<p><div><div><div><div data-show-faces="false" data-height="21" data-width="100" data-layout="button_count" data-send="true" data-href="https://www.r-bloggers.com/august-2017-new-package-picks/"></div></div><div></div></div><div></div></div>
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(This article was first published on <strong><a href="https://rviews.rstudio.com/2017/09/29/august-2017-new-package-picks/"> R Views</a></strong>, and kindly contributed to <a rel="nofollow" href="https://www.r-bloggers.com/">R-bloggers)</a> </div>
<p>August was a relatively slow month for new R packages; “only” 180 new packages stuck to CRAN. Here are my “Top 40” picks organized into seven categories: Data, Machine Learning, Miscellaneous, Science, Statistics, Utilities and Visualizations. Although they have been written for specialized audiences, I have included the three “Science” packages because, in my layman’s opinion, they not only seem to be useful, but they are each documented well enough to give an interested person some idea of what they do.</p>
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<h3>Data</h3>
<p><a rel="nofollow" href="https://cran.r-project.org/package=edgarWebR" target="_blank">edgarWebR</a> v0.1.1: Provides methods to access and parse live filing information from the U.S. <a rel="nofollow" href="https://sec.gov/" target="_blank">Securities and Exchange Commission</a>, including company and fund filings, along with all associated metadata. See the <a rel="nofollow" href="https://cran.rstudio.com/web/packages/edgarWebR/vignettes/edgarWebR.html" target="_blank">vignette</a> for an introduction. <img src="https://i2.wp.com/rviews.rstudio.com/post/2017-09-25-August-Pkgs_files/edgarWebR.png?w=456&ssl=1" data-recalc-dims="1"></p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=forwards" target="_blank">forwards</a> v0.1.0: Anonymized data from surveys conducted by <a rel="nofollow" href="http://forwards.github.io/" target="_blank">Forwards</a>, the R Foundation task force on women and other under-represented groups. Currently, a single data set of responses to a survey of attendees at <a rel="nofollow" href="http://user2016.org/" target="_blank">useR! 2016</a>. The <a rel="nofollow" href="https://cran.rstudio.com/web/packages/forwards/vignettes/Overview.h" target="_blank">vignette</a> provides an overview.</p>
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<img src="https://i2.wp.com/rviews.rstudio.com/post/2017-09-25-August-Pkgs_files/forwards.png?w=456&ssl=1" data-recalc-dims="1">
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<p><a rel="nofollow" href="https://cran.r-project.org/package=GeoMongo" target="_blank">GeoMongo</a> v1.0.1: Utilizes methods from the <a rel="nofollow" href="https://api.mongodb.com/python/current/#" target="_blank"><code>PyMongo</code> library</a> to initialize, insert and query ‘GeoJson’ data. There is a <a rel="nofollow" href="https://cran.rstudio.com/web/packages/GeoMongo/vignettes/the_GeoMongo_package.html" target="_blank">vignette</a>.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=Rnightlights" target="_blank">Rnightlights</a> v0.1.2: Provides an interface to extract raster and zonal statistics from satellite nightlight rasters, downloaded from the United States <a rel="nofollow" href="http://www.noaa.gov/" target="_blank">National Oceanic and Atmospheric Administration</a> free data repositories.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=Knoema" target="_blank">Knoema</a> v0.1.7: Provides an API interface to <a rel="nofollow" href="https://knoema.com/dev/docs" target="_blank">Knoema</a>, one of the largest collections of public data and statistics on the Internet, featuring about 2.5 billion time series from thousands of sources. The <a rel="nofollow" href="https://cran.rstudio.com/web/packages/Knoema/README.html" target="_blank">README</a> file will get you started.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=rwalkr" target="_blank">rwalkr</a> v0.3.1: Provides an API to the Melbourne pedestrian data in tidy data form. See <a rel="nofollow" href="https://cran.rstudio.com/web/packages/rwalkr/README.html" target="_blank">README</a> for an example.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=vegtable" target="_blank">vegetable</a> v0.1.0: Provides functions to import and manipulate data from vegetation-plot databases, especially data stored in <a rel="nofollow" href="https://www.synbiosys.alterra.nl/turboveg" target="_blank">Turboveg</a>. The package also implements import/export routines for exchanging data with <a rel="nofollow" href="http://www.sci.muni.cz/botany/juice" target="_blank">Juice</a>.</p>
