Merge pull request #8 from jfisher-usgs/master

Merge with upstream

.Rbuildignore

@@ -4,7 +4,6 @@
 ^\.Rhistory$
 ^Makefile$
 ^\.travis\.yml$
-
 extdata/.*[.]csv$
 extdata/.*[.]kml$
 extdata/.*[.]md$

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: wrv
 Title: Wood River Valley Groundwater-Flow Model
-Version: 1.1.0.9000
-Authors@R: person("Jason", "Fisher", email="jfisher@usgs.gov", role=c("aut", "cre"))
+Version: 1.1.1
+Authors@R: person(given=c("Jason", "C."), family="Fisher", role=c("aut", "cre"), email="jfisher@usgs.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.
@@ -41,4 +41,4 @@ ByteCompile: true
 LazyData: true
 LazyDataCompression: xz
 VignetteBuilder: knitr
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1

LICENSE.note

@@ -1,5 +1,5 @@
 U.S.Geological Survey Software User Rights Notice
-Copied from http://water.usgs.gov/software/help/notice/ on February 23, 2015. Please check webpage for updates.
+Copied from https://water.usgs.gov/software/help/notice/ on February 23, 2015. Please check webpage for updates.
 
 Software and related material (data and (or) documentation), contained in or furnished in connection with a software distribution, are made available by the U.S. Geological Survey (USGS) to be used in the public interest and in the advancement of science. You may, without any fee or cost, use, copy, modify, or distribute this software, and any derivative works thereof, and its supporting documentation, subject to the following restrictions and understandings.
 

NEWS.md

@@ -1,12 +1,19 @@
-# wrv 1.1.0.9000
+# wrv 1.1.1
 
-- ...
+- Change graphic dimensions for figures in vignettes.
+  Dimensions are now compatible with plotting routines in the latest version of the **inlmisc** package (v0.2.3).
+
+- Set `integer64 = "allow.loss"` (default < rgdal 1.2) in calls to `rgdal::readOGR` function.
+
+- Set `scale.loc = "bottomright"` in calls to `inlmisc::PlotMap` function.
+
+- Update URL links to HTTP Secure
 
 # wrv 1.1.0
 
 - Add suggested package **leaflet**, allows the creation of interactive maps using the 'Leaflet' JavaScript library and the **htmlwidgets** package.
 
-- Update MODFLOW-USG version from 1.2 to 1.3, see [release notes](http://water.usgs.gov/ogw/mfusg/release.txt) for details.
+- Update MODFLOW-USG version from 1.2 to 1.3, see [release notes](https://water.usgs.gov/ogw/mfusg/release.txt) for details.
 
 - Change NEWS file to markdown format.
 

R/GetWellConfig.R

@@ -45,6 +45,9 @@
 #'
 #' @keywords manip
 #'
+#' @import sp
+#' @import raster
+#'
 #' @export
 #'
 #' @examples

R/UpdateWaterBudget.R

@@ -6,7 +6,7 @@
 #'   (2) groundwater pumping at production wells, and
 #'   (3) groundwater underflow in the major tributary valleys.
 #' Specified-flow values are saved to disk by rewriting the
-#' \href{http://water.usgs.gov/ogw/modflow/}{MODFLOW} Well Package file (\file{.wel}).
+#' \href{https://water.usgs.gov/ogw/modflow/}{MODFLOW} Well Package file (\file{.wel}).
 #' Note that this function is executed after each iteration of \href{http://www.pesthomepage.org/}{PEST}.
 #  It may also be run in an interactive \R session to initialize model parameter files.
 #'

