RecreateLibrary function.stringsAsFactors option in all calls to functions data.frame and as.data.frame.Fix inkscape command in render-tables.R script.
Fix bug in SetPolygons that resulted in error.
Fix invalid URL’s.
Import wordcloud2 and webshot packages, and suggest png package. The webshot package has as a dependency the external program PhantomJS.
Add CreateWordCloud, used to create a word cloud from a frequency table of words, and plot to a PNG file.
Add top-level README.Rmd file.
Remove LICENSE.note file from package, and replace witha repo-only LICENSE.md file.
Add DISCLAIMER.md file.
In LaTeX preamble, include new solution for printing fancy header on all pages.
In AddInsetMap, add feature argument, used to add one or more spatial features to the inset map.
In LaTeX preamble, omit group separators in the decimal part when using siunitx package.
In GetColors, type change from diverging to sequential for color schemes: "berlin", "broc", "cork", "lisbon", "oleron", "tofino", and "vik". Results from CPTs not actually having a zero entry.
In PlotMap, fix bug resulting from change in raster::crop that returns an error when the subset is empty, was previously returning NULL.
In FindOptimalSubset, stop setting state of random number generator when seed argument is NULL.
In FindOptimalSubset, add numIslands argument, used to specify the number of islands, was previously dependent on the parallel argument; change default value of elitism argument from 0 to 5-percent of the island population.
Add misc/latex-packages.txt: contains a list of required LaTeX packages that are not included in the default installation of 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, add "turbo" color scheme.
In SetHinge, 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 to PrintPackageHelp. Preserve empty lines in the Examples section of help documentation; 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; 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 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.
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.
SetPolygons, set checkValidity argument to 2 and suppress warnings.Add "usgs_article" template for R Markdown documents. This template is experimental and subject to change in the future.
Set checkValidity argument to 2 (check and try to buffer by zero distance to repair) in many of the rgeos function calls.
In AddColorKey, remove border line around color blocks.
In Grid2Polygons, improved performance; change polygon cropping function from raster::crop to SetPolygons.
In RecreateLibrary, remove github option that allowed package installation from GitHub repositories.
Add PrintHelpPages, used to print the HTML code associated with help pages of a loaded R package.
In BuildVignettes, rearrange order of arguments and add doc argument, used to specify the directory to write vignette output files.
In GetColors, add "bpy" (blue-pink-yellow) color scheme.
In AddPoints, change interval to reflect labels, that is, open at the left and closed at right.
Add AddIntervals, used to add vertical interval symbols to plots. Replaces use of graphics::arrows in PlotGraph, and avoids the warning message resulting from an arrow length less than 1/1000 inch.
In misc/preamble.tex: reduce hyphenation and prevent writing into margin.
In PlotGraph: improve handling of cases where range of y values is zero; extend y-axis limits to prevent symbols from being drawn on an axis limit; change margin line for the main title, axis title, and axis labels; decrease size of upper margin by 0.2 lines; add add.grid argument, determines whether to draw a rectangular grid.
In PrintFigure, allow heading on single figure.
In AddSearchButton, fix bug that prevented popup from opening when openPopup argument is true.
In PlotGraph, change alignment of main title from center to left-hand side of plot.
In ToScientific, add zero argument, used to substitute a string for values of zero.
In PrintTable: allow colheadings argument to be a data table, used to make column headings with spanners; separate multi-table pages using \clearpage.
In misc/preamble.tex: set ‘pdfa’ option to true, tries to avoid violations of PDF/A in code generated by hyperref package; add multirow, footmisc, and siunitx packages; ragged right justification of captions.
Add alphahull, maptools, and remotes to suggested packages.
Remove httr and devtools from suggested packages.
In GetRegionOfInterest: replace obj argument with x and y; add alpha and width arguments, used to compute alpha-shape and expand the region of interest, respectively.
Add BuildVignettes, used to build package vignettes.
In SummariseBudget, improve memory management.
Change package imports by adding data.table and removing dplyr.
Add SetHinge, used to specify a hinge location in a color palette.
In PrintTable: d argument can be of class ‘matrix’; and a default caption is no longer added when title and headnotes arguments are not specified.
Tidy help documentation
Add GetRegionOfInterest, used to calculate the region of interest from spatial points.
In FindOptimalSubset: improve matrix construction of suggestions; change calculation of number of bits in a number.
In AddColorKey, rearrange order of arguments.