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<h3>Machine Learning</h3>
<p><a rel="nofollow" href="https://cran.r-project.org/package=partitionComparison" target="_blank">partitionComparison</a> v0.2.2: Provides several measures (dissimilarity, distance/metric, correlation, entropy) for comparing two partitions of the same set of objects. See the <a rel="nofollow" href="http://www.sciencedirect.com/science/article/pii/S0047259X06002016?via%3Dihub" target="_blank">paper</a> by Marina Meilă for details.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=spm" target="_blank">spm</a> v1.0.0: Introduces hybrid methods of geostatistical and machine learning methods for spatial predictive modelling. The <a rel="nofollow" href="https://cran.rstudio.com/web/packages/spm/vignettes/spm.html" target="_blank">vignette</a> provides an introduction.</p>
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<h3>Miscellaneous</h3>
<p><a rel="nofollow" href="https://cran.r-project.org/package=LearnGeom" target="_blank">LearnGeom</a> v1.0: Provides functions for learning and teaching basic plane Geometry at the undergraduate level, with the aim of being helpful to young students with few programming skills. The <a rel="nofollow" href="https://cran.rstudio.com/web/packages/LearnGeom/vignettes/my-vignette.html" target="_blank">vignette</a> offers several examples.</p>
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<h3>Science</h3>
<p><a rel="nofollow" href="https://cran.r-project.org/package=PGRdup" target="_blank">PGRdup</a> v0.2.3.2: Provides functions to aid the identification of probable/possible duplicates in <a rel="nofollow" href="https://www.ars.usda.gov/northeast-area/geneva-ny/plant-genetic-resources-research/" target="_blank">Plant Genetic Resources</a> collections using ‘passport databases’ comprising information records from each constituent sample. The <a rel="nofollow" href="https://cran.r-project.org/web/packages/PGRdup/vignettes/Introduction.pdf" target="_blank">vignette</a> provides an overview.</p>
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<img src="https://i2.wp.com/rviews.rstudio.com/post/2017-09-25-August-Pkgs_files/PGRdup.png?w=456&ssl=1" data-recalc-dims="1">
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<p><a rel="nofollow" href="https://cran.r-project.org/package=rtimicropem" target="_blank">rtimicropem</a> v1.3: Supports the input and reproducible analysis of RTI MicroPEM output files such as those produced by the <a rel="nofollow" href="http://www.chaiproject.org/" target="_blank">Chai Project</a>. There is an <a rel="nofollow" href="https://cran.rstudio.com/web/packages/rtimicropem/vignettes/vignette_ammon.html" target="_blank">Introduction</a> and a vignette on <a rel="nofollow" href="https://cran.rstudio.com/web/packages/rtimicropem/vignettes/chai_data_cleaning.html" target="_blank">MicroPEM Cleaning</a>.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=snpReady" target="_blank">snpReady</a> v0.9.3: Provides functions to clean, summarize and prepare genomic data sets to Genome Selection and <a rel="nofollow" href="https://en.wikipedia.org/wiki/Genome-wide_association_study" target="_blank">Genome Association</a> analysis and to estimate population genetic parameters. See the <a rel="nofollow" href="https://cran.rstudio.com/web/packages/snpReady/vignettes/snpReady-vignette.html" target="_blank">vignette</a> for details.</p>
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<h3>Statistics</h3>
<p><a rel="nofollow" href="https://cran.r-project.org/package=blink" target="_blank">blink</a> v0.1.0: Implements the model in <a rel="nofollow" href="doi:10.1214/15-BA965SI" target="_blank">Steorts</a>, which performs Bayesian entity resolution for categorical and text data, for any distance function defined by the user. Reproducible experiments are illustrated in the <a rel="nofollow" href="https://cran.rstudio.com/web/packages/blink/vignettes/introEBLink.html" target="_blank">vignette</a>.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=cholera" target="_blank">cholera</a> v0.2.1: Amends errors, augments data and aids analysis of John Snow’s map of the 1854 London cholera outbreak. The original data come from Rusty Dodson and Waldo Tobler’s 1992 digitization of Snow’s map. Those <a rel="nofollow" href="http://www.ncgia.ucsb.edu/pubs/snow/snow.html" target="_blank">data</a> are no longer available. However, they are preserved in the <a rel="nofollow" href="https://cran.r-project.org/package=HistData" target="_blank">HistData</a> package. There are vignettes on <a rel="nofollow" href="https://cran.rstudio.com/web/packages/cholera/vignettes/duplicate.missing.cases.html" target="_blank">Missing Data</a>, <a rel="nofollow" href="https://cran.rstudio.com/web/packages/cholera/vignettes/pump.neighborhoods.html" target="_blank">Pump Neighborhoods</a>, <a rel="nofollow" href="https://cran.rstudio.com/web/packages/cholera/vignettes/roads.html" target="_blank">Roads</a>, <a rel="nofollow" href="https://cran.rstudio.com/web/packages/cholera/vignettes/time.series.html" target="_blank">Time Series</a>, and <a rel="nofollow" href="https://cran.rstudio.com/web/packages/cholera/vignettes/unstacking.fatalities.html" target="_blank">“Unstacking bars”</a>.</p>