R/WriteModflowInput.R

@@ -59,7 +59,7 @@
 #'   listing file (\file{.lst}) and budget file (\file{.bud})
 #'
 #' @details Groundwater flow in the WRV aquifer system is simulated using the
-#'   \href{http://water.usgs.gov/ogw/mfusg/}{MODFLOW-USG} groundwater-flow model.
+#'   \href{https://water.usgs.gov/ogw/mfusg/}{MODFLOW-USG} groundwater-flow model.
 #'   This numerical model was chosen for its ability to solve
 #'   complex unconfined groundwater flow simulations.
 #'   The solver implemented in MODFLOW-USG incorporates the Newton-Raphson formulation for
@@ -68,9 +68,9 @@
 #'   A structured finite-difference grid is implemented in the model to
 #'     (1) simplify discretization,
 #'     (2) keep formats and structures for the MODFLOW-USG packages identical to those of
-#'         \href{http://water.usgs.gov/nrp/gwsoftware/modflow2005/Guide/index.html}{MODFLOW-2005}, and
+#'         \href{https://water.usgs.gov/ogw/modflow/MODFLOW-2005-Guide/index.html}{MODFLOW-2005}, and
 #'     (3) allow any MODFLOW post-processor to be used to analyze the results of the MODFLOW-USG simulation
-#'         (such as \href{http://water.usgs.gov/nrp/gwsoftware/modelviewer/ModelViewer.html}{Model Viewer}).
+#'         (such as \href{https://water.usgs.gov/nrp/gwsoftware/modelviewer/ModelViewer.html}{Model Viewer}).
 #'
 #'   Model input files are written to \code{dir.run} and include the following MODFLOW Package files:
 #'   Name (\file{.nam}), Basic (\file{.ba6}), Discretization (\file{.dis}),
@@ -121,15 +121,18 @@
 #'   Columbus, Ohio State University School of Earth Sciences.
 #'
 #'   Niswonger, R.G., Panday, Sorab, and Ibaraki, Motomu, 2011, MODFLOW-NWT, A Newton formulation for MODFLOW-2005:
-#'   U.S. Geological Survey Techniques and Methods 6-A37, 44 p., available at \url{http://pubs.usgs.gov/tm/tm6a37/}.
+#'   U.S. Geological Survey Techniques and Methods 6-A37, 44 p., available at \url{https://pubs.usgs.gov/tm/tm6a37/}.
 #'
 #'   Panday, Sorab, Langevin, C.D., Niswonger, R.G., Ibaraki, Motomu, and Hughes, J.D., 2013, MODFLOW-USG version 1:
 #'   An unstructured grid version of MODFLOW for simulating groundwater flow and tightly coupled processes using a
 #'   control volume finite-difference formulation: U.S. Geological Survey Techniques and Methods, book 6, chap. A45,
-#'   66 p., available at \url{http://pubs.usgs.gov/tm/06/a45/}.
+#'   66 p., available at \url{https://pubs.usgs.gov/tm/06/a45/}.
 #'
 #' @keywords IO
 #'
+#' @import sp
+#' @import raster
+#'
 #' @export
 #'
 #' @examples