In PlotCrossSection: add bend.label argument, used to place labels at top of the bend-in-section lines; change default value of bg.col argument from "#FFFFFFD8" to NULL, and for scale.loc argument from "bottom" to NULL; make font/line color darker for section breaks and features.
Rename GetTolColors to GetColors. Add additional color schemes; replace start and end arguments with stops, a vector of length 2; change blind argument option from "monochromacy" to "monochrome"; return a variant of the GetColors function when argument n is unspecified.
For leaflet-search plugin, change version from 2.8.0 to 2.9.6 and tidy wrapper functions.
In CreateWebMap, add service argument for specifying the mapping service to use for accessing base-map tiles.
Change required R version from >= 3.2.0 to >= 3.4.0.
Add AddNorthArrow, was previously defined as an internal function.
In AddScaleBar: non-backward compatible argument changes. Remove offset argument and replace with ..., see help documentation for details.
Make dichromat a suggested package.
Remove viridisLite from suggested packages.
Add GetInsetLocation, used to determine the location for a inset graphics in the main plot region.
In AddPoints: add bty, draw.legend, and draw.points arguments.
In PlotGraph: add xpd argument, determines whether point and (or) line symbols are clipped to the plot region; change default color scheme; change contents of fill argument (non-backward compatible) and add a fillcolor argument; provide main argument a default value of NULL.
In FindOptimalSubset, add monitor argument to check on status of GA run.
In GetTolColors: add color schemes; change default scheme from "bright" to "smooth rainbow"; add start, end, bias, reverse, blind, and gray arguments.
In GetTolColors, revise color schemes based of issue 3.0 of technical note.
In PlotGraph, improve placement of tick marks.
Remove colorspace from suggested packages and replace with viridisLite.
In ToScientific, better identify whether to print numeric values in fixed or scientific notation.
In AddScaleBar, non-backward compatible argument changes and formatting improvements.
In PlotGraph: fix bug that resulted in an error when type = "n"; and add main argument for placing a title at the top of the plot.
Make gstat and roxygen2 suggested packages.
Remove httr, maps, and maptools from suggested packages.
In misc/preamble.tex: tidy code; include fix for spacing after number in List of Figures and List of Tables; remove helvet package; and add float package, provides the H float modifier option.
In AddInsetMap: add an optional e argument, a numeric vector describing the extent of the smaller axis-aligned rectangle; add “center” option for loc argument; and add bty argument, determines if a box is to be drawn around the inset map.
Update leaflet-search.min.js and leaflet-search.min.css files to version 2.8.0.
Add PrintFigure, used to print the LaTeX code associated with a figure.
Add GetTolColors, used to access color palettes by Paul Tol.
Avoid importing all functions from a package.
Remove AddCertificate, no longer needed with new version of R (3.4.3).
Add PrintTable, used to print the LaTeX code associated with a data.frame object.
In PlotMap, remove option to map points.
In ReadCodeChunks, remove dependency on knitr-intro.Rmd file in example.
In AddColorKey, replace scientific argument with scipen, see getOption("scipen") command.
In AddColorKey, add log argument to specify axis to be logarithmic.
In AddColorKey, use m x 10^n format for tick labels written in scientific notation.
In RecreateLibrary, add parallel argument to install packages from source using parallel processes.
In ToScientific, add big.mark argument with default value of ",".
In ToScientific, fix bug that formatted 0 as NA when type = "plotmath".
In CreateWebMap, pass ... arguments to leaflet::leaflet function, these arguments were previously passed to the leaflet::leafletOptions function.
In CreateWebMap, add maps argument to specify which base maps to include.
In CreateWebMap, remove coordinates and zoom level information from top of map.
Add AddHomeButton, AddClusterButton, and AddSearchButton, and AddLegend, used to add additional web map elements.
In FindOptimalSubset, allow integer chromosomes to be specified for the suggestions argument.
Add additional argument checks using checkmate package.
In PlotMap, fix bug introduced by previous fix of raster range calculation.
Made AddCertificate an internal function.
Add argument checks using checkmate package.
In PlotMap, fix bug in range calculation of raster values by removing finite = TRUE.
In PlotMap, fix extent of background image, rivers, lakes, and roads using par("usr").
Add FindOptimalSubset, used to identify an optimal subset using a genetic algorithm.
In AddPoints: add option to scale symbol size to radius; revise calculation of symbol size and legend labels.
