<p><div><div><div><div data-width="100" data-show-faces="false" data-send="true" data-layout="button_count" data-height="21" data-href="https://www.r-bloggers.com/march-17-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/2017/04/14/march-17-new-package-picks/"> R Views</a></strong>, and kindly contributed to <a rel="nofollow" href="https://www.r-bloggers.com/">R-bloggers)</a> </div>
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<p>Two hundred and sixteen new packages were added to CRAN in March. The following are my picks for the <em>Top Forty</em>, organized into five categories: Bioscience, Data, Data Science, Statistics and Utilities.</p>
<div>
<h3>Bioscience</h3>
<ul>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/BioInstaller/index.html">BioInstaller</a> v0.0.3: Provides tools to install and download massive bioinformatics analysis software and database, such as NGS analysis tools with its required database or/and reference genome.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/DSAIDE/index.html">DSAIDE</a> v0.4.0: Provides a collection of Shiny Apps that allow users to simulate and explore infectious disease transmission. The <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/DSAIDE/vignettes/DSAIDE.html">vignette</a> will get you started.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/treespace/index.html">treespace</a> v1.0.0: Provides tools for the exploration of distributions of phylogenetic trees. This package includes a Shiny interface which can be started from R. There are vignettes for <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/treespace/vignettes/DengueVignette.html">Dengue trees</a>, <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/treespace/vignettes/TransmissionTreesVignette.html">Transmission trees</a>, and for exploring <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/treespace/vignettes/introduction.html">landscapes of phylogenetic trees</a>. The following plot from the vignette shows clusters of similar trees.</p>
</li>
</ul>
<pre><code>library(treespace)
data(woodmiceTrees)
wm.res &lt;- treespace(woodmiceTrees,nf=3)
wm.groves &lt;- findGroves(wm.res, nclust=6)
plotGrovesD3(wm.groves)</code></pre>
<p>
<div></div>
<p> ### Data<br>
* <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/cropdatape/index.html">cropdatape</a> v1.0.0: Provides access to data from the <a target="_blank" rel="nofollow" href="http://siea.minagri.gob.pe/siea/?q=publicaciones/anuarios-estadisticos">Agricultural Ministry of Peru</a>.</p>
<ul>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/rdataretriever/index.html">rdataretriever</a> v1.0.0: Provides R access to the <a target="_blank" rel="nofollow" href="http://data-retriever.org/">Data Retriever</a> command line interface that automates the tasks of finding, downloading, and cleaning public datasets.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/rnaturalearth/index.html">rnaturalearth</a> v0.1.0: Provides functions to fetch <a target="_blank" rel="nofollow" href="http://www.naturalearthdata.com/">Natural Earth</a> map data. There is an <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/rnaturalearth/vignettes/rnaturalearth.html">introduction</a> and a <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/rnaturalearth/vignettes/what-is-a-country.html">vignette</a> on working with countries.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/ropercenter/index.html">ropercenter</a> v0.1.0: Provides registered users with programmatic, reproducible access to data sets from The <a target="_blank" rel="nofollow" href="https://ropercenter.cornell.edu/">Roper Center for Public Opinion Research</a>, which maintains the largest archive of public opinion data in existence. The <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/ropercenter/vignettes/ropercenter-vignette.htm">vignette</a> shows how to get started.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/statsgrokse/index.html">statsgrokse</a> v 0.1.4: Provides an API for the server containing <a target="_blank" rel="nofollow" href="http://stats.grok.se/">Wikipedia Page View Statistics</a> for the years 2008 to 2015.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/ukds/index.html">ukds</a> v0.1.0: Enables reproducible, programmatic retrieval of datasets from the <a target="_blank" rel="nofollow" href="https://www.ukdataservice.ac.uk/">UK Data Service</a>. The <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/ukds/vigne">vignette</a> shows how to setup and use it.</p>
</li>
</ul>
</div>
<div>
<h3>Data Science</h3>
<ul>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/anomalyDetection/index.html">anomalyDetection</a> v0.1.1: Implements procedures to aid in detecting network log anomalies. The <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/anomalyDetection/vignettes/Introduction.html">vignette</a> provides examples.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/kerasR/index.html">kerasR</a> v0.4.1: Provides an interface to the <a target="_blank" rel="nofollow" href="https://keras.io/">Keras</a> Deep Learning Library, which provides specifications for describing dense neural networks, convolution neural networks (CNN), and recurrent neural networks (RNN) running on top of either <a target="_blank" rel="nofollow" href="https://www.tensorflow.org/">TensorFlow</a> or <a target="_blank" rel="nofollow" href="http://deeplearning.net/software/theano/">Theano</a>. The <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/kerasR/vignettes/introduction.html">vignette</a> contains examples.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/modeval/index.html">modeval</a> v0.1.2: Allows users to easily compare multiple classifications models built with caret functions for small data sets. The <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/modeval/vignettes/modeval.html">vignette</a> provides examples.</p>
</li>
</ul>
<div>
<img src="https://i1.wp.com/rviews.rstudio.com/post/2017-04-13-march-17-new-package-picks_files/modeval.png?w=456&ssl=1" data-recalc-dims="1">
</div>