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<img src="https://i2.wp.com/rviews.rstudio.com/post/2017-09-25-August-Pkgs_files/cholera.png?w=456&ssl=1" data-recalc-dims="1">
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<p><a rel="nofollow" href="https://cran.r-project.org/package=drtmle" target="_blank">drtmle</a> v1.0.0: Provides targeted minimum loss-based estimators for counter-factual means and causal effects that are doubly robust with respect both to consistency and asymptotic normality <a rel="nofollow" href="doi:10.1515/ijb-2012-0038" target="_blank">van der Laan</a>. The extensive <a rel="nofollow" href="https://cran.rstudio.com/web/packages/drtmle/vignettes/using_drtmle.html" target="_blank">vignette</a> does the math.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=esvis" target="_blank">esvis</a> v0.1.0: Provides a variety of methods to estimate and visualize distributional differences in terms of effect sizes, with emphasis on evaluating differences between two or more distributions across the entire scale, rather than at a single point (e.g., differences in means). Look <a rel="nofollow" href="https://github.com/DJAnderson07/esvis" target="_blank">here</a> for an example.</p>
<p><img src="https://i0.wp.com/rviews.rstudio.com/post/2017-09-25-August-Pkgs_files/esvis.png?resize=456%2C342&ssl=1" data-recalc-dims="1"></p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=fuser" target="_blank">fuser</a> v1.0.0: Provides functions for high-dimensional penalized regression across heterogeneous subgroups. The underlying model is described in detail in <a rel="nofollow" href="arxiv:1611.00953" target="_blank">Dondelinger and Mukherjee</a>. The <a rel="nofollow" href="https://cran.rstudio.com/web/packages/fuser/vignettes/subgroup_fusion.html" target="_blank">vignette</a> shows how to use the package for prediction over subgroups.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=gamlss.spatial" target="_blank">gamlss.spatial</a> v1.3.4: Provides functions to fit <a rel="nofollow" href="http://www.maths.lth.se/matstat/climate/ScalingWorkshop2011/JohanLSARMA2011_v3.pdf" target="_blank">Gaussian Markov Random Fields</a> within the Generalized Additive Models for Location Scale and Shape algorithms. The <a rel="nofollow" href="https://cran.rstudio.com/web/packages/gamlss.spatial/vignettes/GAMLSS_GMRF.pdf" target="_blank">vignette</a> introduces the package and provides several examples.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=INLAutils" target="_blank">INLAutils</a> v0.0.4: Provides a number of utility functions for solving models using the Integrated Nested Laplace Approximation <a rel="nofollow" href="http://www.r-inla.org/" target="_blank">INLA</a>, a new approach to statistical inference with latent Gaussian Markov random fields <a rel="nofollow" href="https://en.wikipedia.org/wiki/Markov_random_field" target="_blank">(GMRF)</a>. Look <a rel="nofollow" href="https://github.com/timcdlucas/INLAutils" target="_blank">here</a> for examples and plots.</p>
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<img src="https://i0.wp.com/rviews.rstudio.com/post/2017-09-25-August-Pkgs_files/INLAutils.png?w=456&ssl=1" data-recalc-dims="1">
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<p><a rel="nofollow" href="https://cran.r-project.org/package=missRanger" target="_blank">missRanger</a> v1.0.0: Provides an implementation of the <code>MissForest</code> algorithm for imputing mixed-type data sets by chaining tree ensembles that was introduced by <a rel="nofollow" href="https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btr597" target="_blank">Stekhoven and Buehlmann</a>. Look <a rel="nofollow" href="https://cran.rstudio.com/web/packages/missRanger/README.html" target="_blank">here</a> for an example.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=naniar" target="_blank">naniar</a> v0.1.0: Provides data structures and functions that facilitate the plotting of missing values and examination of imputations. There is a <a rel="nofollow" href="https://cran.rstudio.com/web/packages/naniar/vignettes/getting-started-w-naniar.html" target="_blank">Getting Started Guide</a> and a <a rel="nofollow" href="https://cran.rstudio.com/web/packages/naniar/vignettes/naniar-visualisation.html" target="_blank">Gallery of Missing Data Visualizations</a>.</p>
