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Package Spotlight

 

Each release of Microsoft R Open (and previously Revolution R Open) has a default, fixed repository date. Look below to learn about some of the new and updated packages available with the default repository for that release. Use the `checkpoint` function] to use packages released after the snapshot date listed. Package update data sourced from CRANberries, where you can find a detailed log of R package updates.

logo.jpg Microsoft R Open 3.3.2

By default, Microsoft R Open 3.3.2 uses a fixed CRAN repository snapshot taken on November 1, 2016. The following list spotlights some of the new and updated CRAN packages that were released between 7/1/16 and 10/30/16. These packages and more are available for use with the Microsoft R Open 3.3.2.


Data Munging:

  • anytime: Convert anything that looks vaguely like a date into a POSIXct object. Examples here.

  • fasttime: Fast functions for timestamp manipulation.

  • forcats: Tools for working with categorical variables (factors).

  • roll: Parallel functions for computing rolling statistics of time-series data.

  • stringb: String handling functions with an interface like stringr/stringi, but without the dependencies.

  • tidyverse: A collection of popular packages for data munging from Hadley Wickham. More here.


Data Sources:

  • countyweather: Meterological time series data for U.S. counties, from NOAA.

  • darksky: Interface to the Dark Sky API, which provides current or historical global weather conditions.

  • energyr: Data published by the United States Federal Energy Regulatory Commission.

  • genderNames: API client for genderize.io which will tell you the gender of the name you input.

  • Rlinkedin: (updated): Provides access to the LinkedIn API for people, job, and discussion data.

  • outbreaks: A collection of disease outbreak data, some real, some simulated.

  • rnoaa: Download NOAA weather data. Vignettes provided for many different data types.

  • rpinterest: Access the Pinterest API for data on boards, pins and users.

  • ttbbeer: Beer statistics from the U.S. Department of the Treasury, Alcohol and Tobacco Tax and Trade Bureau.

  • ubeR: Interface to the Uber API.


Graphics:

  • cartogram: Create and plot a continuous area cartogram by a rubber sheet distortion algorithm.

  • colourlovers: Provides access to the COLOURlovers API, which offers color inspiration and color palettes.

  • earthtones: Derive a color palette from a satellite image of a location on Earth. The vignette includes examples.

  • Homeric: Doughnut plots - pie charts with a blank center. The package is named after Homer Simpson.

  • RSVGTipsDevice (updated): An R SVG graphics device with support for dynamic tips and hyperlinks.

  • tweenr (updated): Create smooth animations by interpolating data.


Interfaces:

  • haven (updated): Import and export SPSS, Stata and SAS Files. Details here.

  • readr (updated): Read flat/tabular text files from disk (or a connection). Overview here.

  • SnakeCharmR: Run Python code, make function calls, and assign and retrieve variables from R.

  • sofa: Provides an interface to the NoSQL database CouchDB.

  • sparklyr: Provision, connect and interface to Apache Spark from within R. Details at spark.rstudio.com.

  • XR: Support for interfaces from R to other languages, described in the book “Extending R” by John Chambers.


Programming Tools:

  • checkpoint (updated): Easily use R packages from a specific date for reproducibility (see the vignette). This update adds the ability to delete snapshots and use a local snapshot repository.

  • curl (updated): A modern and flexible web client for R. Vignette included.

  • curry: Partial function application with %<%, %-<%, and %><%.

  • jsonlite (updated): fast JSON parser and generator optimized for statistical data and the web.

  • proto (updated): An object oriented system using object-based rather than class-based object oriented ideas, maintained by Hadley Wickham. Includes this vignette.

  • Rfast: Fast covariance matrix calculation, Mahalanobis distance and column-wise variances and other fast reimplementations of R functions.

  • sticky: Allows objects to be marked as 'sticky' and have resilient attributes that persist during many operations.

  • types: Simple type annotation for R, as a convention to allow other packages to provide error checking, automatic documentation or optimizations.


Reporting:


Statistical Modeling and Analysis:

  • arc: Classification-based on Association Rules (CBA) algorithm for association rule classification (ARC).

  • brms: Bayesian regression models using Stan. Vignette included.

  • CADStat: Provides a GUI to several statistical methods including generalized linear regression, conditional probability calculations, and regression trees. The manual provides more details.

  • endogenous: Classical Simultaneous Equation Models.

  • ensembleR: Functions to use ensembles of several machine learning models specified in caret package.

  • MSGARCH: Markov-Switching GARCH Models.

  • oddsratio: Odds Ratio Calculation for Generalized Additive Models and Generalized Linear Models.

  • pkmon: Least-squares estimators under k-monotony constraint. Pikachu not included.

  • radiant: Business analytics using R and Shiny. Overview here.

  • simputation: Missing value imputation methods that work with the magrittr %>% pipe operator. Vignette included.

  • spikes: Detect election fraud from irregularities in vote-share distributions.

  • SurvDisc: Functions for discrete time survival analysis and longitudinal analysis, from the FDA.


Utilities:

  • convertr: Convert between a broad range of scientific, historical, and industrial unit types.

  • digitize: Extract data from images of printed charts.

  • measurements: Convert between metric and imperial measurement units.

  • qrencoder: Create scannable QR codes and matrix barcodes.

  • optimr: A replacement and extension of the 'optim' function for smooth, possibly box constrained functions of several or many parameters.

  • RDocumentation: Display help files as they appear on RDocumentation.org

  • triangulation: Determine the location of an observer based on the angle towards three known points.


Other:

  • FuzzyR Design and simulate fuzzy logic systems using Type 1 Fuzzy Logic.

  • statquotes Random quotations on topics in statistics, data visualization and science.

  • wfindr Crossword, Scrabble and anagram solver.


Packages on GitHub and Elsewhere

This section highlights some R packages and code that are not (or not yet) available on CRAN.

For a more complete view of what’s trending on GitHub check here.



logo.jpg Microsoft R Open 3.3.1

By default, Microsoft R Open 3.3.1 uses a fixed CRAN repository snapshot taken on July 1, 2016. The following list spotlights some of the new and updated CRAN packages that were released between 6/1/16 and 6/30/16. These packages and more are available for use with the Microsoft R Open 3.3.1.


New Packages

The following list spotlights some of the new and updated CRAN packages that were released between 6/1/16 and 6/30/16. These packages and more are available for use with Microsoft R Open 3.3.1.

  • bigQueryR V0.1.0: Provides an interface to Google's BigQuery. The vignette shows how to use it.

  • bnspatial V0.9: Provides tools for implementing Bayesian Networks in geographical space. The vignette shows how to get started.

  • bunchr V0.1.0: Provides functions to view and analyze bunched data. Read about bunching in the vignette.

  • cointmonitoR V0.1.0: Provides a procedure for detecting the transition from stationary to integrated behavior for time series. Here is the theory.

  • DBItest V1.2: Functions to test Data base backends for confromity to an interface.

  • dlstats V0.0.5: Provides monthly download statistics for CRAN and Bioconductor. The vignette shows some of what you can do.

  • dtplyr V0.0.1: Implements a data table backend for dplyr allowing data.table and dplyr to be used together.

  • extremefit V0.1.1: Extreme value theory calculations to estimate conditional quantiles and probabilities.

  • fuzzr V0.1.0; Functions to test R functions. Here's how.

  • gaussfacts V0.1.1: Provides random "facts" about Carl Friedrich Gauss. Two or three of these and you will be fine again.

  • ggfortify V0.2.0: Provides tools to use ggplot() to plot results from common statistical analyses in a uniform way. There are introductions in English and Chinese and vignettes for probability distirbutions, GLMs, Geospatial data, PCA analyses, survival curves and Time Series.

  • googleAnalyticsR V0.2.1: Provides an interface to the Google Analytics Reporting API. There is a vignette.

  • googleway V1.0.0: Privides functions to retrieve data from 6 google maps.

  • gutenberg V0.1.2: Search and download public domain works in the Project Gutenberg collection. The vignette shows you how.

  • LindelyR V1.1.0: Provides the probability functions for the discrete and continuous Lindley distribution.

  • macleish V0.3.0: Provides functions to data from the Ada & Archibald MacLeish field station in Whately, MA. The vignette shows how to obtain weather data.

  • manhattanly V0.1.0: Uses Plotly.js to create interactive Q-Q and Manhatttan plots. Here is the vignette.

  • mcglm V0.3.0: Provides functions for fitting multivariate covariance generalized linear models McGLMs. There are examples for count, continuous and survey data.

  • microplot V1.0-14: Provides functions to embed microplots into LaTex or HTML tables. Here are some examples.

  • muckrock V0.1.0: Contains public domain information obtained by muckrock through the US Freedom of Information Act.

  • mscstexta4r V0.1.2: Provides an R Client for the Microsoft Cognitive Services Text Analytics REST API.

  • NoiseFilterR V0.1.0: Implements algorithms to preprocess label noise in classification problems. See the vignette on label noise.

  • npROCRegression V1.0.2: Implements kernel-based nonparametric regression modeling. The vignette provides some theory and examples.

  • osi V0.1.0: Provides a conector to the Open Source Initiative API that provides machine --readable data about open source software licenses.

  • pewdata V0.1.0: Provides for reproducible, programmatic retrieval of survey datasets from the Pew Research Center. The vignette shows how to setup and use the package.

