Merge pull request #123 from jfisher-usgs/master

merge with upstream

Author: jfisher-usgs

DESCRIPTION

@@ -46,8 +46,8 @@ Suggests:
     testthat
 License: CC0
 Copyright: This software is in the public domain because it contains materials
-    that originally came from the United States Geological Survey, an agency of
-    the United States Department of Interior.
+    that originally came from the USGS, an agency of the
+    United States Department of Interior.
 URL: https://github.com/USGS-R/inlmisc
 BugReports: https://github.com/USGS-R/inlmisc/issues
 Encoding: UTF-8

NEWS.md

@@ -1,25 +1,32 @@
 # inlmisc 0.4.7.9000
 
+- Add *misc/latex-packages.txt* file: contains a list of required LaTeX packages
+  that are not included in the default installation of [TinyTeX](https://yihui.name/tinytex/);
+  use the `inlmisc:::InstallLatexPackages()` command to install these packages into TinyTeX.
+
+- In LaTeX preamble, replace **xcolor** package with **color**,
+  eliminates an annoying warning when compiling document.
+
 - In `GetColors` function, add `"turbo"` color scheme.
 
-- In `SetHinge` function, non-backward compatible change to allocating colors on each side of hinge.
-  The effect of this change is only perceivable when the number of colors is small (`n < 10`).
+- In `SetHinge` function, non-backward compatible change to allocating colors on each side
+  of hinge, is only perceivable when the number of colors is small (`n < 10`).
 
 - Rename `PrintHelpPages` function to `PrintPackageHelp`.
   Preserve empty lines in the Examples section of help documentation;
-  fix parsing bug on identifying code blocks; tidy main header for each help topic;
+  fix parsing bug associated with identifying code blocks; tidy main header for each help topic;
   add `internal` argument, used to print help pages flagged with keyword `internal`;
-  replace `hr` argument with `sep` argument;
+  replace `hr` argument with `sep`;
   add `title_to_name` argument, used to replace the help-topic "title" with its "name";
   add `notrun` argument, used to remove `## Not run` comments;
-  include internal links for package by default.
+  include internal links by default.
 
 - In `Grid2Polygons`, add `check_validity` argument, used to check the validity of polygons.
 
 - Fix bugs in *raw/build-datasets.R* and *raw/render-tables.R* files
   that incorrectly called `IsColor` function.
 
-- Changed package dependency from R >= 3.4.0 to R >= 3.5.0 because serialized objects
+- Change package dependency from R >= 3.4.0 to R >= 3.5.0 because serialized objects
   in serialize/load version 3 cannot be read in older versions of R.
 
 # inlmisc 0.4.7

R/AddGradientLegend.R

@@ -43,6 +43,8 @@
 #' AddGradientLegend(breaks, pal = GetColors(scheme = "iridescent"),
 #'                   title = "Title", loc = "bottomleft",
 #'                   inset = c(0.2, 0.1))
+#' AddGradientLegend(breaks, pal = GetColors(scheme = "turbo"),
+#'                   loc = "center", labels = FALSE)
 #' breaks <- seq(0, 2e+06, length.out = 5)
 #' AddGradientLegend(breaks, pal = GetColors(scheme = "discrete rainbow"),
 #'                   scientific = TRUE, strip.dim = c(1, 14),

