Merge pull request #16 from jfisher-usgs/master

Merge with upstream
USGS-R · Apr 10, 2018 · 65798d7 · 65798d7
2 parents 22e764e + 58eb367
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,10 @@
 Package: wrv
 Title: Wood River Valley Groundwater-Flow Model
-Version: 1.1.3.9000
-Authors@R: person(given=c("Jason", "C."), family="Fisher", role=c("aut", "cre"), email="jfisher@usgs.gov")
+Version: 1.1.4
+Authors@R: c(
+    person(given=c("Jason", "C."), family="Fisher", role=c("aut", "cre"), email="jfisher@usgs.gov", comment=c(ORCID="0000-0001-9032-8912")),
+    person(given=c("Allan", "H."), family="Wylie", role="ctb", email="Allan.Wylie@idwr.idaho.gov"),
+    person(given="Jennifer", family="Sukow", role="ctb", email="Jennifer.Sukow@idwr.idaho.gov"))
 Description: A processing program for the groundwater-flow model of the Wood
     River Valley aquifer system, south-central Idaho. Included in the package is
     MODFLOW-USG version 1.3, a U.S. Geological Survey groundwater-flow model.
@@ -24,7 +27,7 @@ Suggests:
     rgdal,
     rgeos,
     sfsmisc,
-    viridis,
+    viridisLite,
     xtable
 SystemRequirements: PEST (>= 13.0, optional)
 License: CC0

diff --git a/Makefile b/Makefile
@@ -1,11 +1,18 @@
-# prepare the package for release
+# Prepare package for release
+#
+# Note that 'AppendixC' and 'AppendixD' are built separately using R commands:
+#   setwd("*")
+#   knitr::knit2pdf("sir20165080_Appendix*.Rnw")
+#   tools::compactPDF(paths="sir20165080_Appendix*.pdf", gs_quality="ebook")
+#   knitr::purl("sir20165080_Appendix*.Rnw")
+#
 
 PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
 PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
 PKGSRC  := $(shell basename `pwd`)
 APPXC   := sir20165080_AppendixC
 
-all: docs install check clean
+all: docs rd2tex install check clean
 
 docs:
 	R -q -e 'devtools::document()';\
@@ -30,7 +37,7 @@ rd2tex:
 	$(RM) $(PKGSRC).pdf;\
 	$(RM) -r .Rd2pdf*;\
 
-vignettes: rd2tex
+vignettes:
 	R -q -e 'devtools::build_vignettes()';\
 	R -q -e 'tools::compactPDF(paths='\''inst/doc'\'', gs_quality='\''ebook'\'')';\
 

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,6 @@
-# wrv 1.1.3.9000
+# wrv 1.1.4
+
+- Substitute the recommended **viridis** package for its 'lite' version **viridisLite**.
 
 - In `GetSeasonalMult`, enable extrapolation of time series data.
 

diff --git a/R/zzz.R b/R/zzz.R
@@ -1,21 +1,9 @@
 .onAttach <- function(lib, pkg) {
   if (interactive()) {
     ver <- read.dcf(file.path(lib, pkg, "DESCRIPTION"), "Version")
-    packageStartupMessage(pkg, ": version: ", ver)
-    if (ver < 1 || grepl("\\.9[0-9]{3}$", ver)) {
-      s <- paste("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.")
-      packageStartupMessage(paste(strwrap(s, indent=1), collapse="\n "))
-    }
+    msg <- "USGS Research Package: https://owi.usgs.gov/R/packages.html#research"
+    packageStartupMessage(paste(strwrap(msg), collapse="\n"))
   }
-
   raster::rasterOptions(standardnames=FALSE)
   invisible()
 }
diff --git a/README.md b/README.md
@@ -1,7 +1,6 @@
 # wrv
 
 [![Travis-CI Build Status](https://travis-ci.org/USGS-R/wrv.svg?branch=master)](https://travis-ci.org/USGS-R/wrv)
-[![CC0](https://img.shields.io/badge/license-CC0--1.0-brightgreen.svg)](https://creativecommons.org/publicdomain/zero/1.0/)
 [![USGS Category](https://img.shields.io/badge/USGS-Research-blue.svg)](https://owi.usgs.gov/R/packages.html#research)
 