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<img src="https://i2.wp.com/rviews.rstudio.com/post/2017-09-25-August-Pkgs_files/naniar.png?w=456&ssl=1" data-recalc-dims="1">
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<p><a rel="nofollow" href="https://cran.r-project.org/package=powdist" target="_blank">powdist</a> v0.1.3: Provides density, distribution, and quantile functions, as well as a function for random draws from power and reversal power distributions.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=RATest" target="_blank">RATest</a> v0.1.0: Provides a collection of randomization tests, data sets, and examples currently focusing on permutation tests for baseline covariates in the sharp regression discontinuity design. See <a rel="nofollow" href="https://goo.gl/UZFqt7" target="_blank">Canay and Kamat</a> and the <a rel="nofollow" href="https://cran.rstudio.com/web/packages/RATest/vignettes/RDperm.pdf" target="_blank">vignette</a>.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=skpr" target="_blank">skpr</a> v0.35.1: Is an open-source design of experiments suite, for generating and evaluating optimal designs in R. The <a rel="nofollow" href="https://cran.rstudio.com/web/packages/skpr/README.html" target="_blank">README</a> file shows how to get started. <img src="https://i0.wp.com/rviews.rstudio.com/post/2017-09-25-August-Pkgs_files/skpr.png?w=456&ssl=1" data-recalc-dims="1"></p>
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<h3>Utilities</h3>
<p><a rel="nofollow" href="https://cran.r-project.org/package=blastula" target="_blank">blastula</a> v0.1: Allows users to compose and send HTML email messages that render across a range of email clients and device sizes. Messages are composed using Markdown and a text interpolation system that allows for the injection of evaluated R code within the message body. The <a rel="nofollow" href="https://cran.rstudio.com/web/packages/blastula/README.html" target="_blank">README</a> file describes how to use the package.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=blogdown" target="_blank">blogdown</a> v0.1: Enables users to write blog posts (like this one) and web pages in R Markdown. This package supports the static site generator <a rel="nofollow" href="https://gohugo.io/" target="_blank">Hugo</a> best, but it also supports <a rel="nofollow" href="http://jekyllrb.com/" target="_blank">Jekyll</a> and <a rel="nofollow" href="https://hexo.io/" target="_blank">Hexo</a>.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=cetcolor" target="_blank">cetcolor</a> v0.1.0: Offers a collection of perceptually uniform colour maps described by Peter Kovesi in the paper <a rel="nofollow" href="arxiv:1509.03700" target="_blank">Good Colour Maps: How to Design Them</a>. The <a rel="nofollow" href="https://cran.rstudio.com/web/packages/cetcolor/vignettes/cet_color_schemes.html" target="_blank">vignette</a> shows several examples.</p>
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<img src="https://i2.wp.com/rviews.rstudio.com/post/2017-09-25-August-Pkgs_files/cetcolor.png?w=456&ssl=1" data-recalc-dims="1">
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<p><a rel="nofollow" href="https://cran.r-project.org/package=googledrive" target="_blank">googledrive</a> v0.1.1: See the <a rel="nofollow" href="http://googledrive.tidyverse.org/index.html" target="_blank">googledrive website</a> for an example and instructions for getting started with the package.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=pointblank" target="_blank">pointblank</a> v0.1: Provides functions to validate data in local data frames, local <code>tibble</code> objects, in <code>csv</code> and <code>tsv</code> files, and in <code>PostgreSQL</code> and <code>MySQL</code> database tables. Look at the <a rel="nofollow" href="https://cran.rstudio.com/web/packages/pointblank/README.html" target="_blank">README</a> file for an example.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=reqres" target="_blank">reqres</a> v0.2.0: Provides functions to facilitate parsing of HTTP requests, creation of appropriate responses, and handling of the housekeeping involved in working with HTTP exchanges. See <a rel="nofollow" href="https://cran.rstudio.com/web/packages/reqres/README.html" target="_blank">README</a> to get started.