In PlotMap, let r argument accept any object that can be converted to a RasterLayer class.
In LaTeX preamble: add verbatimbox package; add maketitle format.
In PlotMap, add simplify argument, used to convert raster to polygons prior to plotting.
In Grid2Polygons: allow grd argument to be an object of class SpatialPixelsDataFrame or Raster*; transform coordinate reference system (CRS) of ply argument to match the CRS of the grd argument; and add zlim argument, a limit on the attribute variable.
In ToScientific, add arguments scipen, delimiter, and ...; and rename lab.type argument to type. Code in place for backwards compatibility.
In RecreateLibrary and SavePackageDetails, add support for gzip file compression.
In SavePackageDetails, fix bug that results in an ‘invalid cross-device link’ error on some flavor’s of R.
Rename SavePackageNames to SavePackageDetails.
Add AddCertificate, used to add a X.509 certificate to your CA bundle.
Make httr a suggested package.
In RecreateLibrary, add local argument, file paths of files containing builds of packages.
In AddGradientLegend, add n argument, the desired number of tick-marks to be drawn.
Add Grid2Polygons from the Grid2Polygons package.
Total revision of RecreateLibrary and SavePackageNames.
In ToScientific, improve default value for digits argument.
Add AddGradientLegend, used to add a continuous color gradient legend strip to a plot.
Add RecreateLibrary, used to recreate an existing library on a new installation of R.
Add FormatPval, used to format p-values.
Add bm and makecell packages to LaTeX preamble.
Changes in PlotGraph: Add option for plotting interval censored data by specifying type = "i". Select box-and-whisker plot using type = "w", was previously type = "box". Default for seq.date.by argument changed from "year" to NULL.
Add CreateWebMap, creates a Leaflet map widget using The National Map services.
Tidy help documentation for functions.
endian argument to ReadModflowBinary. Argument describes the endian-ness (or byte-order) of the binary file and is required for calls to the readBin function. Thanks to Professor Brian Ripley for identifying this issue.In SummariseBudget, the desc argument no longer needs to be specified. If missing, all data types are summarized.
In SummariseBudget, remove default for desc argument and add id argument, the auxiliary variable name.
In ReadModflowBinary, enable cell-by-cell budget files to be read when they are not in compact form.
Change legend format for binned point data from [#, ) to ># to #.
Fix bug that resulted in error when plotting a single point location using the AddPoints function.
Add AppVeyor to package.
In PlotMap, PlotCrossSection, and AddColorKey, dynamically adjust vertical plot margins based on the number of lines in the user specified labels.
In AddPoints, remove draw.legend argument and rename pos argument to legend.pos. A NULL value for legend.pos will prevent the legend from being drawn.
Change name from AddBubbles to AddPoints.
In PlotMap and PlotCrossSection, fix layout so color key dimensions don’t change on resize.
In PlotMap function, add file.close argument. A logical that indicates if the graphics device driver should be shut down when the function exits.
In AddBubbles, allow z argument to be an object of class factor.
In AddBubbles, account for aspect ratio when constructing legend.
In AddBubbles, rename bg.pos argument to bg, and set bg.neg = NULL. The bg argument may now be used to specify circle colors for all z values, not just positive values. See help documentation for details.
In AddBubbles, specifying a single numeric value for the inches arguments results in a fixed radius being used for all circle symbols.
In PlotMap, account for z-axis limits prior to removing rows and columns having all missing values.
In PlotMap, change default for scale.loc argument from "leftbottom" to NULL; the scale bar is no longer drawn by default.
In PlotMap, change asp argument from 1 to NULL. Defaults to 1 when data is projected, otherwise, a calculated value based on axes limits is used.
Add POSIXct2Character, used to convert objects from POSIXct to character class.
Update URL links to HTTP Secure
Generalize CITATION file
Change argument name in ReadModflowBinary function from f to path.
Add ReadCodeChunk, reads knitr code chunks into the current session.
Change NEWS file to markdown format.
Remove misc folder from .Rbuildignore file, adds the misc/preamble.tex file back to the package build.
Add file argument to PlotMap and PlotCrossSection. Specifying this argument will start a graphics device driver for producing either a PDF or PNG file.
Width and height of graphics device is no longer calculated when drawing to screen.
Explain the USGS and INL acronyms from the Title in the DESCRIPTION file.
Fix invalid URLs.