R/data.R

@@ -12,7 +12,7 @@
 #' @references Bartolino, J.R., and Adkins, C.B., 2012,
 #'   Hydrogeologic framework of the Wood River Valley aquifer system, south-central Idaho:
 #'   U.S. Geological Survey Scientific Investigations Report 2012-5053, 46 p.,
-#'   available at \url{http://pubs.usgs.gov/sir/2012/5053/}.
+#'   available at \url{https://pubs.usgs.gov/sir/2012/5053/}.
 #'
 #' @keywords datasets
 #'
@@ -39,7 +39,7 @@
 #' @references Bartolino, J.R., and Adkins, C.B., 2012,
 #'   Hydrogeologic framework of the Wood River Valley aquifer system, south-central Idaho:
 #'   U.S. Geological Survey Scientific Investigations Report 2012-5053, 46 p.,
-#'   available at \url{http://pubs.usgs.gov/sir/2012/5053/}.
+#'   available at \url{https://pubs.usgs.gov/sir/2012/5053/}.
 #'
 #' @keywords datasets
 #'
@@ -65,7 +65,7 @@
 #' @references Bartolino, J.R., and Adkins, C.B., 2012,
 #'   Hydrogeologic framework of the Wood River Valley aquifer system, south-central Idaho:
 #'   U.S. Geological Survey Scientific Investigations Report 2012-5053, 46 p.,
-#'   available at \url{http://pubs.usgs.gov/sir/2012/5053/}.
+#'   available at \url{https://pubs.usgs.gov/sir/2012/5053/}.
 #'
 #' @keywords datasets
 #'
@@ -206,7 +206,7 @@
 #'   Blaine County, Idaho: Boise, Idaho Department of Water Resources, Water Information Bulletin 44,
 #'   42 p., 5 plates in pocket, accessed January 31, 2012.
 #'   Also published as U.S. Geological Survey Open-File report 77-456, 66 p.,
-#'   available at \url{http://pubs.er.usgs.gov/pubs/ofr/ofr77456}.
+#'   available at \url{https://pubs.er.usgs.gov/publication/ofr77456}.
 #'
 #' @keywords datasets
 #'
@@ -378,8 +378,8 @@
 #'   Idaho Transverse Mercator projection (\href{https://www.idwr.idaho.gov/GIS/IDTM/}{IDTM}).
 #'
 #' @source U.S. Geological Survey, accessed on March 27, 2015;
-#'   a Keyhole Markup Language (\href{http://en.wikipedia.org/wiki/Kml}{KML}) file created in
-#'   \href{http://www.google.com/earth/}{Google Earth} with polygons drawn by hand in
+#'   a Keyhole Markup Language (\href{https://en.wikipedia.org/wiki/Kml}{KML}) file created in
+#'   \href{https://www.google.com/earth/}{Google Earth} with polygons drawn by hand in
 #'   areas of known drains.
 #'
 #' @keywords datasets
@@ -550,17 +550,17 @@
 #'   \describe{
 #'     \item{Date}{date during which discharge was averaged.}
 #'     \item{13135500}{daily mean discharge in cubic meters per day, recorded at the USGS
-#'       \href{http://waterdata.usgs.gov/id/nwis/uv/?site_no=13135500}{13135500}
+#'       \href{https://waterdata.usgs.gov/id/nwis/uv/?site_no=13135500}{13135500}
 #'       Big Wood River near Ketchum streamgage.}
 #'     \item{13139510}{daily mean discharge in cubic meters per day, recorded at the USGS
-#'       \href{http://waterdata.usgs.gov/id/nwis/uv/?site_no=13139510}{13139510}
+#'       \href{https://waterdata.usgs.gov/id/nwis/uv/?site_no=13139510}{13139510}
 #'       Big Wood River at Hailey streamgage.}
 #'     \item{13140800}{daily mean discharge in cubic meters per day, recorded at the USGS
-#'       \href{http://waterdata.usgs.gov/id/nwis/uv/?site_no=13140800}{13140800}
+#'       \href{https://waterdata.usgs.gov/id/nwis/uv/?site_no=13140800}{13140800}
 #'       Big Wood River at Stanton Crossing near Bellevue streamgage.}
 #'   }
 #'
-#' @source National Water Information System (\href{http://waterdata.usgs.gov/nwis}{NWIS}),
+#' @source National Water Information System (\href{https://waterdata.usgs.gov/nwis}{NWIS}),
 #'   accessed on January 8, 2015
 #'
 #' @keywords datasets
@@ -591,18 +591,18 @@
 #'   \describe{
 #'     \item{Date}{date during which gage height was averaged.}
 #'     \item{13135500}{daily mean gage height in meters, recorded at the USGS
-#'       \href{http://waterdata.usgs.gov/id/nwis/uv/?site_no=13135500}{13135500}
+#'       \href{https://waterdata.usgs.gov/id/nwis/uv/?site_no=13135500}{13135500}
 #'       Big Wood River near Ketchum streamgage.}
 #'     \item{13139510}{daily mean gage height in meters, recorded at the USGS
-#'       \href{http://waterdata.usgs.gov/id/nwis/uv/?site_no=13139510}{13139510}
+#'       \href{https://waterdata.usgs.gov/id/nwis/uv/?site_no=13139510}{13139510}
 #'       Big Wood River at Hailey streamgage.}