 ## Overview
@@ -28,7 +27,7 @@ install.packages("wrv", repos = repos, dependencies = TRUE)
 Or use **devtools** to install the development version from GitHub.
 
 ```r
-devtools::install_github("USGS-R/wrv")
+devtools::install_github("USGS-R/wrv", dependencies = TRUE)
 ```
 
 ## Run
@@ -47,19 +46,20 @@ help(package = "wrv")
 
 See [training material](https://jfisher-usgs.github.io/wrv-training/) for example applications using the **wrv** package.
 
-## Bugs
+## Contact
 
 Please consider reporting bugs and asking questions on the [Issues page](https://github.com/USGS-R/wrv/issues).
 
 ## Disclaimer
 
-This software is in the public domain because it contains materials that originally came from the USGS,
-an agency of the United States Department of Interior.
-For more information, see the
-[official USGS copyright policy](https://www2.usgs.gov/visual-id/credit_usgs.html "official USGS copyright policy").
+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,
+Although this software program has been used by the U.S. Geological Survey (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.
-
-This software is provided "AS IS."
diff --git a/inst/doc/sir20165080.Rnw b/inst/doc/sir20165080.Rnw
@@ -10,11 +10,8 @@
 
 \begin{document}
 
-\title{U.S. Geological Survey \protect\\ Scientific Investigations Report 2016-5080\vspace{2ex}}
+\title{U.S. Geological Survey \protect\\ Scientific Investigations Report 2016-5080}
 \author{}
-\date{}
-\pretitle{\begin{flushleft}\LARGE\bfseries\sffamily}
-\posttitle{\end{flushleft}}
 \maketitle
 
 % =========================================================================

diff --git a/inst/doc/sir20165080_AppendixA.Rnw b/inst/doc/sir20165080_AppendixA.Rnw
@@ -24,11 +24,8 @@ t0 <- Sys.time()
 try(knitr::opts_chunk$set(tidy=FALSE, comment="#", fig.align="center"), silent=TRUE)
 @
 
-\title{Appendix A.\enspace An Introduction to the R-Package `wrv'\vspace{2ex}}
+\title{Appendix A.\enspace An Introduction to the R-Package `wrv'}
 \author{}
-\date{}
-\pretitle{\begin{flushleft}\LARGE\bfseries\sffamily}
-\posttitle{\end{flushleft}}
 \maketitle
 
 \tableofcontents

diff --git a/inst/doc/sir20165080_AppendixC.R b/inst/doc/sir20165080_AppendixC.R
@@ -50,7 +50,7 @@ for (i in files) unzip(i, exdir = dirname(i))
 ## ----download_ned, message=FALSE-----------------------------------------
 ftp <- "ftp://rockyftp.cr.usgs.gov/vdelivery/Datasets/Staged/NED/13/ArcGrid/n44w115.zip"
 file <- file.path(tempdir(), basename(ftp))
-download.file(ftp, file)
+download.file(ftp, file, method = "curl", quiet = TRUE)
 unzip(file, exdir = dir.in)
 
 ## ----create_data_dir-----------------------------------------------------

diff --git a/inst/doc/sir20165080_AppendixC.Rnw b/inst/doc/sir20165080_AppendixC.Rnw
@@ -53,11 +53,8 @@ CheckStatus <- function(s) {
 }
 @
 
-\title{Appendix C. Creating Datasets for the R-Package `wrv'\vspace{2ex}}
+\title{Appendix C. Creating Datasets for the R-Package `wrv'}
 \author{}
-\date{}
-\pretitle{\begin{flushleft}\LARGE\bfseries\sffamily}
-\posttitle{\end{flushleft}}
 \maketitle
 
