Next (#1)

* Minor change

* Mention The National Map in extdata README

* Minor change

* Fix dead url for model archive

* Add additional files to .gitattributes

* Tidy git attributes

* Fix width bug in AddInsetMap

* Remove type equal to both in install.packages

* Minor change

.gitattributes

@@ -1,34 +1,37 @@
-# https://help.github.com/articles/dealing-with-line-endings
+# See https://help.github.com/articles/dealing-with-line-endings
 
-# This setting will tell git to handle the files specified automatically.
+# Auto detect text files and perform LF normalization
 * text=auto
 
-# This setting tells git to always normalize the files specified. When
-# committed they are stored with LF, on checkout they are converted to the OS's
-# native line endings.
-*.bib text
-*.bst text
-*.csv text
-*.f text
-*.inc text
-*.kml text
-*.md text
-*.note text
-*.R text
-*.Rd text
-*.Rmd text
-*.Rnw text
-*.Rprofile text
-*.txt text
+# Committed text files that are stored with LF and converted to native line endings on checkout.
+*.bib          text
+*.csv          text
+*.f            text
+*.inc          text
+*.kml          text
+*.md           text
+*.R            text
+*.Rd           text
+*.Rmd          text
+*.Rnw          text
+*.tex          text
+*.txt          text
+*.xml          text
+.gitattributes text
+.gitignore     text
+.Rbuildignore  text
+inst/CITATION  text
+DESCRIPTION    text
+LICENSE.note   text
+NAMESPACE      text
+NEWS           text
 
-# This setting tells git that the files specified are not text at all, and it
-# should not try to change them.
+# Text files that should always have LF line endings on checkout.
+src/Makevars text eol=lf
+
+# Files that are binary and should not be modified.
 *.exe binary
 *.pdf binary
 *.rda binary
 *.tif binary
 *.zip binary
-
-# This setting tells git that the files specified should always have LF line
-# endings on checkout.
-Makevars text eol=lf

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: wrv
 Type: Package
 Version: 1.0.3
-Date: 2016-07-05
+Date: 2016-8-12
 Title: Wood River Valley Groundwater-Flow Model
 Author: Jason C. Fisher
 Maintainer: Jason C. Fisher <[email protected]>

R/AddInsetMap.R

@@ -24,9 +24,9 @@ AddInsetMap <- function(p, col=c("#D8D8D8", "#BFA76F"),
   ext <- extent(gUnion(p, b))
 
   if (is.null(width)) {
-    dx <- width * (diff(usr[1:2]) / par("pin")[1])
-  } else {
     dx  <- 0.2 * diff(usr[1:2])
+  } else {
+    dx <- width * (diff(usr[1:2]) / par("pin")[1])
   }
   dy <- dx * (diff(ext[3:4]) / diff(ext[1:2]))
 

R/UpdateWaterBudget.R

@@ -39,7 +39,7 @@ UpdateWaterBudget <- function(dir.run, id,
     write.csv(wrv::efficiency, file=f, quote=FALSE, row.names=FALSE)
   eff <- read.csv(f)
 
-  # Read tributary underflow from calibration file
+  # Read tributary underflow control parameters from calibration file
 
   f <- file.path(dir.run, "trib.csv")
   if (!file.exists(f)) {
@@ -59,7 +59,7 @@ UpdateWaterBudget <- function(dir.run, id,
   mult <- GetSeasonalMult(wrv::gage.disch[, c("Date", "13139510")], reduction,
                           d.in.mv.ave, tr.stress.periods)
   mult <- data.frame(Date=head(tr.stress.periods, -1),
-                     multiplier=rep(mult$multiplier, each=3))
+                     multiplier=rep(mult$multiplier, each=3))  # seasonal to monthly
 
   ave.flows <- wrv::tributaries$Flow
   names(ave.flows) <- wrv::tributaries$Name

README.md

@@ -1,10 +1,14 @@
 # wrv
 
-An [R](http://www.r-project.org/ "The R Project for Statistical Computing") package for processing the groundwater-flow model of the Wood River Valley (WRV) aquifer system, south-central Idaho.
-The groundwater-flow model is described in the associated [model report](http://dx.doi.org/10.3133/sir20165080 "USGS Scientific Investigations Report") and
-[model archive](https://www.sciencebase.gov/catalog/item/577507c1e4b07dd077c70746 "USGS Data Release").
-Included in the package is [MODFLOW-USG](http://water.usgs.gov/ogw/mfusg/ "MODFLOW-USG") version 1.2, a U.S. Geological Survey (USGS) computer code that solves the groundwater-flow equation.
-The set of standards used for coding the **wrv** package is documented in [Google's R Style Guide](https://google.github.io/styleguide/Rguide.xml "Google's R Style Guide").
+An [R](http://www.r-project.org/ "The R Project for Statistical Computing") package for processing the
+groundwater-flow model of the Wood River Valley (WRV) aquifer system, south-central Idaho.
+The groundwater-flow model is described in the associated
+[model report](http://dx.doi.org/10.3133/sir20165080 "USGS Scientific Investigations Report") and
+[model archive](http://dx.doi.org/10.5066/F7C827DT "USGS Data Release").
+Included in the package is [MODFLOW-USG](http://water.usgs.gov/ogw/mfusg/ "MODFLOW-USG") version 1.2,
+a U.S. Geological Survey (USGS) computer code that solves the groundwater-flow equation.
+The set of standards used for coding this package is documented in
+[Google's R Style Guide](https://google.github.io/styleguide/Rguide.xml "Google's R Style Guide").
 
