 
-  if(!is.na(surfaces) && 14 != nrow(surfaces)){
+  if(exists("surfaces") && isTRUE(14 != nrow(surfaces))){
     message("\nPlease double check that the surfaces matrix is correctly defined.")
   }
 

R/readNWISDaily.r

@@ -1,8 +1,6 @@
 #' Import NWIS Daily Data for EGRET analysis
 #'
 #' Imports daily data from NWIS web service. This function gets the data from here: \url{https://waterservices.usgs.gov/}
-#' A list of parameter codes can be found here: \url{https://nwis.waterdata.usgs.gov/nwis/pmcodes/}
-#' A list of statistic codes can be found here: \url{https://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
 #'
 #' @param siteNumber character USGS site number.  This is usually an 8 digit number
 #' @param parameterCd character USGS parameter code.  This is usually an 5 digit number.

R/readNWISSample.r

@@ -1,6 +1,6 @@
 #' Import NWIS Sample Data for EGRET analysis
 #'
-#' Imports data from NWIS web service. This function gets the data from here: \url{https://nwis.waterdata.usgs.gov/nwis/qwdata/}
+#' Imports data from NWIS web service. 
 #' A list of parameter and statistic codes can be found here: \url{https://help.waterdata.usgs.gov/codes-and-parameters}
 #' For raw data, use \code{\link[dataRetrieval]{readNWISqw}} from the dataRetrieval package.  This function will retrieve the raw data, and compress it (summing constituents). See
 #' section 3.2.4 of the vignette for more details.

R/runPairs.R

@@ -56,6 +56,15 @@
 #' x20 \tab The results using the CQR for year 2, but using the QD for the entire period. \cr
 #' x22 \tab The results for the CQR for year 2, but using the QD specified by the user for year 2. \cr
 #' }
+#' Additionally, there is an attribute on the data frame "Other", containing
+#' a list that includes minNumObs=minNumObs, minNumUncen, windowY, windowQ, 
+#' windowS, wall, edgeAdjust, QStartDate, QEndDate, PercentChangeConc, and PercentChangeFlux.
+#' 
+#' PercentChangeConc, and PercentChangeFlux are vectors with:
+#' Total Percent Change  is the Total Change divided by x11
+#' CQTC Percent is the CQTC divided by x11
+#' QTC Percent  is the QTC divided by x11
+#' 
 #' @examples 
 #' eList <- Choptank_eList
 #' year1 <- 1985
@@ -321,9 +330,20 @@ runPairs <- function(eList, year1, year2, windowSide,
   cDeltaTotal <- c22 - c11
   cRSpart <- c20 - c10
   cFDpart <- cDeltaTotal - cRSpart
+
   fDeltaTotal <- f22 - f11
   fRSpart <- f20 - f10
   fFDpart <- fDeltaTotal - fRSpart
+
+  totChangePct_conc <- 100*cDeltaTotal/c11
+  totChangePct_flux <- 100*fDeltaTotal/f11
+
+  CQTC_percent_conc <- 100*cRSpart / c11 # CQTC Percent
+  QTC_percent_conc  <- 100*cFDpart / c11 # Q Trend Component Percent
+
+  CQTC_percent_flux <- 100*fRSpart / f11
+  QTC_percent_flux  <- 100*fFDpart / f11
+
   pairResults <- as.data.frame(matrix(ncol = 7, nrow = 2))
   colnames(pairResults) <- c("TotalChange", "CQTC", "QTC", 
                              "x10", "x11", "x20", "x22")
@@ -352,7 +372,13 @@ runPairs <- function(eList, year1, year2, windowSide,
                 wall=wall,
                 edgeAdjust=edgeAdjust,
                 QStartDate = as.Date(QStartDate), 
-                QEndDate = as.Date(QEndDate))
+                QEndDate = as.Date(QEndDate),
+                PercentChangeConc = c("Total Percent Change" = totChangePct_conc, 
+                                      "CQTC Percent" = CQTC_percent_conc, 
+                                      "QTC Percent" = QTC_percent_conc),
+                PercentChangeFlux = c("Total Percent Change" = totChangePct_flux, 
+                                      "CQTC Percent" = CQTC_percent_flux, 
+                                      "QTC Percent" = QTC_percent_flux))
 