 \tableofcontents
@@ -125,7 +122,7 @@ Download the ZIP file to a temporary directory and uncompress.
 <<download_ned, message=FALSE>>=
 ftp <- "ftp://rockyftp.cr.usgs.gov/vdelivery/Datasets/Staged/NED/13/ArcGrid/n44w115.zip"
 file <- file.path(tempdir(), basename(ftp))
-download.file(ftp, file)
+download.file(ftp, file, method = "curl", quiet = TRUE)
 unzip(file, exdir = dir.in)
 @
 

diff --git a/inst/doc/sir20165080_AppendixD.R b/inst/doc/sir20165080_AppendixD.R
@@ -65,7 +65,7 @@ FmtLength <- function(x, u=c("m", "ft"), conv=m.to.ft) {
   return(s)
 }
 FmtFlow <- function(x, u=c("m\\textsuperscript{3}/d", "acre-ft/yr"), conv=m3.per.d.to.af.per.yr) {
-  FUN <- function(i) ToScientific(i, 1)
+  FUN <- function(i) ToScientific(i, digits=1)
   if (length(x) == 1) {
     s <- vapply(c(x[1], x[1] *  conv), FUN, "")
     s <- sprintf("%s~%s (%s~%s)", s[1], u[1], s[2], u[2])
@@ -1750,7 +1750,8 @@ v <- c(paste("Graph showing", paste0(tolower(substr(v, 1, 1)), substr(v, 2, ncha
 ylab <- paste("Groundwater discharge, in", c("cubic meters per day", "acre-feet per year"))
 col <- "#C80C0B"
 PlotGraph(d.drain.2, ylab=ylab, col=col, fill=paste0(col, "66"),
-          conversion.factor=m3.per.d.to.af.per.yr, scientific=TRUE, center.date.labels=TRUE)
+          conversion.factor=m3.per.d.to.af.per.yr, scientific=FALSE,
+          center.date.labels=TRUE, seq.date.by="year")
 
 ## ----echo=FALSE, message=FALSE-------------------------------------------
 # save R objects that will be used to update the water budget

diff --git a/inst/doc/sir20165080_AppendixD.Rnw b/inst/doc/sir20165080_AppendixD.Rnw
@@ -86,7 +86,7 @@ FmtLength <- function(x, u=c("m", "ft"), conv=m.to.ft) {
   return(s)
 }
 FmtFlow <- function(x, u=c("m\\textsuperscript{3}/d", "acre-ft/yr"), conv=m3.per.d.to.af.per.yr) {
-  FUN <- function(i) ToScientific(i, 1)
+  FUN <- function(i) ToScientific(i, digits=1)
   if (length(x) == 1) {
     s <- vapply(c(x[1], x[1] *  conv), FUN, "")
     s <- sprintf("%s~%s (%s~%s)", s[1], u[1], s[2], u[2])
@@ -98,11 +98,8 @@ FmtFlow <- function(x, u=c("m\\textsuperscript{3}/d", "acre-ft/yr"), conv=m3.per
 }
 @
 
-\title{Appendix D.\enspace Uncalibrated Groundwater-Flow Model for the Wood River Valley Aquifer System, South-Central Idaho\vspace{2ex}}
+\title{Appendix D.\enspace Uncalibrated Groundwater-Flow Model for the Wood River Valley Aquifer System, South-Central Idaho}
 \author{}
-\date{}
-\pretitle{\begin{flushleft}\LARGE\bfseries\sffamily}
-\posttitle{\end{flushleft}}
 \maketitle
 
 \tableofcontents
@@ -2799,7 +2796,8 @@ v <- c(paste("Graph showing", paste0(tolower(substr(v, 1, 1)), substr(v, 2, ncha
 ylab <- paste("Groundwater discharge, in", c("cubic meters per day", "acre-feet per year"))
 col <- "#C80C0B"
 PlotGraph(d.drain.2, ylab=ylab, col=col, fill=paste0(col, "66"),
-          conversion.factor=m3.per.d.to.af.per.yr, scientific=TRUE, center.date.labels=TRUE)
+          conversion.factor=m3.per.d.to.af.per.yr, scientific=FALSE,
+          center.date.labels=TRUE, seq.date.by="year")
 @
 
