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(This article was first published on <strong><a href="https://www.rstudio.com/rviews/2016/12/07/november-package-picks/"> RStudio</a></strong>, and kindly contributed to <a rel="nofollow" href="https://www.r-bloggers.com/">R-bloggers)</a> </div>

<p>by Joseph Rickert</p>
<p>November was a prolific month for R developers: 189 new packages landed in CRAN. I have selected more than a quarter of them for this post, but I haven’t listed everything that is worth a look. My November 2016 picks are organized into four categories: Biotech (4 picks), Data (6 picks), Machine Learning (9 picks) , Statistics (9 picks), Time Series (4 picks) and Utilities (20 picks). The relatively large number of Utilities packages listed seriously over-represents this category. However, I have included so many to emphasize the cumulative impact of developers working to improve the R ecosystem at a fairly low level. Also, I believe that these sorts of packages are relatively difficult to discover.</p>
<h2>Biotech</h2>
<p>The packages listed under this heading support analyses in biostatistics, genetics and medicine.</p>
<ul>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/esaddle/">esaddle</a> v0.0.2: Provides functions for fitting the Extended Empirical Saddlepoint (<a target="_blank" rel="nofollow" href="https://arxiv.org/abs/1601.01849">EES</a>) density. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/esaddle/vignettes/esaddle.html">vignette</a> provides examples.</li>
<p><img src="https://i0.wp.com/www.rstudio.com/wp-content/uploads/2016/12/nov_package_pics1.png?w=456" data-recalc-dims="1"></p>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/incidence/">incidence</a> v1.0.1: Provides functions and classes to compute, manipulate and visualize incidence from dated events for defined time intervals. There are three vignettes including this <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/incidence/vignettes/overview.html">overview</a>.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/speaq2/">speaq2</a> v0.1.0: Provides wavelet-based tools for the analysis of NMR spectra. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/speaq2/vignettes/speaq2_illustrations.html">vignette</a> shows how to process a data set.</li>
<p><img src="https://i1.wp.com/www.rstudio.com/wp-content/uploads/2016/12/nov_package_pics2.png?w=456" data-recalc-dims="1"></p>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/starmie/">starmie</a> v0.1.2:Provides data structures and methods for manipulating the output of genetic population structuring algorithms. There is a <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/starmie/vignettes/using-starmie.html">Basic Usage</a> vignette, as well as one on <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/starmie/vignettes/using-starmie-admixture.html">Admixture models</a>.</li>
</ul>
<h2>Data</h2>
<p>The packages here provide access to data through various methods.</p>
<ul>
<li><a target="_blank" rel="nofollow" href="https://mran.revolutionanalytics.com/package/ALA4R/">ALA4R</a> v1.5.3: Provides an interface to the <a target="_blank" rel="nofollow" href="http://www.ala.org.au/">Atlas of Living Australia</a> (ALA) that allows users to access and visualize data on Australian plants and animals. The <a target="_blank" rel="nofollow" href="https://mran.revolutionanalytics.com/web/packages/ALA4R/vignettes/ALA4R.html">vignette</a> shows how to use it.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.revolutionanalytics.com/package/BatchGetSymbols/">BatchGetSymbols</a> v1.0: Makes it easy to download a large amount of trade data from Yahoo or Google Finance. There is a brief <a target="_blank" rel="nofollow" href="https://mran.revolutionanalytics.com/web/packages/BatchGetSymbols/vignettes/BatchGetSymbols-vignette.html">vignette</a>.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.revolutionanalytics.com/package/elasticsearchr/">elasticsearchr</a> v0.1.0: Provides a lightweight interface to <a target="_blank" rel="nofollow" href="https://www.elastic.co/products/elasticsearch">Elasticsearch</a>, a NoSQL search engine and column store database. The <a target="_blank" rel="nofollow" href="https://mran.revolutionanalytics.com/web/packages/elasticsearchr/vignettes/quick_start.html">vignette</a> provides details.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.revolutionanalytics.com/package/hansard/">hansard</a> v0.2.5: Provides functions for downloading data using the <a target="_blank" rel="nofollow" href="http://www.data.parliament.uk/">UK Parliament API</a>. The <a target="_blank" rel="nofollow" href="https://mran.revolutionanalytics.com/web/packages/hansard/vignettes/hansard-example.html">vignette</a> describes how to access information on individual members of parliament, briefings and more.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.revolutionanalytics.com/package/isdparser/">isdparser</a> v0.1.0: Provides tools for parsing NOAA Integrated Surface Database (<a target="_blank" rel="nofollow" href="https://www.ncdc.noaa.gov/isd">ISD</a>) files. The <a target="_blank" rel="nofollow" href="https://mran.revolutionanalytics.com/web/packages/isdparser/vignettes/isdparser_vignette.html">vignette</a> gives the basics on reading and parsing the files.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.revolutionanalytics.com/package/RBMRB/">RBMRB</a> v2.0: Provides an interface to the Biological Magnetic Resonance Data Bank (<a target="_blank" rel="nofollow" href="http://www.bmrb.wisc.edu/">BMRB</a>), along with tools for NMR images. Look <a target="_blank" rel="nofollow" href="https://cdn.rawgit.com/uwbmrb/RBMRB/master/man/RBMRB.html">here</a> for documentation.</li>
