Updates from EGRET.

Merge branch 'master' of github.com:USGS-R/EGRET into usgsEGRET

Conflicts:
	DESCRIPTION
	NAMESPACE
	inst/doc/EGRET.pdf

DESCRIPTION

@@ -10,17 +10,20 @@ Description: Statistics and graphics for streamflow history,
     water quality trends, and the statistical modeling algorithm: Weighted
     Regressions on Time, Discharge, and Season (WRTDS).
 License: CC0
-Date: 2015-05-08
+Date: 2015-07-23
 Depends:
     R (>= 3.0)
 Imports:
     dataRetrieval (>= 2.0.1),
     survival,
     fields,
-    stats,
     lubridate,
     methods,
-    smwrGraphs
+    smwrGraphs,
+    utils,
+    graphics,
+    stats,
+    grDevices
 Suggests:
     xtable,
     knitr,

NAMESPACE

@@ -107,9 +107,12 @@ exportClasses(fluxUnit)
 exportClasses(monthLabel)
 exportClasses(qUnit)
 import(dataRetrieval)
+import(grDevices)
+import(graphics)
 import(methods)
 import(smwrGraphs)
+import(stats)
 import(survival)
+import(utils)
 importFrom(fields,interp.surface)
 importFrom(lubridate,decimal_date)
-importFrom(stats,filter)

R/EGRET.R

@@ -21,6 +21,10 @@
 #'  and produce graphs and tables of data and results from these analyses.
 #'
 #' @name EGRET-package
+#' @import utils
+#' @import graphics
+#' @import stats
+#' @import grDevices
 #' @docType package
 #' @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 
@@ -37,6 +41,8 @@ NULL
 #' @name Choptank_eList
 #' @docType data
 #' @keywords water quality data
+#' @examples 
+#' head(Choptank_eList$Daily)
 NULL
 
 #' Constants included with EGRET

R/modelEstimation.R

@@ -1,3 +1,7 @@
+.onAttach <- function(libname, pkgname) {
+  packageStartupMessage("This information is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The information has not received final approval by the U.S. Geological Survey (USGS) and is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the information. Although this software program has been used by the USGS, no warranty, expressed or implied, is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.")
+}
+
 #' Estimation process for the WRTDS (Weighted Regressions on Time, Discharge, and Season)
 #'
 #' This one function does a jack-knife cross-validation of a WRTDS model, fits the surface
@@ -146,4 +150,3 @@ setUpEstimation<-function(eList,
   return(eList)
 
 }
-

R/populateDaily.r

@@ -22,7 +22,6 @@
 #' Q7 \tab numeric \tab 7 day running average of Q \cr
 #' Q30 \tab numeric \tab 30 day running average of Q \cr
 #' }
-#' @importFrom stats filter
 #' @seealso \code{\link{readNWISDaily}}, \code{\link{readUserDaily}}
 #' @export
 #' @examples

R/readMetaData.r

@@ -108,7 +108,7 @@ readWQPInfo <- function(siteNumber, parameterCd, interactive=TRUE){
     siteInfo$constitAbbrev <- parameterData$parameter_cd
 
   } else {
-    siteInfo <- dataRetrieval::whatWQPsites(siteid=siteNumber, characteristicName=parameterCd)
+    siteInfo <- dataRetrieval::whatWQPsites(siteid=siteNumber, characteristicName=URLencode(parameterCd))
 
     siteInfo$param.nm <- parameterCd
     siteInfo$param.units <- ""