Major changes with much of the src placed in inlmisc

.Rbuildignore

@@ -1,7 +1,10 @@
-.gitattributes
-.gitignore
-.RData
-.Rhistory
+^\.gitattributes$
+^\.gitignore$
+^\.RData$
+^\.Rhistory$
+^Makefile$
+^\.travis\.yml$
+
 extdata/.*[.]csv$
 extdata/.*[.]kml$
 extdata/.*[.]md$

.gitignore

@@ -1,6 +1,9 @@
-/20*/
 /.RData
 /.Rhistory
 /*.tar.gz
 /*.zip
+
+/src-i386
+/src-x64
+
 Thumbs.db

DESCRIPTION

@@ -1,26 +1,44 @@
 Package: wrv
-Type: Package
-Version: 1.0.3
-Date: 2016-8-12
 Title: Wood River Valley Groundwater-Flow Model
-Author: Jason C. Fisher
-Maintainer: Jason C. Fisher <[email protected]>
-Depends: R (>= 3.2.0), sp, rgdal, raster
-Imports: methods, rgeos, igraph, dplyr
-Suggests: RCurl, knitr, xtable, sfsmisc, animation, viridis, colorspace
-SystemRequirements: PEST (>= 13.0, optional)
+Version: 1.1.0
+Authors@R: person("Jason", "Fisher", email="[email protected]", role=c("aut", "cre"))
 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 1.2, a U.S. Geological Survey groundwater-flow model.
+    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.
+Depends:
+    R (>= 3.2.0)
+Imports:
+    dplyr,
+    grDevices,
+    graphics,
+    inlmisc,
+    methods,
+    sp,
+    stats,
+    raster,
+    rgdal,
+    rgeos
+Suggests:
+    animation,
+    dataRetrieval,
+    git2r,
+    knitr,
+    leaflet,
+    sfsmisc,
+    viridis,
+    xtable
+SystemRequirements: PEST (>= 13.0, optional)
 License: CC0
 Copyright: This software is in the public domain because it contains materials
-  that originally came from the United States Geological Survey (USGS), an
-  agency of the United States Department of Interior. For more information, see
-  the official USGS copyright policy at
-  http://www.usgs.gov/visual-id/credit_usgs.html#copyright
+    that originally came from the United States Geological Survey (USGS), an
+    agency of the United States Department of Interior. For more information,
+    see the official USGS copyright policy at
+    https://www2.usgs.gov/visual-id/credit_usgs.html
 URL: https://github.com/USGS-R/wrv
 BugReports: https://github.com/USGS-R/wrv/issues
-ByteCompile: yes
-LazyData: yes
+Encoding: UTF-8
+ByteCompile: true
+LazyData: true
 LazyDataCompression: xz
 VignetteBuilder: knitr
+RoxygenNote: 5.0.1

Makefile

@@ -0,0 +1,50 @@
+# prepare the package for release
+
+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
+
+docs:
+	R -q -e 'devtools::document()';\
+	R -q -e 'devtools::clean_dll()';\
+
+build:
+	cd ..;\
+	R CMD build --no-build-vignettes $(PKGSRC);\
+
+install: build
+	cd ..;\
+	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz;\
+
+check:
+	cd ..;\
+	R CMD check --no-build-vignettes --as-cran $(PKGNAME)_$(PKGVERS).tar.gz;\
+
+rd2tex:
+	cd ..;\
+	R CMD Rd2pdf --no-clean --no-preview --force $(PKGSRC);\
+	cp -f .Rd2pdf*/Rd2.tex $(PKGSRC)/inst/misc;\
+	$(RM) $(PKGSRC).pdf;\
+	$(RM) -r .Rd2pdf*;\
+
+vignettes: rd2tex
+	R -q -e 'devtools::build_vignettes()';\
+	R -q -e 'tools::compactPDF(paths='\''inst/doc'\'', gs_quality='\''ebook'\'')';\
+
+datasets:
+	cd ..;\
+	R -q -e 'knitr::purl(input='\''$(PKGSRC)/vignettes/$(APPXC).Rnw'\'')';\
+	Rscript $(APPXC).R
+	mkdir -p $(PKGSRC)/data;\
+	cp -i data/*.rda $(PKGSRC)/data;\
+	$(RM) $(APPXC).R;\
+	$(RM) -r data;\
+
+clean:
+	cd ..;\
+	$(RM) -r $(PKGNAME).Rcheck/;\
+
+.PHONY: all docs build install check rd2tex vignettes datasets clean

NAMESPACE

@@ -1,44 +1,9 @@
-
-importFrom("grDevices", "axisTicks", "col2rgb", "dev.cur", "dev.new", "dev.off",
-           "dev.size", "extendrange", "grey", "png", "rainbow", "xy.coords")
-importFrom("graphics", "abline", "arrows", "axTicks", "axis", "axis.Date",
-           "box", "grconvertX", "grconvertY", "layout", "matplot", "mtext",
-           "par", "plot.new", "plot.window", "polygon", "rect", "segments",
-           "strheight", "strwidth", "symbols", "title")
-importFrom("methods", "as", "slot", "slot<-")
-importFrom("stats", "approxfun", "dist", "integrate", "median", "na.omit", "sd")
-importFrom("utils", "read.csv", "untar", "unzip", "write.csv", "write.table")
-
-import("sp", "rgdal", "raster")
-
-importFrom("rgeos", "append.poly", "gArea", "gBuffer", "gCentroid",
-           "gDifference", "gDistance", "gIntersection", "gIntersects",
-           "gIsValid", "gUnaryUnion", "gUnion")
-importFrom("igraph", "clusters")
-importFrom("dplyr", "arrange", "bind_rows", "filter", "group_by_", "left_join",
-           "mutate", "summarise_")
-
-export("AddBubbles",
-       "AddColorKey",
-       "AddInsetMap",
-       "AddScaleBar",
-       "BumpDisconnectCells",
-       "BumpRiverStage",
-       "DownloadFile",
-       "ExportRasterStack",
-       "ExtractAlongTransect",
-       "GetDaysInMonth",
-       "GetSeasonalMult",
-       "GetWellConfig",
-       "PlotCrossSection",
-       "PlotGraph",
-       "PlotMap",
-       "ReadModflowBinary",
-       "ReplaceInTemplate",
-       "RmSmallCellChunks",
-       "RunWaterBalance",
-       "SetPolygons",
-       "SummariseBudget",
-       "ToScientific",
-       "UpdateWaterBudget",
-       "WriteModflowInput")
+# Generated by roxygen2: do not edit by hand
+
+export(GetSeasonalMult)
+export(GetWellConfig)
+export(RunWaterBalance)
+export(UpdateWaterBudget)
+export(WriteModflowInput)
+import(raster)
+import(sp)