   attr(pairResults, "Other") <- Other
 
@@ -364,23 +390,23 @@ runPairs <- function(eList, year1, year2, windowSide,
         as.character(sample1EndDate), "\n")
   cat("\n Change estimates ", year2, " minus ", year1, "\n")
   totChange <- format(pairResults[1, 1], digits = 3)
-  totChangePct <- format(100 * ((c22 - c11)/c11), digits = 2)
+  totChangePct_conc_f <- format(totChangePct_conc, digits = 2)
   cat("\n For concentration: total change is ", totChange, 
       "mg/L")
-  cat("\n expressed as Percent Change is ", totChangePct, "%")
-  pctRS <- format(100 * (cRSpart/c11), digits = 2)
-  pctFD <- format(100 * (cFDpart/c11), digits = 2)
+  cat("\n expressed as Percent Change is ", totChangePct_conc_f, "%")
+  pctRS <- format(CQTC_percent_conc, digits = 2)
+  pctFD <- format(QTC_percent_conc, digits = 2)
   cat("\n\n Concentration v. Q Trend Component ", pctRS, "%\n       Q Trend Component            ", 
       pctFD, "% \n\n")
   totChange <- format(pairResults[2, 1], digits = 3)
-  totChangePct <- format(100 * ((f22 - f11)/f11), digits = 2)
+  totChangePct_flux_f <- format((totChangePct_flux), digits = 2)
   cat("\n For flux: total change is ", totChange, "million kg/year")
-  cat("\n expressed as Percent Change is ", totChangePct, "%")
-  pctRS <- format(100 * (fRSpart/f11), digits = 2)
-  pctFD <- format(100 * (fFDpart/f11), digits = 2)
+  cat("\n expressed as Percent Change is ", totChangePct_flux_f, "%")
+  pctRS <- format(CQTC_percent_flux, digits = 2)
+  pctFD <- format(QTC_percent_flux, digits = 2)
   cat("\n\n Concentration v. Q Trend Component ", pctRS, "%\n       Q Trend Component            ", 
       pctFD, "% \n\n")
-  print(pairResults, digits = 2)
+  print(pairResults[,1:7], digits = 2)
   return(pairResults)
 
 }

README.Rmd

@@ -20,7 +20,6 @@ knitr::opts_chunk$set(
 # EGRET 
 
 [![travis](https://travis-ci.org/USGS-R/EGRET.svg?branch=master)](https://travis-ci.org/USGS-R/EGRET)
-[![Build status](https://ci.appveyor.com/api/projects/status/i2hr35abwxx85vgs?svg=true)](https://ci.appveyor.com/project/ldecicco-USGS/EGRET)
 [![Coverage Status](https://coveralls.io/repos/github/USGS-R/EGRET/badge.svg?branch=master)](https://coveralls.io/github/USGS-R/EGRET?branch=master)
 [![status](https://img.shields.io/badge/USGS-Research-blue.svg)](https://owi.usgs.gov/R/packages.html#research)
 [![CRAN version](http://www.r-pkg.org/badges/version/EGRET)](https://cran.r-project.org/package=EGRET)

README.md

@@ -2,8 +2,6 @@ EGRET
 =====
 
 [![travis](https://travis-ci.org/USGS-R/EGRET.svg?branch=master)](https://travis-ci.org/USGS-R/EGRET)
-[![Build
-status](https://ci.appveyor.com/api/projects/status/i2hr35abwxx85vgs?svg=true)](https://ci.appveyor.com/project/ldecicco-USGS/EGRET)
 [![Coverage
 Status](https://coveralls.io/repos/github/USGS-R/EGRET/badge.svg?branch=master)](https://coveralls.io/github/USGS-R/EGRET?branch=master)
 [![status](https://img.shields.io/badge/USGS-Research-blue.svg)](https://owi.usgs.gov/R/packages.html#research)