<ul>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/supc/index.html">supc</a> v0.1: Implements the self-updating process clustering algorithms proposed in <a target="_blank" rel="nofollow" href="doi:10.1080/00949655.2015.1049605">Shiu and Chen</a>. The <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/supc/vignettes/supc.html">vignette</a> contains examples.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/tensorflow/index.html">tensorflow</a> v0.7: Provides an interface to <a target="_blank" rel="nofollow" href="https://www.tensorflow.org/">TensorFlow</a>, an open-source software library for numerical computation using data flow graphs.</p>
</li>
</ul>
</div>
<div>
<h3>Statistics</h3>
<ul>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/frailtyEM/index.html">frailtyEM</a> v0.5.4: Contains functions for fitting shared frailty models with a semi-parametric baseline hazard using the Expectation-Maximization algorithm. The <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/frailtyEM/vignettes/frailtyEM_manual.pdf">vignette</a> explains the math.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/FRK/index.html">FRK</a> v0.1.1: Provides functions to build, fit and predict spatial random effects, fixed rank kriging models with large datasets. The <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/FRK/vignettes/FRK_intro.pdf">vignette</a> introduces the theory and shows some examples.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/hmi/index.html">hmi</a> v0.6-3: Allows users to build single-level and multilevel imputation models using functions provided, or functions from the mice and MCMCglmm packages. There is a <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/hmi/vignettes/my-vignette.html">vignette</a>.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/margins/index.html">margins</a> v0.3.0: Ports Stata’s <code>margins</code> command for calculating marginal (or partial) effects. There is an <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/margins/vignettes/Introduction.html">introduction</a>, a vignette on the <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/margins/vignettes/TechnicalDetails.pdf">Technical Implementation Details</a>, and a comparison with the <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/margins/vignettes/Stata.html">Stata Command</a>.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/mlrMBO/index.html">mlrMBO</a> v1.0.0: Provides a toolbox for Bayesian, model-based optimization. There is an <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/mlrMBO/vignettes/mlrMBO.html">introduction</a> and vignettes for <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/mlrMBO/vignettes/mixed_space_optimization.html">Mixed Space Optimization</a>, <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/mlrMBO/vignettes/noisy_optimization.html">Noisy Optimization</a>, and <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/mlrMBO/vignettes/parallelization.html">Parallelization</a>.</p>
</li>
</ul>
<div>
<img src="https://i2.wp.com/rviews.rstudio.com/post/2017-04-13-march-17-new-package-picks_files/mlrMBO.png?w=456&ssl=1" data-recalc-dims="1">
</div>
<ul>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/MonteCarlo/index.html">MonteCarlo</a> v1.0.0: Simplifies Monte Carlo simulation studies by providing functions that automatically set up loops to run over parameter grids, parallelize the computations, and generate output in LaTeX tables. The <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/MonteCarlo/vignettes/MonteCarlo-Vignette.html">vignette</a> shows how to use it.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/RankingProject/index.html">RankingProject</a> v0.1.1: Provides functions to generate plots and tables for comparing independently sampled populations. There is an <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/RankingProject/vignettes/intro.html">introduction</a> and a <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/RankingProject/vignettes/primer.pdf">vignette</a> that reproduces the figures from “A Primer on Visualizations for Comparing Populations, Including the Issue of Overlapping Confidence Intervals” by Wright, Klein, and Wieczorek (2017, The American Statistician, in press).</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/rjmcmc/index.html">rjmcmc</a> v0.2.2: Provides functions to perform <a target="_blank" rel="nofollow" href="doi:10.2307/2337340">reversible-jump MCMC</a> with the restriction introduced by <a target="_blank" rel="nofollow" href="doi:10.1080/00031305.2013.791644">Barker &amp; Link</a>. The <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/rjmcmc/vignettes/rjmcmcVignette.pdf">vignette</a> shows how to calculate posterior probabilities from the MCMC output.</p>
</li>
</ul>
</div>
<div>
<h3>Utilities</h3>
<ul>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/canvasXpress/index.html">canvasXpress</a> v1.5.2: Enables creation of visualizations using <a target="_blank" rel="nofollow" href="http://canvasxpress.org/">CanvasXpress</a>, a stand-alone JavaScript library for reproducible research. The <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/canvasXpress/vignettes/getting_started.html">vignette</a> shows how to get started.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/collapsibleTree/index.html">collapsibleTree</a> v0.1.4: Provides functions to build interactive Reingold-Tilford tree diagrams created using D3.js, where every node can be expanded and collapsed by clicking on it. There are some <a target="_blank" rel="nofollow" href="https://adeelk93.github.io/collapsibleTree/">examples</a> on the GitHub site.</p>
</li>
</ul>
<div>
<img src="https://i0.wp.com/rviews.rstudio.com/post/2017-04-13-march-17-new-package-picks_files/collapsibleTree.png?w=456&ssl=1" data-recalc-dims="1">
</div>