</ul>
<h2>Machine Learning</h2>
<p>The packages listed here are geared towards machine-learning applications.</p>
<ul>
<li><a target="_blank" rel="nofollow" href="https://mran.revolutionanalytics.com/package/bcROCsurface/">bcROCsurface</a> v1.0-1: Offers functions to compute bias-corrected estimates of ROC curves. There is a <a target="_blank" rel="nofollow" href="https://mran.revolutionanalytics.com/web/packages/bcROCsurface/vignettes/example.html">guide</a>.</li>
<p><img src="https://i0.wp.com/www.rstudio.com/wp-content/uploads/2016/12/nov_package_pics3.png?w=456" data-recalc-dims="1"></p>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/BiBitR/">BiBitR</a> v0.1.0: raps the Java BiBIt biclustering algorithm for extracting bit-patterns from binary data sets. See the <a target="_blank" rel="nofollow" href="http://bioinformatics.oxfordjournals.org/content/27/19/2738.abstract">Bioinformatics paper</a> for details.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/cleanNLP/">cleanNLP</a> v0.24: Provides a Tidy Data model based on dplyr for converting a textual corpus into a set of normalized tables. The underlying NLP pipeline is based on Stanford’s <a target="_blank" rel="nofollow" href="http://stanfordnlp.github.io/CoreNLP/">CoreNLP</a> library.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/ffstream/">ffstream</a> v0.1-5: Provides an implementation of the adaptive forgetting factor algorithm for estimating the mean and variance of a data stream in order to detect multiple checkpoints. The details are in the <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/ffstream/vignettes/ffstream_html.html">vignette</a>.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/FTRLProximal/">FTRLProximal</a> v0.1.2: Implements the <a target="_blank" rel="nofollow" href="https://courses.cs.washington.edu/courses/cse599s/12sp/scribes/Lecture8.pdf">Regularized Leader Proximal algorithm</a> for online training of large-scale regression models using a mixture of L1 and L2 regularization</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/IDmining/">IDmining</a> v1.0.0: Contains functions for mining large high-dimensional data sets using the Intrinsic Dimension technique. This <a target="_blank" rel="nofollow" href="https://arxiv.org/abs/1608.05581">paper</a> describes the idea.</li>
<li><a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/mltools/index.html">mltools</a> v0.1.0: Provides a collection of machine learning helper functions for exploratory analysis. The <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/mltools/README.html">README file</a> provides some details.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/OpenML/">OpenML</a> v1.1: Provides an interface to the <a target="_blank" rel="nofollow" href="http://www.openml.org/">OpenML</a> online machine-learning platform. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/OpenML/vignettes/OpenML.pdf">vignette</a> provides an example of how to use it.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/rucrdtw/">rucrdtw</a> v0.1.1: Provides R bindings for functions from the <a target="_blank" rel="nofollow" href="http://www.cs.ucr.edu/~eamonn/UCRsuite.html">UCR Suite</a> (Rakthanmanon et al. 2012), which enables ultrafast subsequence search under both Dynamic Time Warping and Euclidean Distance. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/rucrdtw/vignettes/using_rucrdtw.html">vignette</a> shows how to use the package.</li>
</ul>
<h2>Statistics</h2>
<p>The packages listed under this heading mostly offer algorithms to support statistical analyses. Notable are queuecomputer, which implements a discrete event simulation, and regtools, which could have also been listed under the Machine Learning heading.</p>
<ul>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/bayesplot/">bayesplot</a> v1.0.0: Provides plotting functions for posterior analysis, model checking, and MCMC diagnostics. There are vignettes for <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/bayesplot/vignettes/MCMC-diagnostics.html">MCMC diagnostics</a>, plotting <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/bayesplot/vignettes/MCMC.html">MCMC draws</a>, and <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/bayesplot/vignettes/PPC.html">graphical posterior checks</a>.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/eMLEloglin/">eMLEloglin</a> v1.0.1: Provides functions for fittlin log-linear models of sparse contingency tables. See the <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/eMLEloglin/vignettes/User_manual.pdf">user manual</a> for the math.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/POT/">POT</a> v1.1-6 : Implements functions to perform <a target="_blank" rel="nofollow" href="https://arxiv.org/pdf/1509.01051.pdf">Peaks Over Threshold</a> analysis, useful in Extreme Value Theory. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/POT/vignettes/POT.pdf">vignette</a> explains the math.