  • polmineR V0.6.1: Provides text mining tools for the analysis of large corpora using the IMS Open Corpus Workbench (CWB) as he backend. There is a vignette to get you started.

  • preprosim V0.1.0: Provides functions to simulate artificial data. There is a short vignette.

  • rAmCharts V2.0.2: Provides an interface for using the Javascript AmCharts library. Look here to get started

  • RFinfer V0.2.0: Provides a prediction variance function and other tools for Random Forests. There are Introduction and Jackknife vignettes.

  • rmapshaper V0.1.0: Is a wrapper around the javascript mapshaper API to edit "geojson" spatial objects. A vignette introduces the basics.

  • roseteApi V1.0: Interface to the Rosette text analysis toolkit.

  • rvcheck V0.0.2: Allow you to check the latest version R and R packages on both CRAN and Bioconductor.

  • simstudy V0.1.1: Simulates data sets. The vignette shows how.

  • sjstats V0.2.0: Provides a collection of functions for common statistical computations not directly provided in {base} or {stats}.

  • tableHTML V0.2.10: Provides functions to create and style HTML tables that are compatible with Shiny.

  • vembdedr V0.1.0: Functions to generate the HTML to embed hosted video into R Markdown documents and Shiny apps. There is a vignette.


Packages on GitHub and Elsewhere

This section highlights some R packages and code that are not (or not yet) available on CRAN. For a more complete view of what’s trending on GitHub check here.

 

logo.jpg Microsoft R Open 3.3.0

By default, Microsoft R Open 3.3.0 uses a fixed CRAN repository snapshot taken on June 1, 2016. The following list spotlights some of the new and updated CRAN packages that were released between 5/1/16 and 5/31/16. These packages and more are available for use with the Microsoft R Open 3.3.0.


New Packages

The following list spotlights some of the new and updated CRAN packages that were released between 5/1/16 and 5/31/16. These packages and more are available for use with Microsoft R Open 3.3.0.

  • cocor V1.1-3: Implements tests for the comparison of correlations. There is a nice website.

  • dataone V2.0.0: The dataone R package enables R scripts to search, download and upload science data and metadata to the DataONE Federation. There are several vignettes including this overview.

  • eechidna V0.1: Provides the data from the 2013 Australian Federal Election and tools to analyze it. There are several nicely done vignettes.

  • extremeStat V0.5.16: Provides code to fit and plot several extreme value functions. See the vignette on quantile estimation.

  • fakeR V1.0: Generates fake data based on a given data set for both time dependent and time independent variables. See the vignette.

  • feather V0.0.1: Provides functions to read and write feather files.

  • flexdashboard V0.2.0: Provides a format for converting an R Markdown document to a grid oriented dashboard.

  • GRANBase V1.1.14: Provides tools for creating continuously integrated package repositories from manifests. See the overview.

  • heatmaply V0.3.2: Allows you to create interactive heatmaps that are usable from the Rstudio IDE, R Markdown documents and Shiny apps, based on ggplot2. There is a nice vignette.

  • jose V0.1: Functions for reading and wroting JSON web tokens which are useful for securely transferring claims. See the vignettes on JSON web keys and JSON web tokens.

  • mvtboost V0.5.0: Fits a multivariate decision tree model for multiple continuous outcome variables. See vignettes mpg example and Well-being example.

  • nasadata V0.9.0: Provides an interface to NASA's Earth Imagery and Assets API and Earth Observatory and Natural Event Tracker.

  • netdiffuseR V1.16.5: Provides functions for simulating diffusion processes and calculating network diffusion statistics. There is an example of the diffusion of medical innovations and vignettes for simulation, data importing and exporting and susceptibility and infection.

  • profvis V0.3.2: Provides interactive visualizations for profiling R Code.

  • riem V0.1.0: Fetches weather data from ASOS stations. See the vignette.

  • rmsfact V0.0.2: Provides random quotes from Richard M. Stallman. To be used when gaussfacts doesn't quite do it for you.

  • TippingPoint V1.1.0: Implements the tipping point method of Campbell, Pennello and Yue to visualize missing data and calculate the point that would change the result of a study. There is a very nice vignette.

  • vembdedr V0.1.0: Functions to generate the HTML to embed hosted video into R Markdown documents and Shiny apps. There is a vignette.

  • waterfalls V0.1.0: Contains a single function to produce waterfall charts in ggplot2.


Packages on GitHub and Elsewhere

This section highlights some R packages and code that are not (or not yet) available on CRAN. For a more complete view of what’s trending on GitHub check here.

  • R/qtl: Provides functions for mapping quantitative trait loci in experimental crosses.

 

logo.jpg Microsoft R Open 3.2.5

By default, Microsoft R Open 3.2.5 uses a fixed CRAN repository snapshot taken on May 1, 2016. The following list spotlights some of the new and updated CRAN packages that were released between 4/1/16 and 4/30/16. These packages and more are available for use with the Microsoft R Open 3.2.5.


New Packages

The following list spotlights some of the new and updated CRAN packages that were released between 4/1/16 and 4/30/16. These packages and more are available for use with Microsoft R Open 3.2.5.

  • asymmetry V1.0: Provides functions to implement the slide vector model for the analysis and graphical display of asymmetry of a proximity matrix.

  • bootTimeInference V0.1.0: Provides functions for hypothesis testing with the Sharpe Ratio. The details are in the JEF paper.

  • bridgedist V0.1.0: Provides and implementation of the Bridge Distribution with Logit-Link. The vignette introduces the basics.

  • BWStest V0.1.0: Performs the Baumgartner-Weiss-Schindler two-sample test of equal probability distributions.

  • ClusterRankTest V1.0: Provides Nonparametric rank based tests (rank-sum tests and signed-rank tests) for clustered data, especially useful for clusters having informative cluster size and intra-cluster group size. See the paper

  • deeplearning V0.1.0: Employes Rectifier Linear Unit functions to implement a deeplearning neural network and trains the network with stochastic gradient descent method with batch normalization.

  • factoextra V1.0.3: Contains some nice functions to extract and visualize the output of multivariate data analyses. See the web page.

  • fbRads V0.2: Provides wrapper functions for the Facebook Marketing API.

  • FuzzyAHP V0.6.1: Provides functions for calculating an Analytic Hierarchy Process with classic and fuzzy weights based on Saaty's pairwise comparison method for determination of weights. This vignette provides examples.

  • fuzzyjoin V0.1: Provides functions to j oin tables together based not on whether columns match exactly, but whether they are similar by some comparison. The vignette shows how to use the package.

  • gencve V0.3: Provides functions to facilitate the cross validation of many regression and prediction algorithms.

  • ggsci V1.1: A collection of 'ggplot2' color palettes inspired by scientific journals and science fiction TV shows. The vignette is very nice.

  • grpSLOPE V0.1.0: Implements the penalized linear regression method of Brzyski et al. for the adaptive selection of groups of significant predictors in a high-dimensional linear model. Have a look at the vignette.

  • haplotyper V0.1: Provides tools for Clustering Genotypes in Haplotypes. The vignette provides examples.

  • hextri V0.1: Provides functions to display hexagonally binned scatterplots for multi-class data, using colored triangles to show class proportions. - Very cool vignette.

  • imputeTestbench V0.1.0: Provides a test bench for comparison of missing data imputation methods. There is a vignette.

  • janeaustenrV0.1.0: Contains the full text of Jane Austen's six completed novels.

  • machine V0.1.3: Provides functions to connect to machi.na, create time series, and run backtests on a selected portfolio.

  • mixedsde V1.0: Proposes 3 methods for density estimation in the special context of stochastic differential equation with linear random effects in the drift.

  • msmtools V1.0: Provides functions for structuring longitudinal data to work with the msm package for analyzing continuous time Markov Chains. There is a nice vignette.

  • mvcluster V1.0: Implements multi-view bi clustering algorithms.

  • nmfgpu4R V0.2.4: Is a wrapper package for the nmfgpu library, which implements several Non-negative Matrix Factorization algorithms for CUDA platforms.

  • ParallelTree V0.1.0: Provides functions to create parallel tree plots, a variation of parallel coordinate plots.

  • postGIStools V0.1.0: Provides gunctions to convert geometry and 'hstore' data types from 'PostgreSQL' into standard R objects, as well as to simplify the import of R data frames. There is a vignette.

  • RFc V0.1-1: Fetch environmental data such as air temperature, precipitation rate and wind speed from the FetchClimate Web service based on user specified arguments such as geographical regions or coordinates and time bounds.

  • rnpn V0.1.0: Monitor the effects of climate change with this interface to the National Phenology Network.

  • roahd V1.0: Provides functions for the robust analysis of high dimensional functional data. See the vignette for details.

  • roll V1.0.0: Contains parallel functions for computing rolling statistics of time-series data

  • rrefine V1.0: Provides an interface to the OpenRefine Library of functions for dealing with messy data. The vignette provides examples.

  • ShapePattern V1.0: Provides tools for analyzing planar shapes.

  • sparsesvd V0.1: Provides a wrapper around the SVDLIBC library for truncated singular value decomposition of a sparse matrix.

  • tidytext V0.1.0: Based dplyr, broom and tidyr this package contains functions to facilitate text mining by converting text to tidy formats and switching between tidy tools and existing text mining packages. See the vignette to get started.

