NEWS.md

In USGS-R/inlmisc: Miscellaneous Functions for the USGS INL Project Office

inlmisc 0.5.5

• Stop running example in RecreateLibrary function.

inlmisc 0.5.4

• Explicitly set stringsAsFactors option in all calls to functions data.frame and as.data.frame.

inlmisc 0.5.3

• Fix inkscape command in render-tables.R script.

• Fix bug in SetPolygons that resulted in error.

• Fix invalid URL's.

inlmisc 0.5.2

• Fixed invalid URL's.

inlmisc 0.5.1

• 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.

inlmisc 0.5.0

• 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.

inlmisc 0.4.9

• 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.

inlmisc 0.4.8

• 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.

inlmisc 0.4.7

• In SetPolygons, set checkValidity argument to 2 and suppress warnings.

inlmisc 0.4.6

• 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.

inlmisc 0.4.5

• 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.

inlmisc 0.4.4

• 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.

inlmisc 0.4.3

• 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.

inlmisc 0.4.2

• 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.

inlmisc 0.4.0

• 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.

inlmisc 0.3.5

• In PlotMap, fix bug introduced by previous fix of raster range calculation.

• Made AddCertificate an internal function.

• Add argument checks using checkmate package.

inlmisc 0.3.4

• 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.

inlmisc 0.3.3

• 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.

inlmisc 0.3.2

• 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.

inlmisc 0.3.1

• 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.

inlmisc 0.3.0

• 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.

inlmisc 0.2.7

• 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.

inlmisc 0.2.6

• Add 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.

inlmisc 0.2.5

• 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.

inlmisc 0.2.4

• Fix bug that resulted in incorrect dimensions for saved graphics.

inlmisc 0.2.3

• 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

inlmisc 0.2.2

• 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.

inlmisc 0.2.1

• Fix invalid URLs.

inlmisc 0.2.0

• 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.

inlmisc 0.1.2

• Explain the USGS and INL acronyms from the Title in the DESCRIPTION file.

• Fix invalid URLs.

inlmisc 0.1.0

• First version of inlmisc

USGS-R/inlmisc documentation built on Sept. 17, 2022, 2:38 a.m.