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/queuecomputer/">queuecomputer</a> v0.5.1: Provides computationally efficient solutions for simulating queues with arbitrary arrival and service times. There is a vignette describing how to <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/queuecomputer/vignettes/Howto.html">use the package</a> and one showing how to <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/queuecomputer/vignettes/MMk_queues.html">simulate M/M/k queues</a>.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/regtools/">regtools</a> v1.0.1: Provides novel tools for linear and nonlinear regression, and nonparametric regression and classification. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/regtools/vignettes/regtools.html">vignette</a> contains examples.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/revdbayes/">revdbayes</a> v1.0.0: Provides functions for the Bayesian analysis of extreme value models. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/revdbayes/vignettes/revdbayes-vignette.html">vignette</a> contains several interesting examples and references.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/slim/">slim</a> v0.1.0: Provides functions to fit singular linear models to longitudinal data. The theory is described in this <a target="_blank" rel="nofollow" href="http://biomet.oxfordjournals.org/content/early/2010/01/20/biomet.asp068.abstract">Biometrika paper</a>, and the <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/slim/vignettes/slim.pdf">vignette</a> provides examples.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/varband/">varband</a> v0.9.0: Implements the variable banding procedure described in a <a target="_blank" rel="nofollow" href="https://arxiv.org/abs/1604.07451">paper</a> by Yu and Bien for modeling local dependence and estimating precision matrices. The vignette shows how to use the package. The following plot shows the sparsity patterns of the true model, and the sample covariance matrix for one of the examples.</li>
<p><img src="https://i1.wp.com/www.rstudio.com/wp-content/uploads/2016/12/nov_package_pics4.png?w=456" data-recalc-dims="1"></p>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/xyz/">xyz</a> v0.1: Implements an <a target="_blank" rel="nofollow" href="https://arxiv.org/pdf/1610.05108v1.pdf">algorithm</a> by Thanei, Meinshausen and Shah for finding strong interactions in almost linear time. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/xyz/vignettes/xyz-vignette.html">vignette</a> contains an example.</li>
</ul>
<h2>Time Series</h2>
<p>The packages listed here explicitly call out time series applications.</p>
<ul>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/GeomComb/">GeomComb</a> v1.0: Provides an eigenvector-based method for combining time series forecasts.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/ptest/">ptest</a> v1.0-8: Implements p-value computations for testing periodicity in short time series. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/ptest/vignettes/Introduction_to_the_ptest_package.html">vignette</a> provides examples and references.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/tsdisagg2/">tsdisagg2</a> v0.1.0: Provides functions to disaggregate low frequency time series data to higher frequency series. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/tsdisagg2/vignettes/tsdisagg2manual.pdf">vignette</a> describes the math and provides references.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/zoocat/">zoocat</a> v0.2.0: Extends the zoo class and provides tools for manipulating multivariate time series data. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/zoocat/vignettes/my-vignette.html">vignette</a> contains an example.</li>
</ul>
<h2>Utilities</h2>
<p>The packages listed here are a varied collection of convenience utilities, package extensions, gateways to other software, and low-level computing functions. Notable are flock and subprocess, which feel like systems-level programming.</p>
<ul>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/batchtools/">batchtools</a> v0.9.0: As a successor of the packages ‘BatchJobs’ and ‘BatchExperiments’, this package provides a parallel implementation of the Map function for high-performance computing systems managed by schedulers such as ‘IBM Spectrum LSF’ (), ‘OpenLava’ (), and others. There are four vignettes, including this one on <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/batchtools/vignettes/ErrorHandling.html">error handling</a>.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/benchr/">benchr</a> v0.1.0: Provides infrastructure to accurately measure and compare the execution times of R expressions. Usage is described <a target="_blank" rel="nofollow" href="https://gitlab.com/artemklevtsov/benchr">here</a>.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/bindr/">bindr</a> v0.1: Provides an interface for creating active binding where the bound function accepts additional arguments. Usage is described <a target="_blank" rel="nofollow" href="https://github.com/krlmlr/bindr">here</a>.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/bytescircle/">bytescircle</a> v1.0: Shows statistics about bytes contained in a file as a circle graph of deviations from mean in sigma increments. The following plot from the <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/bytescircle/vignettes/bytescircle.pdf">vignette</a> shows byte values mapped as an archimedean spiral, where each byte value is represented as a color circle and size indicates the deviation from sigma.</li>