  • utiml V0.1.0: Provides functions for multi-label learning and classification. There is a vignette.

  • wbstats V0.1: Provides tools for searching and downloading data and statistics from the World Bank Data and the World Bank Data Catalog. There is a vignette.

  • weightr V1.0: Provides functions for estimating the Vevea and Hedges weight-function model for publication bias. There is a Shiny app.

  • xkcdcolors V1.0: Contains the sRGB hex values for the top 1K colors from the xkcd color survey.


Updated Packages

The following list spotlights some CRAN packages that were updated between 4/1/16 and 4/30/16. These packages are notable either because many changes were made or because they have not been updated in quite some time.

  • distr V2.6: A package providing tools for creating distributions has had its first update in a couple of years.

  • gmailr V0.7.1: An interface to the gmail API has had its print functions reworked.

  • imputeTS V1.5: A package for time series imputation has had several improvements including the addition of functions to deal with NAs and the improvement fo the code examples.

  • miniCRAN V0.2.5: The package that makes it possible to create internally consistent repositories has had its first update in a year.

  • rmarkdown V0.9.6: Quite a few changes have been made including the ability to render collections of functions within a directory, the ability fo define html document navigation using yaml format and the addition of an option for Google Analytics ioslides presentations

  • simmer V3.2.1: Two new vignettes on queueing systems and Continuous-Time Markov Chains have been added to this package for discrete event simulation.


GitHub Packages

This section highlights some R packages that are only available on GitHub. For a more complete view of what’s trending on GitHub check here.

  • ggtree: Is a package for visualizing and annotating phylogenic trees with different types of meta-data.

  • r-graph-catalog: The repo for the R Graph Catalog maintained by Joanna Zhao and Jennifer Bryan.  

logo.jpg Microsoft R Open 3.2.4

By default, Microsoft R Open 3.2.4 uses a fixed CRAN repository snapshot taken on April 1, 2016. The following list spotlights some of the new and updated CRAN packages that were released between 1/1/16 and 3/31/16. These packages and more are available for use with the Microsoft R Open 3.2.4.


New Packages

The following list spotlights some of the new and updated CRAN packages that were released between 1/1/16 and 3/31/16. These packages and more are available for use with Microsoft R Open 3.2.4.

  • bayesboot V0.2.0: Implements the Bayesian bootstrap from Rubin's 1981 paper.

  • dCovTShttps V1.0: implements the distance covariance and correlation metrics for univariate and multivariate time series. These are relatively new metrics published by Z. Zhou in a 2012 paper in which he adapted the distance correlation metric developed by Szekely et al to measure non-linear dependence in time series.

  • deepboost V0.1.4: provides an interface to google's Deep Boasting algorithm as described in this paper by Cortes et al. It contains functions for training, evaluation, predicting and hyper parameter optimizing using grid search and cross validation.

  • fastAdaboost V1.0.0: Implements Adaboost on a C++ backend.

  • fermicatsR V1.4 provides data on gammaray sources from NASA's Large Area Telescope on board the Fermi gamma-ray satellite.

  • formatR V 1.3: provides the function tidy_source() to format R Source code. See the vignette.

  • fuzzyforest V1.0.1: A variation of the Random Forests algorithm designed to reduce bias in feature selection due to correlated features.

  • genie V1.0.0: contains the chlust() function to cluster data using the Gini index. hclust2() implements a hierarchical clustering technique that is billed as being outlier resistant.

  • ggbeeswarm V0.5.0: Provides two methods for plotting categorical scatter plots.

  • ggraptR V 0.1 enables users to create interactive data visualizations without writing code.

  • GLMMRR V0.1.2: fits GLMM lme4 models to binary, randomized response data and provides Cauchit, Log-log, Logistic and Probit link functions.

  • glmmsr V0.1.1: provides some alternatives to the Laplace method for approximating likelihood functions in the lme4 pckage. The vignette does a good job of explaining the new alternatives.

  • graphTweets V0.3; Provides functions to visualize Twitter interactions.

  • gunsales V0.1.1: Provides a statistical analysis of monthly background checks of gun purchases for the New York Times story "What Drives Gun Sales: Terrorism, Obama and Calls for Restrictions". There is a vignette. Also see: Gun Sales Soar After Obama Calls for New Restrictions.

  • kmlShape V0.9.5 contains functions to do hierarchical clustering on longitudinal data using the Frechet's distance metric to group trajectories.

  • lavaan.shiny V1.0: contains a single function to launch an interactive tutorial on latent variable analysis based on the lavaan package.

  • livechatR V0.1.0: Provides a wrapper for the LiveChat's API enabling the ectraction of raw chat data.

  • MultivariateRandomForests V1.0: contains functions to fit multivariate Random Forests models and make predictions.

  • permGPU V0.14.9: uses GPUs to carry out permutation resampling for RNA microarray studies.

  • Qtools V1.0 provides functions for working with conditional and unconditional quantiles. There is a vignette.

  • quickReg V0.0.1 provides functions to extract results from regression Models and plot effect size. Have a look at the vignette.

  • rEDM V0.4.7: brings empirical dynamic modeling EDM to R. The vignette makes a nice case for why attractors and chaos belong in R.

  • RtutoR V0.1: launches a Shiny-based interactive R tutorial that, so far, includes sections on basic operations on a data set, data manipulation, loops and functions, and basic model development

  • survMisc V0.5.0: extends the survival package by providing functions to help with the analysis of right censored data.

  • tweenr V0.1.2: provides functions for the gganimate package to smooth animations.

  • WaverR V1.0: Provides a function to estimate missing data using the weighted average of all possible regressions on available data.

  • WHO V0.1: Provides access to the World Health Organization API. The vignette shows how to use it.


Updated Packages

The following list spotlights some CRAN packages that were updated between 1/1/16 and 3/31/16. These packages are noteable either because many changes were made or because they have not been updated in quite some time.

  • BalancedSampling V1.5.1: Which contains functions for balanced and spatially balanced sampling has had its first update since 2014.

  • KFAS V1.2.2: a package for Kalman filtering, smoothing, forecasting and simulation of exponential family state space models has had a number of improvements and bug fixes since last year.

  • miceadds V1.7-8: a package which contains auxiliary functions for multiple imputation with mice has had several additions and improvements.

  • ModelMap V3.3.2: A package for modeling and map production using Random Forests and Stochastic Gradient Boosting has had several recent fixes and additions including the addition of new model types quantile regression forests (QRF) and conditional inference forests (CF), as well as new exploratory function 'model.explore()'. Also there are two new vignettes.

  • RcmdrPlugin.MPAStats V1.2.0; A package which extends R Commander with a menue of pre-existing statistical functions has been updated with new templates and rearranged menu items.

  • rfordummies V0.1.2: Contains the code examples for the book R for Dummies

  • RNetLogo V1.0-2 now supports NetLogo 5.3.

  • RSQLServer V0.1.1: Which wraps the jTDS Project's JDBC 3.0 SQL Server driver and extends the RJDBC classes and DBI methods has had several upgrades including the implementation of a SQL backend to dplyr and Azure hosted SQL Server support.

  • SocialMediaMiner V0.2: provides tools for determining the popularity and reach of URLs. The get_twitter function was removed from package as a result of Twitter's decision of discontinuing the Tweet share count API endpoint in November 2015.

  • SpatialEPI V1.2.2: Which contains methods for cluster detection and disease mapping has had its first update since 2014.

  • Unicode V8.0.0-1: A package which provides unicode data and utilities has had its first updates since 2014.

  • USAboundaries V 0.2.0: which provides boundaries for geographical units in the US has added contemporary boundaries for states, counties, and congressional districts. It imports fewer packages and provides high resolution data in the USAboundariesData package.


GitHub Packages

This section highlights some R packages that are only available on GitHub. For a more complete view of what’s trending on GitHub check here.

logo.jpg Microsoft R Open 3.2.3

By default, Microsoft R Open 3.2.3 uses a fixed CRAN repository snapshot taken on Jan 1, 2016. The following list spotlights some of the new and updated CRAN packages that were released between 9/1/15 and 12/31/15. These packages and more are available for use with the Microsoft R Open 3.2.3.


New Packages

The following list spotlights some of the new and updated CRAN packages that were released between 9/1/15 and 12/31/15. These packages and more are available for use with Microsoft R Open 3.2.3.

  • ameco V0.1: Contains the entire European Commission Annual macro-economic (AMECO) database in a format amenable to analysis in R.

  • antitrust V0.95: Provides tools for antitrust practitioners, including the ability to calibrate different consumer demand systems. The vignette describes the Bertrand Pricing Game , Auction Models and more.

  • assertive.code V0.0-1: Contains a set of predicates and assertions for checking properties of code. This is just one of a whole series of assertive.xx packages including assertive.base, assertive.data, assertive.numbers. Search MRAN for more.

  • batteryreduction V0.1.0: Provides a single function to implement the Battery Reduction method of feature selection.

  • Blossom V1.2: Provides permutation test tools for making statistical comparisons and for testing parameters estimated in linear models.

  • bmeta V0.1 Provides functions for performing Bayesian meta-analyses and meta-regression. The author's website is a good read.

  • brainGraph V0.55: Provides tools for performing graph theory analysis of brain MRI data.

  • cartography V1.1: Provides functions to integrate maps into R workflows. There is a vignette to get you started.