 % =========================================================================

diff --git a/inst/doc/sir20165080_AppendixE.Rnw b/inst/doc/sir20165080_AppendixE.Rnw
@@ -64,11 +64,8 @@ credit <- paste("Base derived from U.S. Geological Survey National Elevation Dat
                 "Idaho Transverse Mercator projection; North American Datum of 1983.", sep="\n")
 @
 
-\title{Appendix E.\enspace Tributary Basin Underflow into the Wood River Valley Aquifer System, South-Central Idaho\vspace{2ex}}
+\title{Appendix E.\enspace Tributary Basin Underflow into the Wood River Valley Aquifer System, South-Central Idaho}
 \author{}
-\date{}
-\pretitle{\begin{flushleft}\LARGE\bfseries\sffamily}
-\posttitle{\end{flushleft}}
 \maketitle
 
 \tableofcontents

diff --git a/inst/doc/sir20165080_AppendixF.Rnw b/inst/doc/sir20165080_AppendixF.Rnw
@@ -60,15 +60,14 @@ credit <- paste("Base derived from U.S. Geological Survey National Elevation Dat
                 "Idaho Transverse Mercator projection; North American Datum of 1983.", sep="\n")
 @
 
-\title{Appendix F.\enspace Natural Groundwater Recharge and Discharge in the Wood River Valley Aquifer System, South-Central Idaho\vspace{2ex}}
+\title{Appendix F.\enspace Natural Groundwater Recharge and Discharge in the Wood River Valley Aquifer System, South-Central Idaho}
 \author{}
-\date{}
-\pretitle{\begin{flushleft}\LARGE\bfseries\sffamily}
-\posttitle{\end{flushleft}}
 \maketitle
 
 \tableofcontents
 
+\newpage
+
 \renewcommand*\listfigurename{Figures}
 \listoffigures
 

diff --git a/inst/doc/sir20165080_AppendixG.Rnw b/inst/doc/sir20165080_AppendixG.Rnw
@@ -59,11 +59,8 @@ credit <- paste("Base derived from U.S. Geological Survey National Elevation Dat
                 "Idaho Transverse Mercator projection; North American Datum of 1983.", sep="\n")
 @
 
-\title{Appendix G.\enspace Incidental Groundwater Recharge and Pumping Demand in the Wood River Valley Aquifer System, South-Central Idaho\vspace{2ex}}
+\title{Appendix G.\enspace Incidental Groundwater Recharge and Pumping Demand in the Wood River Valley Aquifer System, South-Central Idaho}
 \author{}
-\date{}
-\pretitle{\begin{flushleft}\LARGE\bfseries\sffamily}
-\posttitle{\end{flushleft}}
 \maketitle
 
 \tableofcontents

diff --git a/inst/doc/sir20165080_AppendixH.Rnw b/inst/doc/sir20165080_AppendixH.Rnw
@@ -58,11 +58,8 @@ credit <- paste("Base derived from U.S. Geological Survey National Elevation Dat
                 "Idaho Transverse Mercator projection; North American Datum of 1983.", sep="\n")
 @
 
-\title{Appendix H.\enspace Calibration of the Wood River Valley Groundwater-Flow Model\vspace{2ex}}
+\title{Appendix H.\enspace Calibration of the Wood River Valley Groundwater-Flow Model}
 \author{}
-\date{}
-\pretitle{\begin{flushleft}\LARGE\bfseries\sffamily}
-\posttitle{\end{flushleft}}
 \maketitle
 