R/PrintFigure.R

@@ -60,23 +60,22 @@
 #'     "\\usepackage[labelsep=period, labelfont=bf]{caption}",
 #'     "\\usepackage{subcaption}",
 #'     "\\captionsetup[figure]{skip=10pt}",
-#'     "\\captionsetup[subfigure]{skip=-10pt, labelfont={bf, it}}",
+#'     "\\captionsetup[subfigure]{skip=0pt, labelfont={bf, it}}",
 #'     "\\renewcommand{\\thesubfigure}{\\Alph{subfigure}}",
 #'     "\\begin{document}",
 #'     "<<id, echo=FALSE, fig.width=3, fig.height=2, results='asis'>>=",
 #'     "par(mar=c(2.1, 2.1, 1.1, 1.1))",
-#'     "n <- 9",
-#'     "fig <- sprintf('plot(runif(%s))', seq_len(n))",
-#'     "headings <- sprintf('Subfigure caption, n=%s', seq_len(n))",
-#'     "PrintFigure(fig, 3, 2, 'id', title='Figure caption', headings=headings)",
+#'     "n <- 10",
+#'     "fig <- sprintf('inlmisc::PlotGraph(runif(%s))', 2:n)",
+#'     "headings <- sprintf('Subfigure caption, $n=%s$', 2:n)",
+#'     "PrintFigure(fig, 3, 2, 'id', title='Caption', headings=headings)",
 #'     "@",
 #'     "\\end{document}",
 #'     file = "figure-example.Rnw", sep = "\n")
-#' knitr::knit2pdf("figure-example.Rnw", clean = TRUE)  # requires TeX installation
+#' knitr::knit2pdf("figure-example.Rnw", clean = TRUE)  # requires LaTeX
 #' system("open figure-example.pdf")
 #'
-#' unlink("figure-example.*")
-#' unlink("figure", recursive = TRUE)
+#' unlink(c("figure-example.*", "figure"), recursive = TRUE)
 #' }
 #'
 

R/PrintTable.R

@@ -123,7 +123,7 @@
 #' PrintTable(d, colheadings, align)
 #' cat("\\end{document}\n")
 #' sink()
-#' tinytex::pdflatex("table-example.tex")  # requires TeX
+#' tinytex::pdflatex("table-example.tex")  # requires LaTeX
 #' system("open table-example.pdf")
 #'
 #' file.remove("table-example.tex", "table-example.pdf")

R/usgs_article.R

@@ -16,7 +16,7 @@
 #' @examples
 #' \dontrun{
 #' # install LaTeX distribution
-#' if (Sys.which("pdflatex") == "" && !tinytex:::is_tinytex())
+#' if (Sys.which("pdflatex") == "")
 #'   tinytex::install_tinytex()
 #'
 #' # install LaTeX packages
@@ -123,7 +123,8 @@ usgs_article <- function(...) {
 }
 
 
-# install required LaTeX packages into TinyTeX
+# install required LaTeX packages that are not included
+# in the default installation of TinyTeX
 InstallLatexPackages <- function() {
   file <- system.file("misc", "latex-packages.txt", package="inlmisc")
   pkgs <- readLines(file)

README.md

@@ -16,14 +16,14 @@ Idaho National Laboratory (INL) [Project Office](https://www.usgs.gov/centers/id
 
 ## Install
 
-You can install the stable version from [CRAN](https://CRAN.R-project.org/package=inlmisc "The Comprehensive R Archive Network")
-using the following command:
+The current release is available on [CRAN](https://CRAN.R-project.org/package=inlmisc "The Comprehensive R Archive Network"),
+which you can install using the following command:
 
 ```r
 install.packages("inlmisc", dependencies = TRUE)
 ```
 
-Or use the **remotes** package to install the development version from GitHub.
+To install the development version, you need to clone the repository and build from source, or run:
 
 ```r
 remotes::install_github("USGS-R/inlmisc", dependencies = TRUE)

inst/misc/latex-packages.txt

@@ -16,5 +16,4 @@ siunitx
 symbol
 tocloft
 verbatimbox
-xcolor
 xpatch

inst/misc/preamble.tex

@@ -189,7 +189,7 @@
 
 \usepackage[multiple]{footmisc}  % typesetting of footnotes
 
-\usepackage{xcolor}  % control colors
+\usepackage[]{color}  % control colors
 \definecolor{Red}{rgb}{0.7,0,0}
 \definecolor{Blue}{rgb}{0,0,0.8}
 

inst/rmarkdown/templates/usgs_article/skeleton/usgs.sty

@@ -148,7 +148,7 @@
 
 \RequirePackage[multiple]{footmisc}  % typesetting of footnotes
 
-\RequirePackage{xcolor}  % control colors
+\RequirePackage[]{color}  % control colors
 \definecolor{Red}{rgb}{0.7,0,0}
 \definecolor{Blue}{rgb}{0,0,0.8}