  • censusr V0.0.2: Provides an interface to the US Census API.

  • chunked V0.1.1: Provides tools to process text data in chunks using dplyr allowing text files too large to fit into memory to be processed.

  • clusrank V0.1-0: Implements the Wilcoxon Rank Sum Test for Clustered Data.

  • corkscrew V1.1: Allows you to bin categorical variables into a smaller number of categories based on t-tests and provides functions to explore the relationship between the response variable and predictor variables.

  • cowsay V0.4.0: Lets cows, cats, frogs and other ASCII animals deliver messages and warnings. But what the fox say?

  • ckanr V0.1.0: Provides and interface to the Comprehensive Knowledge Archive Network CKAN.

  • ddR V0.1: Provides distributed data structures for distributed computing with R.

  • dieZeit V0.1.0: Provides access to Die Zeit's online content.

  • easyVerification V0.1.8: Provides tools to simplify the verification of ensemble forecasts for large data sets. See the vignette for how to use it.

  • ecb V0.1: Provides an interface to the European Central Bank's Statistical Warehouse API. There is a vignette to get you started.

  • ECOSolveR V0.1-1: Provides a couple of functions to interface to ECOS, a C library for solving convex problems. The vignette works through a linear programming example.

  • ELMR V1.0: Provides training and prediction functions for the Extreme Learning Machine algorithm; a single hidden layer, feed forward neural network.

  • eva V0.1.2: Provides functions for extreme value analysis with goodness of fit testing. There is a vignette.

  • forestmodel V0.4.0: Uses ggplot to produce forest plots for regression models; really nice if you are working with survival data and hazard ratios.

  • geomnet V0.1.1: Provides a new geom, geom_net, for plotting networks in ggplot2.

  • gesis V0.1: Provides an interface to the GESIS Catalogue of data sets maintained by the Leibniz-Institute of the Social Sciences. There is a vignette.

  • ggfortify V0.0.4: Provides some very nice plotting tools for common statistical models such as GLM, PCA, survival analysis and clustering.

  • glm.ddR V0.1.0: Implements a distributed GLM algorithm using the ddR infrastructure for large data sets.

  • gmum.r V0.2.1: Provides an interface to the support vector machine libraries and GMUM group machine learning libraries.

  • gpuR V1.0.1: Provides GPU enabled functions for R objects. The vignette demonstrates how to do GPU matrix multiplication int R.

  • gtrendsR V1.3.0: Provides functions to perform and display Google Trend queries.

  • hdr V0.1: Provides an interface to the United Nations Development Program Human Development Report API. There is a vignette.

  • heemod V0.1.0: Provides tools for applying Markov models to Health Care Economics. Vignettes cover both homogenous and time varying models.

  • hellno V0.0.1: A package for those made crazy by stringsAsFactors = TRUE.

  • homomorpheR V0.1-1: Implements homomorphic, privacy preserving functions.

  • inegiR V1.0.2: Provides functions to download and parse information form the official Mexican statistics agency: INEGI.

  • jrvFinance V1.03: Provides functions for calculating properties of cash flows, bond pricing, Black-Scholes option pricing and more.

  • littler V0.3.0: Provides full support for "sebang"-style scripting at Unix shell prompt.

  • lucr V0.1.1: Contains functions for currency formatting and conversion.

  • maddison V0.1: Contains the Maddison Project database which provides estimates of GDP per capita for all countries between AD 1 and 2010. There is a vignette.

  • maGUI V1.0: Provides a comprehensive graphical user interface for analysis of Affymetrix, Agilent, Illumina, Nimblegen and other microarray data.

  • mldr.datasets V0.3.1: Contains a large collection of multi-label data sets.

  • mogsvs V1.0.1: Provides a genetic algorithm for variable selection in regression that claims to be faster than algorithms that rely on complete enumeration and, hence, suitable for data sets with large numbers of variables.

  • NlcOptin V0.1: Provides a single function to solve non-linear optimization problems with non-linear constraints.

  • pageviews V0.1.1: Provides an API client for [Wikimedia] (www.wikimedia.org) traffic data.

  • PAactivPAL V1.0: Provides functions to summarize accelerometer data from a wearable device.

  • pangaear V0.1.0: Provides tools for interacting with the PANGAEA database. - should be of interest to environmental scientists.

  • peakPick V0.11: Implements two algorithms for detecting peaks in 1-dimensional data based on heuristics that have worked well with genomic data.

  • pcev V1.1.1: Provides functions to implement the Principal Component of Explained Variance algorithm.

  • PiecewiseSEM V1.0.0: Provides functions for implementing piecewise structural equation models. There is a vignette.

  • poisson V1.0: Contains functions for simulating homogenous as well as non-homogenous Poisson processes.

  • prism V0.0.7: Allows you to download and visualize climate data from Oregon State's PRISM Project. There is a vignette to get started.

  • PsiHat V1.0: Provides a suite of functions for estimating local false discovery rates.

  • r.jive V1.2: Provides functions to implement the Joint and Individual Variation Explained (JIVE) method of integrated dimension reduction and visualization of multiple, high-throughput data sources. It is generalization of PCA for multi-source data. The vignette works through and example.

  • randomForest.ddR V0.1.0: Provides a distributed random forest algorithm using the ddR API.

  • rglwidget V0.1.1434: provides an htmlwidgets for rgl.

  • rGroovy V1.0: Provides an interface to the Groovy language for working with the Java platform.

  • RImagePalette V0.1.0: Uses the median cut algorithm to extract the dominant colors from an R image.

  • Rknots V1.3.0: Provides functions for the topological Analysis of Knotted Proteins, Biopolymers and 3D structures.

  • rPowerSampleSize V1.0: Provides functions for performing sample size calculations while controlling for the generalized family-wise error rate.
  • rrepast V0.2: Provides an interface to the Repast Symphony system for building agent based mocels.

  • rsvd V0.3: Implements a fast probabilistic algorithm to compute an approximate, low rank singular value decomposition for large data sets.

  • rstatscn V1.0: Provides functions to query Chinese National Data.

  • simmer V3.1.1: Provides a system for doing discrete event simulation (DES) in R. There are 3 vignettes including a very nice Introduction.

  • SocialMedialab V0.19.0: Provides tools to collect data from Instagram, Facebook, Twitter and YouTube, construct networks and plot them.

  • sodium V0.2: Provides an interface to libsodium, software for encryption/decryption, password hashing and more. This vignette could launch your crypto career.

  • subspace V1.0.4: Provides and interface to the OpenSubspace framework for subspace clustering algorithms.

  • SurvRegCensCov V1.4: Provides a function for Weibull Regression for right-censored and interval-censored endpoints. See the vignette for the math.

  • swirlify V0.4: Provides functions to help create R courses on swirl. Give it a look if you find yourself teaching R.

  • textmineR V1.5.1: Provides functions that facilitate topic modeling.

  • textreuse V0.1.1: Might be the ultimate weapon for the good guys in the plagiarism wars. It contains functions for measuring similarity among documents and detecting reused passages. There are multiple vignettes including this Introduction to get you started.

  • TLBC V1.0 Provides functions to train and fit 2-level Random Forest and hidden Markov models for human behavior classification from raw tri-axial accelerometer and / or GPS data.

  • treescape V1.8.15: A new package for exploring phylogenetic trees includes a Shiny interface.

  • tuber V0.1: Provides a client to the youtube API

  • urlshorteneR V0.8.8: Provides a wrapper to the Bit.ly, Goo.gl and Is.gd URL shortening services.

  • vipor V0.3.2: Contains functions for making violin plots of categorical variables. There is a vignette to get you started.

  • wakefield V0.2.0: Provides functions for generating random data sets including data frames, lists and vectors.

  • wingui V0.2: Provides tools interfacing with the Windows (and other) operating system.

  • wordbankr V0.1: Contains functions for connecting to Wordbank, Stanford's database of children's development vocabulary that spans 14 languages. There is a vignette.


Updated Packages

The following list spotlights some CRAN packages that were updated between 9/1/15 and 12/31/15. These packages are noteable either because many changes were made or because they have not been updated in quite some time.

  • caret V6.0-15: the library unifying machine learning models has had several updates including bug fixes and changes to ggplot.train() and trainControl() functions.

  • darch V0.10.0: A package for building and training deep, multilayer neural nets has had its first update in a year.

  • doParallel V1.0.10: Provides a parallel backend for the %dopar% functon. This release provides a bug fix for the stopImplicitCluster() function.

  • doSnow V1.0.14: Provides a parallel backend for the snow package. This release offers improved foreach loop execution.

  • dygraphs V1.1: Now allows for explicit specification of series periodicity when creating a graph.

  • ergm V3.5.1: The package for fitting and simulating exponential random graph models has been updated to provide a bigger boost from parallel execution along with other improvements.

  • GGally V1.0.0: Updates to GGally, a package that extends ggplot2, include 5 new vignettes: ggmatrix shows how to manage multiple plots in a matrix-like layout.

  • ggplot2 V2.0: The R plotting package based on the Grammar of Graphics now provides a formal extension mechanism allowing package authors to create new geoms and plot types. Learn More

  • git2r V0.13.1: A package for accessing Git repositories has recently been updated with new features and bug fixes.

  • glmx V0.1-1: This package which provides extended techniques for GLMs, now has a predict method.