 \tableofcontents

diff --git a/inst/misc/Rd2.tex b/inst/misc/Rd2.tex
@@ -14,7 +14,7 @@ \chapter*{}
 \raggedright{}
 \inputencoding{utf8}
 \item[Title]\AsIs{Wood River Valley Groundwater-Flow Model}
-\item[Version]\AsIs{1.1.3}
+\item[Version]\AsIs{1.1.4}
 \item[Description]\AsIs{A processing program for the groundwater-flow model of the Wood
 River Valley aquifer system, south-central Idaho. Included in the package is
 MODFLOW-USG version 1.3, a U.S. Geological Survey groundwater-flow model.}
@@ -34,7 +34,7 @@ \chapter*{}
 rgdal,
 rgeos,
 sfsmisc,
-viridis,
+viridisLite,
 xtable}
 \item[SystemRequirements]\AsIs{PEST (>= 13.0, optional)}
 \item[License]\AsIs{CC0}

diff --git a/inst/misc/miscellaneous.Rnw b/inst/misc/miscellaneous.Rnw
@@ -20,7 +20,7 @@ try(knitr::opts_chunk$set(tidy=FALSE, comment="#", fig.align="center"), silent=T
 grDevices::pdf.options(useDingbats=FALSE)
 options(preferRaster=TRUE, scipen=0, digits=2)
 library(wrv)
-loadNamespace("viridis")
+loadNamespace("viridisLite")
 loadNamespace("xtable")
 
 # Device dimension in inches (width, height)
@@ -369,7 +369,7 @@ breaks <- pretty(log10(x), n=15, na.rm=TRUE)
 at <- breaks[c(TRUE, FALSE)]
 labels <- ToScientific(10^at, digits=1, type="plotmath")
 
-Pal <- function(...) viridis::viridis(...)
+Pal <- function(...) viridisLite::viridis(...)
 FUN <- function(r) {
   r[] <- log10(r[])
   PlotMap(r, breaks=breaks, xlim=usr.map[1:2], ylim=usr.map[3:4],
@@ -935,7 +935,7 @@ PlotMap(crs(hill.shading), xlim=usr.map[1:2], ylim=usr.map[3:4],
 plot(alluvium.extent, border="#FFFFFFCC", add=TRUE)
 xy <- coordinates(getSpatialLinesMidPoints(trib.lines))
 z <- trib.lines@data$mean.flow
-Pal <- function(...) rev(viridis::viridis(..., alpha=0.8))
+Pal <- function(...) rev(viridisLite::viridis(..., alpha=0.8))
 AddPoints(xy, z=z, inches=c(0.03, 0.3), fg="#FFFFFF65", format="d",
           title="Average groundwater flow rate", subtitle="in cubic meters per day",
           bg=Pal, legend.loc="topright", quantile.breaks=TRUE)

diff --git a/vignettes/sir20165080_AppendixC.Rnw b/vignettes/sir20165080_AppendixC.Rnw
@@ -122,7 +122,7 @@ Download the ZIP file to a temporary directory and uncompress.
 <<download_ned, message=FALSE>>=
 ftp <- "ftp://rockyftp.cr.usgs.gov/vdelivery/Datasets/Staged/NED/13/ArcGrid/n44w115.zip"
 file <- file.path(tempdir(), basename(ftp))
-download.file(ftp, file)
+download.file(ftp, file, method = "curl", quiet = TRUE)
 unzip(file, exdir = dir.in)
 @
 

diff --git a/vignettes/sir20165080_AppendixD.Rnw b/vignettes/sir20165080_AppendixD.Rnw
@@ -2796,7 +2796,8 @@ v <- c(paste("Graph showing", paste0(tolower(substr(v, 1, 1)), substr(v, 2, ncha
 ylab <- paste("Groundwater discharge, in", c("cubic meters per day", "acre-feet per year"))
 col <- "#C80C0B"
 PlotGraph(d.drain.2, ylab=ylab, col=col, fill=paste0(col, "66"),
-          conversion.factor=m3.per.d.to.af.per.yr, scientific=TRUE, center.date.labels=TRUE)
+          conversion.factor=m3.per.d.to.af.per.yr, scientific=FALSE,
+          center.date.labels=TRUE, seq.date.by="year")
 @
 
 % =========================================================================

diff --git a/vignettes/sir20165080_AppendixF.Rnw b/vignettes/sir20165080_AppendixF.Rnw
@@ -66,6 +66,8 @@ credit <- paste("Base derived from U.S. Geological Survey National Elevation Dat
 
 \tableofcontents
 
+\newpage
+
 \renewcommand*\listfigurename{Figures}
 \listoffigures