<p><img src="https://i1.wp.com/www.rstudio.com/wp-content/uploads/2016/12/nov_package_pics5.png?w=456" data-recalc-dims="1"></p>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/crul/">crul</a> v0.1.0: Implements a simple HTTP client for making HTTP requests. Look at the <a target="_blank" rel="nofollow" href="https://github.com/ropensci/crul">GitHub README file</a> for information on where to start.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/datapasta/">datapasta</a> v1.0.0: Provides three addins for copying and pasting tables and vectors from Excel, Jupyter, and websites into the RStudio editor. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/datapasta/vignettes/how-to-datapasta.html">vignette</a> provides an example.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/debugme/">debugme</a> v1.0.1: Offers functions to specify debugging messages as special string constants, and control package debugging via environment variables. Look here for <a target="_blank" rel="nofollow" href="https://github.com/gaborcsardi/debugme#readme">an example</a>.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/errorizer/">errorizer</a> V0.1.1: Creates “errorized” versions of existing R functions with enhanced capabilities for logging and error handling. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/errorizer/vignettes/errorize.html">vignette</a> provides an example and describes the limitations of the method.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/fauxpas/">fauxpas</a> v0.1.0: Provides methods for general-purpose HTTP error handling. Integrates with packages crul, curl and httr. Look <a target="_blank" rel="nofollow" href="https://github.com/ropenscilabs/fauxpas">here</a> for crul and curl examples.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/flock/">flock</a> v0.7: Nitty-gritty package that implements synchronization between R processes using file locks.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/ggforce/">ggforce</a> v0.1.1: Offers new stats and geoms to be used with ggplot2. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/ggforce/">vignette</a> provides several examples.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/ggstance/">ggstance</a> v0.3: an extension to ggplot2 that provides flipped components and horizontal versions of stats and geoms. The package <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/ggstance/README.html">README file</a> contains examples.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/naptime/">naptime</a> v1.2.0: Provides a “near drop-in” replacement for base::Sys.sleep() that allows for more control of delays. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/naptime/vignettes/naptime.html">vignette</a> explains the why and how of napping.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/packagedocs/">packagedocs</a> v0.4.0: Should make writing package vignettes a little easier by providing functions for building websites of Package Documentation. See the <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/packagedocs/vignettes/docs.html">quick start manual</a> and <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/packagedocs/vignettes/rd.html">package reference manual</a>.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/reactR/">reactR</a> v0.1.0: Provides an interface to the <a target="_blank" rel="nofollow" href="https://facebook.github.io/react/">React</a> Javascript library for building user interfaces. There is an <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/reactR/vignettes/intro_reactR.html">introduction</a>.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/rly/">rly</a> v1.0.1: Another nitty-gritty package, it provides an R implementation of the parsing tools <a target="_blank" rel="nofollow" href="http://dinosaur.compilertools.net/">lex and yacc</a>. See the <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/rly/README.html">README file</a> for examples.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/spark.sas7bdat/">spark.sas7bdat</a> V1.0: Allows R users to read SAS data files into Spark. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/spark.sas7bdat/vignettes/spark_sas7bdat_examples.html">vignette</a> indicates how to read SAS data in parallel.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/startup/">startup</a> v0.3.0: Provides new directories to specify R’s startup configuration that makes it possible to keep private / secret variables separate from other environment variables. See the <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/startup/README.html">README file</a>.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/subprocess/">subprocess</a> v0.7.4 : Brings systems-level programming to R, with the capability to create, interact with and control the life cycle of child processes. The <a target="_blank" rel="nofollow" href="https://mran.microsoft.com/web/packages/subprocess/vignettes/intro.html">vignette</a> shows how.</li>
<li><a target="_blank" rel="nofollow" href="https://mran.microsoft.com/package/tesseract/">tesseract</a> v1.2: Allows text to be extracted from an image. This is an OCR engine with unicode (UTF-8) support that can recognize over 100 languages. See the <a target="_blank" rel="nofollow" href="https://cran.r-project.org/web/packages/tesseract/README.html">README file</a>.</li>
</ul>
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