  • jaatha V3.0.0: This package which provides simulation methods for maximum likelihood parameter estimation has been completely rewritten and the documentation has been revised.

  • matrixStats V0.50.1: Provides functions for row and column operations on matrices has had a major feature update with performance improvements.

  • pixiedust V0.5: A package for producing beautifully formatted tables has had several improvements including a new vignette Advanced Magic, support for HTML, the use of the pipe operator %>%, a new function glance-foot for placing summary statistics at the foot of a table and more.

  • plotly V2.0.16: A package for creating interactive web graphics now provides the capability to translate ggplot2 plots into interactive, web-based graphs.

  • plotROC V2.0.0: A package for plotting ROC curves based on ggplot2 now supports faceting and grouping.

  • PRIMscr V0.6.3: Provides a uniform treatment of Bump Hunting by the Patient Rule Induction Method for Survival, Regression and Classification models. It has had several updates including changing random splitting in the cross-validation step to random stratified splitting by conservation of events.

  • PythonInR V0.1-3: A package for interacting with Python from R has been updated with additional documentation and use cases. R swallows Python.

  • randomForest V4.6-12: This latest update to R's primary implemation of Breiman and Cutler's random forests algorithm includes changes to the inbag and ncat components of the model object.

  • rapport V1.0: A package with templates for creating reproducible statistical reports has been changed quite a bit since its last update in 2013. Many functions have been outsourced to pander.

  • Rcpp V0.12.2: This fundamental package that provides seamless R and C++ integration has had several updates recently including providing a transpose operator for Matrix classes and the operator <<() for complex types.

  • RcppArmadillo V0.6.200.2.0: Has had quite a few updates including improvements to diagmet(), trace() norm() and normalize().

  • RcppOctave V0.18.1: A problem for installation on Windows with R version 3.2 or newer has been fixed. This package provides a direct interface to Octave.

  • rebus V0.1-0: A package for building regular expressions, has been extended with several new packages including: rebus.unicode, rebus.numbers and rebus.datetimes.

  • rotations V1.4: Which provides functions for working with rotation data, including simulations from the SO(2) rotation group has been updated to include a Maxwell-Boltzman distribution function. The vignette shows some beautiful math applied to practical problems

  • snow V0.4-1: Is the first update of this essential package for simple parallel computing since 2013.

  • spatstat V1.43-0: Several changes including added dependencies, bug fixes, and new features have been added to this toolbox for analyzing spatial data.

  • taxize V0.6.6: A package for interacting with web APIs for verifying taxonomic information has several improvements and bug fixes

  • VGAM V1.0-0: A fundamental change to the code to this package for fitting Vector Generalized Linear and Additive Models means that models fitted under <= VGAM 0.9-9 and saved might not work under >= VGAM 1.0-0.


GitHub Packages

This section highlights some R packages that are only available on GitHub. For a more complete view of what’s trending on GitHub check here.

  • cartodb-r Provides an R wrapper for the API for CartoDB software for mapping and analyzing location data.

  • MEFM Contains tools for implementing the Monash Electricity Forecasting Model described in the paper by Hyndman and Fan

  • openml: An R package for interfacing to OpenML.

  • R-Box An R package for Sublime Text

 

logo.jpg Revolution R Open 3.2.2

By default, Revolution R Open 3.2.2 uses a fixed CRAN repository snapshot taken on Aug 27, 2015. The following list spotlights some of the new and updated CRAN packages that were released between 7/1/15 and 8/27/15. These packages and more are available for use with Revolution R Open.


New Packages

The following list spotlights some of the new and updated CRAN packages that were released between 7/1/15 and 8/27/15. These packages and more are available for use with Revolution R Open.

  • AutoModel V0.4.9: Contains functions to facilitate the process of building hierarchical multiple regression models. The vignettewalks through an example including assumptions checking.
  • AzureML V0.1.1: Provides and interface to Microsoft Azure to discover web services and publish R functions and models as web services. The vignette gets you started.
  • bnclassify V0.3.0: Implements algorithms for learning discrete Bayesian network classifiers from data.
  • bstruct V1.0: Implements various algorithms for Bayesian network structure learning from data with missing values.
  • circlize V0.3.1: Provides a framework for constructing circular visualizations in R. There are several vignettes including an Introduction, Circular phylogenetic tree and Make genomic plots.
  • credule V0.1 Provides functions to bootstrap Credit Curves from market quotes. There is a vignette.
  • edgar V1.01: Provides functions to download EDGAR forms from the Securities and Exchange Commission.
  • EPGLM V1.0: Provides functions to compute the expectation propagation approximation of a Bayesian probit/logit models with Gaussian prior.
  • fasttime V1.0-1: Contains fast functions for timestamp manipulation that avoid system calls and facilitate operations on very large data.
  • FCNN4R V0.3.4: Provides an interface to the kernel routines from the FCNN (http://fcnn.sourceforge.net/) C++, neural net library.
  • flowr V0.9.7.5: Provides an interface to streamline the design of workflows and their deployment to a high performance computing cluster. Support several different clusters. Provides several vignettes.
  • fulltext V0.1.0: Provides a single interface for searching for scholarly articles from several sources. There are 3 vignettes including this introduction.
  • ggplot2movies V0.0.1: The movies data set that used to be in ggplot2 now has its own package.
  • googlePublicData V0.15.7.28: Provides functions for working with the Google Public Data
  • graticule V0.1.0: Provides functions to create graticule lines and labels for maps as described in the vignette.
  • HistogramTools V0.3.2: Provides (1) functions for manipulating large histograms, including methods to trim, subset, merge buckets and histograms and more, (2) a protocol buffer representation of the default R histogram class for MapReduce environments. 3 vignettes, including this really nice Quick Reference Guide
  • imputeTS V0.1: Provides functions for imputing missing vales in univariate time series.
  • iotools V0.1-12: Provides I/O tools for streaming.
  • JacobiEigen V0.1: Implements the classical Jacobi (1846) algorithm for the eigenvalues of a real symmetric matrix, both in pure R and using Rcpp.
  • RKlout V1.0: Provides an R interface to the Klout API for Twitter Ranking application.
  • lazyWeave V3.0.0: Provides the functionality to write LaTeX code from within R without having to learn LaTeX.
  • MBTAr V1.0.0: An interface to the API for accessing data from the Massachusetts Bay Transportation Authority
  • Mediana V1.0" Provides a general framework for simulating clinical trials based on the Clinical Scenario Evaluation approach. There is an online manual and a case studies R file.
  • [momr] () V1.1: Contains routines fro biomarker identification and exploration. It is the core package of the MetaOMineR suite of packages.
  • mvtboost V0.2.1: An extension to the gbm package that fits a multivariate decision tree model for multiple, continuous outcome variables. See and example in the vignette.
  • nhanesA V0.4 Provides functions to retrieve data from the National Health and Nutrition Examination Survey (NHANES).
  • nordklimdata1 V1.2: Contains the Nordklim data set: 100 years worth of climate observations from over 100 Nordic stations.
  • OTE V1.0: Provides functions to obtain ensembles of optimal trees for regression, classification.
  • packcircles V0.1.1: Provides an algorithm to pack circles into a rectangle. Just for fun, have a look at this paper on computational geometry as well as the vignette.
  • pixiedust V0.1.1: Provides functions to create customized output from the tidy data created with the broom package. There is a nice vignette.
  • pystr V1.0.0: A package for those who miss Python's string operations while working in R. Really, R has everything.
  • QFRM V1.0.1: Provides functions for options pricing based on the text: Options, Futures and Other Derivatives, 9ed by John C.Hull, 2014. Prentice Hall.
  • qualvar V0.1-0: Implements indices of qualitative variation proposed by Wilcox in 1973 as described in the vignette. Eventually, R will have almost everything.
  • ranger V0.2.6: Provides a fast implementation of the random forests algorithm for high dimensional data based on Rcpp.
  • RcppShark V 0.1: Provides an R interface to the C++/ Boost Shark machine learning library. There is a tutorial.
  • rgeolocate V0.4.1 Provides functions to geolocate IP addresses. There is a vignette.
  • Rgnuplot V1.0.3: Provides an interface to the freely distributed Gnuplot graphing system.
  • rotl V0.4.1: Provides an interface to the Open Tree of LIfe API to retrieve phylogenetic trees. This vignette will get you started.
  • ROptimizely V 0.2.0 Provides functions to extract results and test information from the Optimizely API.
  • rpca V0.2.3: Given a matrix that is a superposition of a low rank component and a sparse component, rcpa uses a robust PCA method to recover these components. See Robust Principal Component Analysis by Candes et. al.
  • rstan V2.7.0-1: Provides functions to parse, compile, test, estimate and analyze Bayesian models built with Stan. This interface is described in the vignette.
  • rstpm2 V1.2.2: Provides an R implementation with extensions of Stata's stpm2 function for flexible link-based survival models. There is a vignette.
  • simplr V1-1: Provides basic functions for symbolic expression simplification.
  • SwarmSVM V0.1: Provides three ensemble methods for training support vector machines as described in the vignette.
  • UpSetR V0.0.5: Provides functions to visualize intersecting sets and attribute plots that are based on ggplot2. Additional vignettes describe [Basic Usage] (/web/packages/UpSetR/vignettes/basic.usage.html) and [Querying the Data] ()
  • wbsts V0.1: Implements the Wild Binary Segmentation method to estimate the number and location of change-points in nonstationary time series
  • weatherr V0.1: Contains a function to obtain weather forecast data from the Norwegian Meteorological Institute API.
  • wiod V0.3.0: Contains data sets from the World Input Output Database, for the years 1995-2011. See the wiod working paper for explanations.