 #'     \item{13140800}{daily mean gage height in meters, recorded at the USGS
-#'       \href{http://waterdata.usgs.gov/id/nwis/uv/?site_no=13140800}{13140800}
+#'       \href{https://waterdata.usgs.gov/id/nwis/uv/?site_no=13140800}{13140800}
 #'       Big Wood River at Stanton Crossing near Bellevue streamgages.}
 #'   }
 #'
 #' @source Data queried from the National Water Information System
-#'   (\href{http://waterdata.usgs.gov/nwis}{NWIS}) database on December 15, 2014,
+#'   (\href{https://waterdata.usgs.gov/nwis}{NWIS}) database on December 15, 2014,
 #'   by Ross Dickinson (USGS).
 #'   Records recorded on May 26-28, 1991 and March 15-22, 1995 were reassigned
 #'   quality assurance codes of \sQuote{I} because of assumed ice build-up.
@@ -666,7 +666,7 @@
 #' @source U.S. Department of Commerce, U.S. Census Bureau,
 #'   Geography Division/Cartographic Products Branch.
 #'   A simplified representation of the State of Idaho from the 2014 Census Bureau's
-#'   MAF/\href{http://www.census.gov/geo/maps-data/data/tiger.html}{TIGER} geographic database.
+#'   MAF/\href{https://www.census.gov/geo/maps-data/data/tiger.html}{TIGER} geographic database.
 #'
 #' @keywords datasets
 #'
@@ -820,18 +820,18 @@
 #'   The spatial grid is composed of 565 rows and 429 columns,
 #'   and has cell sizes that are constant at 100 meters by 100 meters.
 #'
-#' @source The National Elevation Dataset (\href{http://ned.usgs.gov/}{NED})
+#' @source The National Map (\href{https://nationalmap.gov/elevation.html}{TNM})
 #'   1/3-arc-second raster (Gesch, 2007; Gesch and others, 2002),
 #'   accessed on December 1, 2015.
 #'   This dataset can be downloaded in a Esri ArcGRID format using the
-#'   \href{http://viewer.nationalmap.gov/viewer/}{National Map Viewer}.
-#'   NED data are distributed in geographic coordinates in units of decimal degrees,
+#'   \href{https://viewer.nationalmap.gov/viewer/}{The National Map Viewer}.
+#'   Elevation datasets are distributed in geographic coordinates in units of decimal degrees,
 #'   and in conformance with the NAD 83.
 #'   Elevation values are in meters above the NAVD 88.
 #'   The west, east, south, and north bounding coordinates for this dataset are
 #'   -115, -114, 43, and 44 decimal degrees, respectively.
 #'   Post-processing includes:
-#'     (1) project the values of the NED dataset into the \code{\link{alluvium.thickness}}
+#'     (1) project the values of the elevation dataset into the \code{\link{alluvium.thickness}}
 #'         spatial grid using bilinear interpolation, and
 #'     (2) set values in cells where the elevation of the alluvium bottom is missing to NA.
 #'
@@ -1173,10 +1173,10 @@
 #' @source Idaho Department of Water Resources, accessed on April 24, 2015
 #'
 #' @references National Oceanic and Atmospheric Administration's National Weather Service
-#'   (\href{http://www.nws.noaa.gov/om/coop/}{NWS}) Cooperative Observer Program
+#'   (\href{https://www.ncdc.noaa.gov/data-access/land-based-station-data/land-based-datasets/cooperative-observer-network-coop}{NWS}) Cooperative Observer Program
 #'
 #'   U.S. Bureau of Reclamation's Cooperative Agricultural Weather Network
-#'   (\href{http://www.usbr.gov/pn/agrimet/}{AgriMet})
+#'   (\href{https://www.usbr.gov/pn/agrimet/}{AgriMet})
 #'
 #' @seealso \code{\link{precip.zones}}, \code{\link{swe}}
 #'
@@ -1433,7 +1433,7 @@
 #'
 #' @references Bartolino, J.R., 2014, Stream seepage and groundwater levels, Wood River Valley,
 #'   south-central Idaho, 2012--13: U.S. Geological Survey Scientific Investigations Report 2014-5151,
-#'   34 p., \url{http://dx.doi.org/10.3133/sir20145151}.
+#'   34 p., \url{https://dx.doi.org/10.3133/sir20145151}.
 #'
 #' @keywords datasets
 #'
@@ -1526,7 +1526,7 @@
 #'   North American Datum of 1983 (NAD 83), and placed in the
 #'   Idaho Transverse Mercator projection (\href{https://www.idwr.idaho.gov/GIS/IDTM/}{IDTM}).
 #'
-#' @source National Water Information System (\href{http://waterdata.usgs.gov/nwis}{NWIS}),
+#' @source National Water Information System (\href{https://waterdata.usgs.gov/nwis}{NWIS}),
 #'   accessed on May 29, 2015.
 #'
 #' @keywords datasets
@@ -1636,7 +1636,7 @@