<ul>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/cronR/">cronR</a> v0.3.0: Allows users to schedule R scripts and processes on Unix/Linux systems, while <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/taskscheduleR/index.html">taskscheduleR</a> allows the same from Windows. See the <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/cronR/vignettes/cronR.html">cronR vignette</a> and the <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/taskscheduleR/vignettes/taskscheduleR.html">taskscheduleR vignette</a>.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/doctr/index.html">doctr</a> v0.2.0: Provides tools to help check the consistency and quality of a dataset. There are vignettes for <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/doctr/vignettes/doctr_compare.html">Comparing Tables</a>, <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/doctr/vignettes/doctr_diagnose.html">Dataset Diagnostics</a>, and <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/doctr/vignettes/doctr_examine.html">EDA Automation</a>.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/geojsonR/index.html">geojsonR</a> v1.0.1: Provides functions to process <a target="_blank" rel="nofollow" href="https://en.wikipedia.org/wiki/GeoJSON">GeoJson objects</a>. The <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/geojsonR/vignettes/the_geojsonR_package.html">vignette</a> gives the details.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/ggedit/index.html">ggedit</a> v0.2.1: Provides an interactive layer and theme aesthetic editor for ggplot2. The <a target="_blank" rel="nofollow" href="vhttps://metrumresearchgroup.github.io/ggedit/">ggedit gitbook</a> explains how to use it.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/implyr/index.html">implyr</a> v0.1.0: Provides a SQL backend to dplyr for <a target="_blank" rel="nofollow" href="https://impala.apache.org/">Apache Impala</a>.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/officer/index.html">officer</a> v0.1.0: Provides functions to manipulate <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/officer/vignettes/word.html">Microsoft Word</a> and <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/officer/vignettes/powerpoint.html">Microsoft Powerpoint</a> documents. This is a companion package to flextable.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/flextable/index.html">flextable</a> v.1.0: Includes functions to create tables in Word, PowerPoint, and HTML documents. There is an <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/flextable/vignettes/overview.html">overview</a>, and vignettes for <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/flextable/vignettes/format.html">explaining objects</a> and <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/flextable/vignettes/layout.html">table layout</a>.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/pivottabler/index.html">pivottabler</a> v0.1.0: Allows users to create complex pivot tables and pivot tables with irregular layouts in R. There are multiple vignettes, including an <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/pivottabler/vignettes/introduction.html">introduction</a>, a <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/pivottabler/vignettes/styling.html">styling guide</a>, a <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/pivottabler/vignettes/shiny.html">Shiny example</a> and explanations of <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/pivottabler/vignettes/calculations.html">calculations</a> and <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/pivottabler/vignettes/datagroups.html">data groups</a>.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/Polychrome/index.html">Polychrome</a> v0.8.2: Provides tools for creating, viewing, and assessing qualitative palettes with many (20-30 or more) colors. There is a colorful <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/Polychrome/vignettes/polychrome.html">vignette</a></p>
</li>
</ul>
<pre><code>library(Polychrome)
pal2 &lt;- alphabet.colors(26)
rancurves(pal2)</code></pre>
<p><img src="https://i2.wp.com/rviews.rstudio.com/post/2017-04-13-march-17-new-package-picks_files/figure-html/unnamed-chunk-2-1.png?w=450&ssl=1" data-recalc-dims="1"></p>
<ul>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/RApiDatetime/index.html">RApiDatetime</a> v0.0.3: Provides a C-level API to allow packages to access C-level R date and datetime code.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/Rcssplot/index.html">Rcssplot</a> v0.2.0.0: Provides tools to style plots with cascading style sheets. The <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/Rcssplot/vignettes/Rcssplot.pdf">vignette</a> shows how.</p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/reticulate/index.html">reticulate</a> v0.7: Implements an R interface to Python modules, classes, and functions. When calling into Python, R data types are automatically converted to their equivalent Python types. When values are returned from Python to R, they are converted back to R types. There is an <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/reticulate/vignettes/introduction.html">overview</a> and a vignette describing <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/reticulate/vignettes/arrays.html">arrays in R and Python</a></p>
</li>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/shinyWidgets/index.html">shinyWidgets</a> v0.2.0: Provides custom input widgets for Shiny apps. See the <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/shinyWidgets/README.html">README</a> for examples.</p>
</li>
</ul>
<div>
<img src="https://i1.wp.com/rviews.rstudio.com/post/2017-04-13-march-17-new-package-picks_files/shinyWidgets.png?w=456&ssl=1" data-recalc-dims="1">
</div>
<ul>
<li>
<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/shinyjqui/index.html">shinyjqui</a> v0.1.0: An extension to shiny that brings interactions and animation effects from the <code>jQuery UI</code> library. There is an <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/shinyjqui/vignettes/introduction.html">introduction</a> and a <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/shinyjqui/vignettes/orderInput.html">vignette</a> with examples.</p>
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<p><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/valaddin/index.html">valaddin</a> v0.1.0: Provides tools to transform functions into functions with input validation checks, in a manner suitable for both programmatic and interactive use. The <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/valaddin/vignettes/valaddin.html">vignette</a> shows how.</p>
</li>
</ul>
</div>
<p>
<div>
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