Updated Packages

The following list spotlights some CRAN packages that were updated between 7/1/15 and 8/27/15. These packages are noteable either because many changes were made or because they have not been updated in quite some time.

  • Cairo V1.5-8: Fixes a premature memory release in locator handling for raster back-ends.
  • DescTools V0.99.13: A memory access error has been fixed for this package which contains a number of functions to assist with basic statistics.
  • drat V0.1.0: A package for supporting the creation and use of local repositories has had several updates this month including an update to the vignette with respect to support for binary packages on OS X and Windows
  • FastRWeb V1.1-1; A package for creating dynamic web content now imports Cairo. This is the first update since 2012.
  • GEVStableGarch V1.0: A package for ARMA-GARCH modeling has had a few enhancements since its last update in 2014 including the addition of the gsSelect() function.
  • gridExtra V2.0.0: Which provides user level functions to enhance grid graphics has had its first ugdate since 2012. Several minor changes to parameters such as base_color and base_size were made.
  • markovchain V0.2.4: Now has functions to fit higher order markov chains.
  • mcmcse V1.1-1: This package which provides functions for computing Monte Carlo standard errors in MCMC setting has had its first update in 3 years.
  • mmand V1.2.0: A package which provides tools for performing mathematical morphology operations in multiple dimensions has been updated with a new function for thresholding arrays.
  • NlsyLinks V2.0.2: Which provides utilities and kinship information for behavior genetics and developmental research has had its first update since 2013. The SurveyDate data set now provides survey details by subject and year. There is a FAQ a vignette for the NLS investigator and one for ACE Models.
  • partitions V1.9-18: Which enumerates the partitions, unequal partitions, and restricted partitions of an integer has had its first update in two years.
  • powerSurvEpi V 0.0.9: Which provides functions for power and sample size calculations for main and interaction effects in survival analysis has had its first update in 3 years. The optim function is now explicitly imported into the namespace.
  • quanteda V0.8.2-1: Which provides functions for analyzing textual data has had a number of improvements including functions to sample documents from a corpus and dfm and a fix to enable the Mac binary to build on CRAN. There is both a Getting Started Guide and a Design Principles vignette.
  • rattle V3.5: the R GUI for data mining has had a number of changes including replace xlsx::read.xlsx() with readxl::read_excel() to removereliance on Java.
  • ReporteRs V0.8.2: A package for creating Microsoft Word and Powerpoint documents and HTML documents has had several changes since the May 0.7.8 release.
  • rjava V0.9-7: Which provides a low level interface to the Java VM has had a couple new updates dealing with the handling of NAs.
  • RSclient V0.7-3: Is the client for RServe. This update fixes an error when handling OOB if no handlers are registered.
  • rtkpp V0.9.2: Which privodes C++ classes for statistics and linear algebra functions using Rcpp now supports kernel mixture models.
  • rts V1.0-10: A package which provides a classes and methods for manipulating raster time series has had its first update since 2012.
  • sjmisc V1.1 A package which contains a number of utility functions to help transition users from SAS, SPSS and Strata to R has had a number of new functions added.


GitHub Packages

This section highlights some R packages that are only available on GitHub. For a more complete view of what’s trending on GitHub check here.

  • AnomalyDetection implements Twitter's Seasonal Hybrid ESD (S-H-ESD) algorithm for detecting anomalies in time series data.
  • Awsome R: Not a package, but a very nice curated list of R frameworks, packages and software.
  • bench-ml: a simplified but incomplete benchmark for machine learning libraries.
  • CausalImpact: A google package for causal inference using Bayesian structural time-series models.
  • ggfortify: Provides functions to allow ggplot2 handle objects from some popular R packages.
  • mason: A tool for building R packages.

logo.jpg Revolution R Open 3.2.1

By default, Revolution R Open 3.2.1 uses a fixed CRAN repository snapshot taken on July 1, 2015. The following list spotlights some of the new and updated CRAN packages that were released between 5/1/15 and 7/1/15. These packages and more are available for use with Revolution R Open.


New Packages

The following list spotlights some of the new and updated CRAN packages that were released between 5/1/15 and 7/1/15. These packages and more are available for use with Revolution R Open.

  • ApacheLogProcessor: V0.1.5 provides functions to extract data from Apache log files into data frames
  • arqas V1.0: provides functions for computing the performance metrics for a number of queueing networks in the M/M/s/k family and for open and closed Jackson networks. There are also functions to simulate networks in the G/G/s/K family.
  • bcrypt: V0.1 provides an R interface to the OpenBSD Blowfish password hashing algorithm.
  • BinaryEPPM V1.0: provides functions for the mean and variance modeling of under and over dispersed binary data using Poisson process models.
  • biorxivr V0.1.1: provides the ability to bulk download Biology papers from the bioRxiv preprint server. The vignette will get you started.
  • brms V0.2.0: provides functions to fit Bayesian Regression Models using STAN.
  • CausalFX V1.0.1: provides functions to implement various methods of estimating the causal effects of one variable on another. Currently only handles binary data.
  • ClustMMDD V1.0.1: provides functions for discrete data variable selection using mixtures of multinomial models. It treats the twin problems of variable selection and clustering as a model selection problem.
  • ColorPalette V1.0-0: provides methods to create color palettes based on a specified color and the number of colors to be created
  • commT V0.1.1: provides functions for comparative phylogeographic analysis allowing users to measure the difference between constrained and unconstrained gene tree distributions using various metrics.
  • coreNLP V0.4-1: provides an interface to Stanford’s coreNLP suite of Natural Language Processing tools.
  • covr V1.0.0: Code coverage, a measure of the percentage of code covered by tests, is a measure of code quality. covr functions track and report code coverage and optionally upload the results to the services Codecov and Coveralls. There is a vignette.
  • cranlogs V 2.0.2: provides an interface to the API for the database of CRAN package downloads maintained in the RStudio CRAN mirror.
  • CryptRndTest V1.0.5: provides functions to perform cryptographic randomness tests on sequences of random integers or bits.
  • d3heatmap V0.6.0: provides functions to create interactive 3D heatmaps using the htmlwidgets and the JavaScript D3.js library.
  • distcomp V0.25.1: provides functions to fit models with data distributed over networks without sharing data and without aggregation. This blog post may be helpful.
  • fbroc V0.2.1: implements a fast C++ algorithm to bootstrap ROC curves.
  • fermicatsR V1.3: provides data that is out of this world: astrophysical gamma ray sources detected by NASA’ s Large Area Telescope.
  • fheatmap V1.0.0: provides functions to plot elegant heatmaps using ggplot2
  • filemax: V1.0 ia an "all R" package for working with large ( ~ 1 terabyte) file-backed matrices.
  • forestFloor V1.4: Contains functions to visualize random forests models.
  • hierband V1.0: implements the convex banding procedure using a hierarchical group lasso for covariance estimation. The details are in the vignette. This is the sort of thing that you are likely to see first in R.
  • hiertest V1.1: implements the convex hierarchial testing (CHT) algorithm introduced by Bien, Simon, and Tibshirani.
  • [leaflet] (/package/leaflet) V1.0 provides functions to create and customize interactive maps using the 'Leaflet' JavaScript library and the htmlwidgets package.
  • loo V0.1.0: provides functions to approximate leave-one-out cross-validation (LOO) using VGIS, a new procedure for regularizing importance weights. See the vignette for getting started with STAN and R.
  • manifestoR V1.0-1: provides an interface to the coded election programmes of the Manifesto Project which collects and analyzes election programs to measure the political preferences of parties.
  • metaSEM V0.9.4: provides a collection of functions for conducting meta-analyses using Structural Equation Models.
  • metricsgraphics V0.8.5: provides an htmlwidgets widgets interface to the MetricsGraphics.js D3 JavaScript library for plotting time series data. The vignette shows what it can do.
  • MInt V1.0.1: provides a function for estimating direct interaction networks as described in the vignette.
  • mitmlV0.2-2: provides tools for multiple imputation of missing data in multilevel models.
  • MLmetrics V1.0.1: provides a collection of metrics to measure the performance of regression and classification algorithms.
  • odeintr V1.0: wraps the Boost odeint library.
  • oglmx V1.0.2: provides functions for estimating ordered probit and ordered logit models without assuming a constant variance across observations. Users can specify a variance model.
  • openMX V2.2.4: is a package for advanced structural equation modeling. It provides several method for specifying SEMs. See the website for some details.
  • palr V0.4-0: provides some color palettes for data.
  • pcaBootPlot V0.1.0: contains a single function to draw a 2 dimensional principal components plot with bootstrapped confidence intervals.
  • PoisBinOrdNor V1.0: Provides functions to simultaneously generate values from multiple-count binary, ordinal and normal random variables given marginal information.
  • progress V1.01: provides functions to implement configurable progress bars that may include percentage complete, elapsed time and estimated time to complete.
  • qrmtools V0.0-1: provides tool for quantitative risk management including functions to compute the Black Scholes model and the generalized extreme value distribution. Follows the book: Quantitative Risk Management: Concepts, Techniques and Tools
  • RedditextractoR V1.0.0: provides an R interface to the API for Reddit, the online bulletin board.
  • Rlinkedin V0.1: provides an interface to the Linkedin API
  • rotationForest V0.1: provides an implementation of the new Rotation Forest binary ensemble classifier described in the paper by Rodriguez et. al.
  • rriskDistributions V2.1: contains functions for fitting distributions either to data or to known quantiles.
  • PREnsemble V0.2: implements the random projection ensemble classifier for high dimensional data as described in the paper by Cannings and Samworth.
  • RANN V2.5: provides a wrapper to the ANN C++ library for performing approximate nearest neighbor searching.
  • Rtts V0.2.5: contains functions to convert text into 'mp3' or 'wav' format speech files with APIs offered by Google Translate and ITRI TTS.
  • signmedian.test V1.5.1: contains a single function to perform the nonparametric, sign median test.
  • smcfcs V1.0.0: provides functions for the multiple imputation of covariates using the Substantive Model Compatible Fully Conditional Specification as described in the vignette.
  • smoof V1.0: provides several single and multiple objective test functions for benchmarking numerical optimization algorithms.
  • stationaRy V0.2: provides functions to identify meteorological stations around the world and fetch hourly data from them.
  • statnetWeb V0.3.4: provides a GUI for network modeling with the statnet software.
  • STMedianPolish Provides functions for the analysis of spatial-temporal tata usning n dimenional arrays and the median polish technique.
  • switchr V0.9.6: provides an abstraction for installing and managing multiple package libraries and switch between them in an effort to maintain strict, package-version-specific reproducibility.
  • TDAmapper V1.0: provides functions for Topological Data Analysis using Discrete Morse Theory.
  • threejs V0.2.1: contains functions to create interactive 3D scatter plots and globe plots using the three.js visualization library.
  • xml2 V0.1.1: provides a consistent interface for working with XML files