 #'       its geometry is represented as the lower-half of an ellipse with
 #'       width and height equal to \code{TribWidth} and \code{BdrkDepth}, respectively.}
 #'     \item{DarcyFlow}{groundwater flow rate, in cubic meters per day, calculated using a
-#'       \href{http://en.wikipedia.org/wiki/Darcy_law}{Darcian} analysis.}
+#'       \href{https://en.wikipedia.org/wiki/Darcy_law}{Darcian} analysis.}
 #'     \item{BasinArea}{land-surface area defined by the basin above the cross-sectional transect line.}
 #'     \item{BasinAreaType}{label that describes the relative basin size; where
 #'       \code{"big"} indicates a basin area greater than 10 square miles (25.9 square kilometers), and
@@ -1653,16 +1653,16 @@
 #'   Idaho Transverse Mercator projection (\href{https://www.idwr.idaho.gov/GIS/IDTM/}{IDTM}).
 #'
 #' @source U.S. Geological Survey, accessed on July 2, 2015;
-#'   a Keyhole Markup Language (\href{http://en.wikipedia.org/wiki/Kml}{KML}) file created in
-#'   \href{http://www.google.com/earth/}{Google Earth} with polygons drawn by hand in
+#'   a Keyhole Markup Language (\href{https://en.wikipedia.org/wiki/Kml}{KML}) file created in
+#'   \href{https://www.google.com/earth/}{Google Earth} with polygons drawn by hand in
 #'   areas of known specified flow boundaries.
 #'   Transect lines are defined by the polygon boundaries within the extent of
 #'   alluvium aquifer (see \code{\link{alluvium.extent}} dataset).
 #'   The land surface gradient (\code{LandGrad}) was estimated from the
 #'   \code{\link{land.surface}} dataset.
 #'   Hydraulic conductivity (\code{K}) is the average of two geometric means of hydraulic conductivity
 #'   in the unconfined aquifer taken from table 2 in Bartolino and Adkins (2012).
-#'   The U.S. Geologic Survey \href{http://water.usgs.gov/osw/streamstats/}{StreamStats} tool
+#'   The U.S. Geologic Survey \href{https://water.usgs.gov/osw/streamstats/}{StreamStats} tool
 #'   (Ries and others, 2004) was used to delineate the basin area (\code{BasinArea}) and
 #'   estimate the precipitation rate (\code{PrecipRate}).
 #'   See the appendix C. Package Dataset Creation for the \R code used to calculate the
@@ -1671,12 +1671,12 @@
 #' @references Bartolino, J.R., and Adkins, C.B., 2012, Hydrogeologic framework of the
 #'   Wood River Valley aquifer system, south-central Idaho: U.S. Geological Survey
 #'   Scientific Investigations Report 2012-5053, 46 p.,
-#'   available at \url{http://pubs.usgs.gov/sir/2012/5053/}.
+#'   available at \url{https://pubs.usgs.gov/sir/2012/5053/}.
 #'
 #'   Ries, K.G., Steeves, P.A., Coles, J.D., Rea, A.H., and Stewart, D.W., 2004,
 #'   StreamStats--A U.S. Geological Survey web application for stream information:
 #'   U.S. Geological Survey Fact Sheet FS-2004-3115, 4 p., available at
-#'   \url{http://pubs.er.usgs.gov/usgspubs/fs/fs20043115}.
+#'   \url{https://pubs.er.usgs.gov/publication/fs20043115}.
 #'
 #' @keywords datasets
 #'
@@ -1784,13 +1784,13 @@
 #'   Idaho Transverse Mercator projection (\href{https://www.idwr.idaho.gov/GIS/IDTM/}{IDTM}).
 #'
 #' @source This dataset is from Plate 1 in Skinner and others (2007), and available on the
-#'   \href{http://water.usgs.gov/GIS/metadata/usgswrd/XML/sir2007-5258_oct2006wl.xml}{WRD NSDI Node}.
+#'   \href{https://water.usgs.gov/GIS/metadata/usgswrd/XML/sir2007-5258_oct2006wl.xml}{WRD NSDI Node}.
 #'
 #' @references Skinner, K.D., Bartolino, J.R., and Tranmer, A.W., 2007,
 #'   Water-resource trends and comparisons between partial development and
 #'   October 2006 hydrologic conditions, Wood River Valley, south-central, Idaho:
 #'   U.S. Geological Survey Scientific Investigations Report 2007-5258, 30 p.,
-#'   available at \url{http://pubs.usgs.gov/sir/2007/5258/}
+#'   available at \url{https://pubs.usgs.gov/sir/2007/5258/}
 #'
 #' @keywords datasets
 #'
@@ -1820,7 +1820,7 @@
 #' @references Bartolino, J.R., and Adkins, C.B., 2012, Hydrogeologic framework of the
 #'   Wood River Valley aquifer system, south-central Idaho:
 #'   U.S. Geological Survey Scientific Investigations Report 2012-5053, 46 p.,
-#'   available at \url{http://pubs.usgs.gov/sir/2012/5053/}.
+#'   available at \url{https://pubs.usgs.gov/sir/2012/5053/}.
 #'
 #' @keywords datasets
 #'