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=rmapzen" target="_blank">rmapzen</a> v0.3.3: Provides an interface to the <a rel="nofollow" href="https://mapzen.com/documentation" target="_blank">Mapzen</a> API for geographic search and geocoding, isochrone calculation, and vector data to draw map tiles. Look <a rel="nofollow" href="https://tarakc02.github.io/rmapzen/" target="_blank">here</a> for examples.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=spelling" target="_blank">spelling</a> v1.0: Provides spell checking for common document formats including latex, markdown, manual pages, and description files.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=splashr" target="_blank">splashr</a> v0.4.0: Provides tools to work with the <a rel="nofollow" href="https://github.com/scrapinghub/splash" target="_blank">Splash</a> <code>JavaScript</code> Rendering and Scraping Service. There is an <a rel="nofollow" href="https://cran.rstudio.com/web/packages/splashr/vignettes/intro_to_splashr.html" target="_blank">Introduction</a> and vignettes on <a rel="nofollow" href="https://cran.rstudio.com/web/packages/splashr/vignettes/splashr_helpers.html" target="_blank">Helper Functions</a> and <a rel="nofollow" href="https://cran.rstudio.com/web/packages/splashr/vignettes/the_splashr_dsl.html" target="_blank">Working with the splashrDSL</a>.</p>
<p><a rel="nofollow" href="https://cran.r-project.org/package=writexl" target="_blank">writexl</a> v0.2: Implements a portable, light-weight data-frame-to-<code>xlsx</code> exporter based on <a rel="nofollow" href="https://libxlsxwriter.github.io/" target="_blank">libxlsxwriter</a>. No ‘Java’ or ‘Excel’ required.</p>
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<h3>Visualizations</h3>
<p><a rel="nofollow" href="https://cran.r-project.org/package=billboarder" target="_blank">billboarder</a> v0.0.3: Provides an <code>htmlwidgets</code> interface to <a rel="nofollow" href="https://naver.github.io/billboard.js/" target="_blank">billboard.js</a>, a re-usable, easy interface to the JavaScript chart library, based on D3 v4+. Chart types include line charts, scatter plots, bar charts, pie/donut charts, and gauge charts. There is an <a rel="nofollow" href="https://cran.rstudio.com/web/packages/billboarder/vignettes/billboarder-intro.html" target="_blank">Introduction</a> and a vignette on <a rel="nofollow" href="https://cran.rstudio.com/web/packages/billboarder/vignettes/billboarder-options.html" target="_blank">Options for Styling Charts</a>.</p>
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<img src="https://i1.wp.com/rviews.rstudio.com/post/2017-09-25-August-Pkgs_files/billboarder.png?w=456&ssl=1" data-recalc-dims="1">
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<p><a rel="nofollow" href="https://cran.r-project.org/package=cdparcoord" target="_blank">cdparcoord</a> v1.0.0: Provides functions for plotting parallel coordinates with resolutions for large data sets and missing values. The <a rel="nofollow" href="https://cran.r-project.org/web/packages/cdparcoord/vignettes/cdparcoord.html" target="_blank">vignette</a> offers several examples.</p>
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<img src="https://i1.wp.com/rviews.rstudio.com/post/2017-09-25-August-Pkgs_files/cdparcoord.png?w=456&ssl=1" data-recalc-dims="1">
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<p><a rel="nofollow" href="https://cran.r-project.org/package=gggenes" target="_blank">gggenes</a> v0.2.0: Provides a <code>ggplot2</code> geom and helper functions for drawing gene arrow maps.</p>
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<img src="https://i0.wp.com/rviews.rstudio.com/post/2017-09-25-August-Pkgs_files/gggene.png?w=456&ssl=1" data-recalc-dims="1">
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<p><a rel="nofollow" href="https://cran.r-project.org/package=quickPlot" target="_blank">quickplot</a> v0.1.1: Offers a high-level plotting system, built using ‘grid’ graphics, which is optimized for speed and modularity. The <a rel="nofollow" href="https://cran.rstudio.com/web/packages/quickPlot/vignettes/iii-plotting.html" target="_blank">vignette</a> provides examples.</p>
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<img src="https://i2.wp.com/rviews.rstudio.com/post/2017-09-25-August-Pkgs_files/quickplot.png?w=456&ssl=1" data-recalc-dims="1">
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<p><a rel="nofollow" href="https://cran.r-project.org/package=treemapify" target="_blank">treemapify</a> v2.3.2: Provides <code>ggplot2</code> geoms for drawing treemaps. There is a <a rel="nofollow" href="https://cran.rstudio.com/web/packages/treemapify/vignettes/introduction-to-treemapify.html" target="_blank">vignette</a> with examples.</p>
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