Updated Packages

The following list spotlights some CRAN packages that were updated between 5/1/15 and 7/1/15. These packages are noteable either because many changes were made or because they have not been updated in quite some time.

  • BaBoon 0.2-0: a package for Bayesian bootstrap predictive mean modeling, has had quite a few updates since its previous 2011 release including the use of RcppArmadillo, changes in code structure and new auxiliary functions.
  • bamdit V2.0: a package for the Bayesian meta-analysis of diagnostic tests has had its first update since 2011.
  • bcv V1.0.1: which provides methods for choosing the rank of an SVD approximation via cross validation has had its first update since the package was released in 2009.
  • biwavelet V0.17.10: which provides functions for univariate and biwavelet analysis now has the ability to handle custom color palettes in its plot method.
  • beeswarm V0.2.0: which contains a function to implement the 1 dimensional “Bee Swarm” scatterplot now allows swarms to grow on only one side of the plot.
  • FatTailsR V1.2-0: in this first update since the package was released in 2014, the title has been changed to FatTailsR: Kiener Distributions and Fat Tails in Finance and a new quantile based algorithm, estimkienerX, has been added.
  • leafletR V0.3-3: This package for creating interactive, web based maps based on the javaScript library has had a couple of updates during the last two months with bug fixes and a few new features such as maps without a base, and factor to character conversion in the toGeoJson function.
  • ordPens V0.3-1: which provides methods for the selection and smoothing of ordinally scaled variables using a group lasso or ridge regression has had its first update in two years.
  • qtbase V1.0.9: provides an interface to the Nokia Qt library, an application framework, best known for its collection of GUI widgets. This is the first update in three years.
  • MixSim V1.1-1: which provides functions for simulating mixtures of Gaussian has been updated for the first time in two years.
  • RVsharing V1.3.4: which provides functions to estimate the probability of related individuals sharing a rare variant has had its first update since being released in 2013.
  • spsurvey V3.0: which provides algorithms for the design and analysis of probability surveys now has a new class, SpatialDesign, for the output of the functions grts() and irs() as well as new S3 and S4 methods for SpatialDesign plots and summary
  • stabledist V0.7-0: which provides skew stable distribution functions has had its first update since June 2013.
  • TESS V2.0.0: a package for diversification rate estimation and simulation of phylogenetic trees has had a number of new features added since the 2013 1.2.1 release including skyline birth-death models for piecewise constant and linear rates and reversible jump MCMC algorithms to estimate rate changes and the number of mass extinctions.
  • XML V3.98-1.2: provides tools for parsing and generating XML. This is the first update since 2013.


GitHub Packages

This section highlights some R packages that are only available on GitHub. For a more complete view of what’s trending on GitHub check here.

  • AnomalyDetection: provides functions for anomaly detection with R
  • awesome-R: contains a curated list of R framworks, packages and software
  • causalImpact: provides functions for causal inference using bayesian structural time-series models.
  • data: contains data and code behind the stories and interactive FiveThirtyEight stories
  • engsoccerdata: contains English and European soccer resuts for the years 1871 to 2014.
  • FootballData: is a collection of JSON and CSV Football/Soccer data
  • SparkR-pkg: provides an R frontend for Spark
  • swirl_courses: is a collection of interactive courses for the swirl R package

logo.jpg Revolution R Open 3.2.0

By default, Revolution R Open 3.2.0 uses a fixed CRAN repository snapshot taken on May 1, 2015. The following list spotlights some of the new and updated CRAN packages that were released between 4/1/15 and 5/1/15. These packages and more are available for use with Revolution R Open.


New Packages

  • ADPclust V0.6.3: Contains functions to implement a clustering algorithm based on Adaptive Density Peak Detection. See the vignette.
  • BCRA V1.0: Provides functions to calculate the risk of developing invasive breast cancer using the GAIL model of the National Cancer Institute.
  • cellranger V0.1.0: Provides helper functions to translate “A1:D10” spreadsheet ranges to rows and columns.
  • cqrReg V1.2 Contains functions to fit quantile and composite quantile regression models with the adaptive lasso penalty.
  • crunch V1.0.2: Provides functions for manipulating Crunch data sets from R. See the vignette describing how to create and load data sets.
  • csrplus V1.03-0: COntains two functions to evaluate the hypothesis of complete spatial randomness in point processes.
  • emg V1.0.6: Provides the basic distribution functions for the exponentially modified Gaussian distribution (EMG) which is a mixture of exponential and Gaussian random variables.
  • fpCompare V0.1.0: Implements 4 relational operators for floating point comparisons.
  • geojsonio V0.1.0: Provides functions to convert data to and from geoJSON and topoJSON formats. See the vignette.
  • HarmonicRegression V1.0: Contains functions to fit the first harmonics in a Fourier expansion to one or more time series. See the brief vignette.
  • HighDimOut V1.0.0: Implements 3 different algorithms for outlier detection in high dimensional data. See the brief vignette.
  • icenReg V1.1.1: Provides functions to fit Cox PH regression models on interval censored data.
  • mixedMem V1.0.2: Contains functions to fit mixed membership models with discrete multivariate data using the framework of Erosheva 2004. See the very nice vignette.
  • mongolite V0.3: Provides a high-level MongoDB client. See the vignette for getting started with MongoDB in R.
  • ngramrr V0.1.1: A simple n-gram tokenizer to be used with the 'tm' package with no 'rJava'/'RWeka' dependency.
  • PortfolioAnalytics V1.0.3636: Is a new package for portfolio analytics designed with the goal of allowing the use of many different portfolio solvers on the same portfolio specification problem. There are 5 vignettes including this introduction.
  • qrng V0.0-1: Contains a function to generate quasi-random numbers in high dimensions.
  • quanteda V0.7.2: A toolset for the management, processing and analysis of text data. There is a vignette quickstart guide.
  • randNames V0.2: A nicer utility for generating random user names with fake demographic data.
  • RandomFieldsUtils V0.0.1: Provides a function that checks the sparsity of the matrix before solving a linear equation.
  • rcorpora V1.0.1: A collection of small text corpora.
  • RcppTOML V0.0.3: Provides Rcpp bindings to parser for Tom’s Obvious/Own Minimal/Markup Language.
  • readr V0.1.0: Contains functions to read flat and tabular text files from disk.
  • RRTCS V0.0.1: Provides functions for point and interval estimation of parameters in survey models using stratified and clustered sampling.
  • SLOPE V0.1.1: Implements efficient procedures for performing Sorted LI Penalized Estimation as described in the paper by Bogdan et. al. See the vignette.
  • shinydashboard V0.4.0: Provides a theme on top of Shiny to create dashboards.
  • shinyjs V0.0.3.3: Provides wrappers for several useful javascript functions that can be called from Shiny applications.
  • TickExec V1.0: Provides functions to execute orders (LimitBuy / Sell, MarketBuy / Sell) in backtesting using tick data.
  • timetree V1.0: Provides an interface to the time tree of life database.
  • treeperm V1.6: An implementation of permutation tests that uses tree algorithms to estimate p-values. Supports both exact tests and asymptotic K sample test of data locations.
  • TSmisc V2015.1-3: Provides functions to retrieve various time series data sets including quote data from Yahoo and Oanda. See the vignette.
  • uniqtag V1.0: A handy utility to abbreviate strings to short, unique identifiers.
  • WikipediaR V1.0: Implements a web based client to the Wikipedia API.
  • xml2 V0.1.0: Provides functions for working with xml files.