 ## Install
 
@@ -15,7 +19,7 @@ Next, open an R session and install user-contributed R packages from CRAN and th
 
 ```r
 repos <- c("http://owi.usgs.gov/R", getOption("repos"))
-install.packages("wrv", repos = repos, dependencies = TRUE, type = "both")
+install.packages("wrv", repos = repos, dependencies = TRUE)
 ```
 
 ## Run
@@ -38,8 +42,10 @@ Please consider reporting bugs and asking questions on the [Issues page](https:/
 
 ## 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](http://www.usgs.gov/visual-id/credit_usgs.html#copyright/ "official USGS copyright policy").
+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](http://www.usgs.gov/visual-id/credit_usgs.html#copyright/ "official USGS copyright policy").
 
 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,

inst/doc/sir20165080_AppendixA.R

@@ -5,7 +5,7 @@ try(knitr::opts_chunk$set(tidy=FALSE, comment="#", fig.align="center"), silent=T
 ## ----eval=FALSE----------------------------------------------------------
 #  repos <- c("http://owi.usgs.gov/R", getOption("repos"))
 #  update.packages(ask = FALSE, repos = repos)
-#  install.packages("wrv", repos = repos, dependencies = TRUE, type = "both")
+#  install.packages("wrv", repos = repos, dependencies = TRUE)
 
 ## ----warning=FALSE, message=FALSE, results="hide"------------------------
 library("wrv")

inst/doc/sir20165080_AppendixA.Rnw

@@ -75,7 +75,7 @@ That is, start an \R{} session and type the following commands in your \R{}-cons
 <<eval=FALSE>>=
 repos <- c("http://owi.usgs.gov/R", getOption("repos"))
 update.packages(ask = FALSE, repos = repos)
-install.packages("wrv", repos = repos, dependencies = TRUE, type = "both")
+install.packages("wrv", repos = repos, dependencies = TRUE)
 @
 
 \noindent Once the packages are installed, load the \textbf{wrv} package in the current \R{} session:

inst/extdata/README.md

@@ -5,6 +5,8 @@ processing occurs in stages, and the "processed data" from one stage may be cons
 Many of these datasets are composed entirely of data collected from the study site;
 however, a few of the datasets are the result of a preliminary stage of data processing.
 For example, evapotranspiration and precipitation datasets are the result of processing that is not explicitly shown in the **wrv** package.
+The only unprocessed dataset used during model construction and not included under this folder is located on the
+[The National Map](http://nationalmap.gov/) and represents the land surface elevation within the study area.
 
 ## File and Folder Structure
 

inst/misc/readme-template.txt

@@ -222,7 +222,7 @@
 
             repo <- "https://mran.revolutionanalytics.com/snapshot/@{packageDescription('wrv', fields = 'Date')}/"
             pkgs <- c($(pkgs))
-            install.packages(pkgs, repos = repo, type = "both")
+            install.packages(pkgs, repos = repo)
 
         Install the R-package wrv from a distribution file contained within
         the data release. Specify the absolute path to the model archive folder

man/AddInsetMap.Rd

@@ -42,7 +42,7 @@ Used for the side-effect of a inset map drawn on the current graphics device.
 
 \examples{
 PlotMap(alluvium.thickness@crs, bg.image = hill.shading, reg.axs = FALSE)
-AddInsetMap(idaho, width = 1, main.label = list("IDAHO", adj = c(-0.4, -4.9)),
+AddInsetMap(idaho, main.label = list("IDAHO", adj = c(-0.4, -4.9)),
             sub.label = list("Map area", adj = c(0.5, 2.5)), loc = "topright")
 
 graphics.off()

man/UpdateWaterBudget.Rd

@@ -43,8 +43,6 @@ And a binary data file \file{model.rda} containing the following serialized \R o
 \dQuote{lay1.top}, \dQuote{lay1.bot}, \dQuote{lay2.bot}, and \dQuote{lay3.bot}.
 These raster layers describe the geometry of the model grid; that is,
 the upper and lower elevation of model layer 1, and the bottom elevations of model layers 2 and 3.
-In addition to these layers, \code{rs} includes ancillary raster layers \dQuote{lay1.zones}, \dQuote{lay2.zones}, and \dQuote{lay3.zones}
-describing the distribution of hydrogeologic zones in the model grid.
 Missing cell values (equal to \code{NA}) indicate inactive model cells lying outside of the model domain.
 
 \code{misc} is a \code{data.frame} object with miscellaneous seepage,

vignettes/sir20165080_AppendixA.Rnw

@@ -75,7 +75,7 @@ That is, start an \R{} session and type the following commands in your \R{}-cons
 <<eval=FALSE>>=
 repos <- c("http://owi.usgs.gov/R", getOption("repos"))
 update.packages(ask = FALSE, repos = repos)
-install.packages("wrv", repos = repos, dependencies = TRUE, type = "both")
+install.packages("wrv", repos = repos, dependencies = TRUE)
 @
 
 \noindent Once the packages are installed, load the \textbf{wrv} package in the current \R{} session:

vignettes/sir20165080_AppendixD.Rnw

@@ -2811,10 +2811,10 @@ invisible(dev.off())
 
 <<echo=FALSE, message=FALSE>>=
 # save R objects that will be used to update the water budget
-layers <-  c("lay1.top", sprintf("lay%s.bot", 1:3), sprintf("lay%s.zones", 1:3))
+layers <-  c("lay1.top", sprintf("lay%s.bot", 1:3))
 rs <- subset(rs.model, layers)
 save(rs, misc, trib, tr.stress.periods, ss.stress.periods, reduction, d.in.mv.ave,
-     file=file.path(dir.run, "model.rda"), compress=FALSE)
+     file=file.path(dir.run, "model.rda"))
 
 # read raster data from from reference file and store in stack
 FUN <- function(f, mv.flag=1e+09) {