README.md

@@ -4,21 +4,21 @@
 
 ## Overview
 
-The [R](http://www.r-project.org/) package **wrv** is for processing the
+The [R](https://www.r-project.org/) package **wrv** is 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 1.3,
+[model report](https://dx.doi.org/10.3133/sir20165080 "USGS Scientific Investigations Report") and
+[model archive](https://dx.doi.org/10.5066/F7C827DT "USGS Data Release").
+Included in the package is [MODFLOW-USG](https://water.usgs.gov/ogw/mfusg/ "MODFLOW-USG") version 1.3,
 a U.S. Geological Survey (USGS) computer code that solves the groundwater-flow equation.
 
 ## Install
 
-You can install the stable version of **wrv** from [GRAN](http://owi.usgs.gov/R/gran.html),
-and its dependencies from [CRAN](http://cran.r-project.org/), using the following commands:
+You can install the stable version of **wrv** from [GRAN](https://owi.usgs.gov/R/gran.html),
+and its dependencies from [CRAN](https://cran.r-project.org/), using the following commands:
 
 ```r
-repos <- c("http://owi.usgs.gov/R", getOption("repos"))
+repos <- c("https://owi.usgs.gov/R", "https://cloud.r-project.org/")
 install.packages("wrv", repos = repos, dependencies = TRUE)
 ```
 
@@ -61,4 +61,4 @@ and no responsibility is assumed by the USGS in connection therewith.
 
 This software is provided "AS IS."
 
-[![CC0](http://i.creativecommons.org/p/zero/1.0/88x31.png)](http://creativecommons.org/publicdomain/zero/1.0/)
+[![CC0](https://i.creativecommons.org/p/zero/1.0/88x31.png)](https://creativecommons.org/publicdomain/zero/1.0/)