Updated Packages

The following list spotlights some CRAN packages that were updated between 4/1/15 and 5/1/15. These packages are noteable either because many changes were made or because they have not been updated in quite some time.

  • candisc V0.6-7 which contains functions for performing generalized canonical discriminant analyses and canonical correlation analysis for multivariate linear models now uses rgl for 3d plots.
  • Comp2ROC V1.1 Contains functions to compare ROC Curves. (Last updated in May 2013.)
  • gcmr V0.7.0: Which contains functions to Gaussian copula marginal regression models, was updated with new examples and a new plot method.
  • GWRM V2.0: Contains functions to fit and validate a Generalized Waring Regression Model. (This is the first update to the package since it was released in 2010.)
  • Hmisc V3.16: Updates include a new colorFacet function, ggplot.summaryP which sizes points according to denominators and knitrSet, a new function to setup knitr with nice defaults for books, etc.
  • migui V1.1: Implements a GUI for the user through the fantastic mi package, (This is the first update since 2011.)
  • rainbow V.3.3: provides functions for visualizing functional time series. (This is the first update in a couple of years.) See the vignette, which describes how functional time series differ from multivariate time series.
  • pcaL1 V 1.3: provides implementations of 3 PCA algorithms using the L1 norm. This update (the first since 2012) provides support for user defined starting points and an interface to R’s internal random number generator.
  • R2admb V0.7.13: provides an interface to the AD Model Builder, a stand alone package that finds the coefficients that minimize a negative log-likelihood function (and more) through “automatic differentiation” (last updated in 2013). See the vignette.
  • Renext V 2.1-10 provides functions for extreme value analysis using the peaks over threshold method (last updated in 2013).
  • StatDA V 1.6.9 provides functions for analysing environmental data was (last updated in August 2013).
  • softImpute V1.4: provides nuclear-norm regularization iterative methods for matrix completion (updated for the first time since it was introduced in 2013). See the vignette.
  • stringr V1.0.0 A very popular package that provides a consistent interface for common string operations (last updated in 2012).
  • TSdbi V2015.1-1: Provides a common interface to time series databases. This update (the first in 2 years) contains several minor fixes and enhancements.

GitHub Packages

This section highlights some R packages that are only available on GitHub. For a more complete view of what’s trending on GitHub, check here.

  • explainr translates S3 objects into text using standard templates. See Hilary Parker’s presentation from the recent NY R Conference.
  • fivethirtyeight provides the data and code behind the stories at FiveThirtyEight.
  • ML_for_Hackers provides the code to accompany the book “Machine Learning for Hackers”.
  • PAPPOR is a privacy technology that allows inferring statistics about populations while preserving the privacy of individual users.
  • sjPlot provides functions for data visualization of social science statistics.
  • slidify lets you generate reproducible html5 slides from R markdown.

 

 

logo.jpg Revolution R Open 8.0.3

By default, Revolution R Open 8.0.3 uses a fixed CRAN repository snapshot taken on April 1, 2015.

The following list spotlights some of the new and updated CRAN packages that were released between 3/1/15 and 4/1/15. These packages and more are available for use with Revolution R Open.

 

New Packages

  • Ake - V1.0: Associated Kernel Estimations uses the kernels associated with probability functions to estimate continuous probability density functions and discrete probability mass functions.
  • CARBayesdata - V1.0: contains three spatial data sets from Scotland that are used in the vignette for the CARBayes package.
  • cOde - V0.1: Provides functions for working with ordinary differential equations, including functions to symbolically compute Jacobians. It generates all of the necessary C functions for working with the compiled code interface of ode() {deSolve} and bvptwp() {bvpSolve}
  • Conake V1.0: Provides functions for continuous smoothing of probability density functions on compact or semi-infinite support and includes a function to select the optimal value of the bandwidth parameter based on cross validation.
  • Coxnet - V0.1-1: Provides functions to fit regularized Cox models with lasso (L1), exlatic-net (L1 and L2) or L1 plus Laplacian regularization. See the paper by Friedman, Hastie and Tibshirani for some theory.
  • GameTheory - V1.0: Provides functions to implement a common set of punctual solutions for Cooperative Game Theory. There is a vignette on cooperative games.
  • gapminder - V0.1.0: An excerpt of the data available at http://gapminder.org.
  • gdm - V1.0 Generalized Dissimilarity Modeling is a statistical technique for modelling biotic compositional dissimilarity between pairs of geographical locations. gdm provides basic functions to fit, plot, predict and summarize gdms.
  • ggExtra - V0.1.0: Provides a collection of functions and layers to enhance ggplot2. Among other things, the vignette shows examples of adding marginal histograms to scatter plots.
  • gsheet - V0.1.0: Contains two functions to download Google sheets using just the sharing link
  • kmodR - V0.1.0: Provides an implementation of the k-means-- algorithm proposed by Chawla and Gionis in the paper: A unified approach to clustering and outlier detection.
  • longclust - V1.2: Enables clustering and classification of longitudinal data based on mixtures of t or Gaussian distributions
  • MCL - V1.0: Contains and implementation of the Markov cluster algorithm proposed by van Dongen in his 2000 thesis for finding clusters in networks and graphs.
  • MixAll - V1.0.2: Provides algorithms and methods for estimating parametric mixture models with missing data. Has the vignette: Generative Clustering with missing values using the Mixall package.
  • nnlasso - V0.2: Provides functions to estimate lasso penalized glms subject to non-negativity constraints.
  • NPBayesImpute - V0.5: Provides functions for multiple imputations of missing values for categorical data based on Dirichlet process mixtures of multinomial distributions.
  • prais - V0.1.1: Implements Prais-Winsten method, an iterative recursive algorithm, that takes into account serial correlation of type AR(1) in estimating the coefficients of a linear model.
  • pRF - V1.0: Provides functions for estimating false discovery rates for importance functions in random forest runs.
  • RLumShiny - V0.1.0: Contains a collection of Shiny applications for the package Luminescence. Releasing Shiny front ends for R packages might just be the next big thing.
  • Rmonkey - V0.2.11: Provides programmatic access to the Survey Monkey API.
  • ROCS - V1.2: Plots the Receiver Operating Characteristics Surface for class skewed data, calculates the volume under the surface and the FDR-Controlled Area Under the Curve.
  • rscala - V1.01: Implements a bi-directional interface between R and Scale with callbacks
  • sadists - V0.2.0: Provides the pdf, cdf, quantile and generation functions for some additional obscure probability distributions, including the doubly non-central t, F, Beta, and Eta distributions; Lecoutre's lambda-prime and K-prime and more. There is a vignette for this package whose name apparently describes its author and users.
  • StatMeasures - V1.0; provides functions for data manipulation and data quality and statistical checks for data in both data frame and data.table object.
  • TSPred - V 2.0: Provides functions for time series predictions and accuracy assessment using automatic ARIMA modeling.
 

Updated Packages

The following list spotlights some CRAN packages that were updated between 3/1/15 and 4/1/15. These packages are noteable either because many changes were made or because they have not been updated in quite some time.

 

GitHub Packages

This section highlights some R packages that are only available on GitHub. For a more complete view of what’s trending on GitHub, check here.

  • DiagrammeR - Provides functions for creating graphs and flowcharts which may be displayed at the R console, in R Markdown documents and in Shiny Apps.
  • dmpe / R - Aggregates aR exercises from Udacity, Coursera and other sources.
  • htmlwidgets - provides a framework for creating R bindings to JavaScript libraries. Widgets created using the framework can be used at the R console, embedded in R markdown and Shiny and saved as stand alone web pages.
  • oce - A package for processing oceanographic data. The webpage contains examples and documentation.
  • Rfacebook - Provides an R API to Facebook.
  • rstan - Provides an R interface to the Stan Bayesian Engine.
  • logo.jpg Revolution R Open 8.0.2 Beta

    By default, Revolution R Open 8.0.2 Beta uses a fixed CRAN repository snapshot taken on March 1, 2015.

    The following list spotlights some of the new and updated CRAN packages that were released between 12/1/14 and 3/1/15. These packages and more are available for use with Revolution R Open.

     

    New Packages

    • ald - V1.0: Provides functions to describe and simulate the Asymmetric Laplace Distribution.
    • assertive - V0.2-1: Provides readable check functions to ensure code integrity.
    • BinOrdNonNor - V1.0: Provides functions to generate samples from a mix of binary, ordinal and continuous random variables with a pre-specified correlation matrix and marginal distributions.
    • BLCOP - V0.3.1: Implements the Black-Litterman Model along with Atilio Meucci’s copula pooling framework. The vignette provides an overview of the Black-Litterman model.
    • CEoptim - V1.0: Provides an optimization solver based on the Cross-Entropy method allowing multi-extremal optimization problems involving discrete, continuous, and mixed variables to be solved.
    • DiagrammeR - V0.4: allows you to create diagrams and flowcharts in R. A “Markdown-like” describes a diagram and lets code and diagrams be integrated.
    • drat - V0.0.2: Provides functions to create and use R repositories and to make repository information available in the current R session. Supports gh-pages at GitHub and local repositories.
    • elastic V0.3.0: Provides an interface to the elasticsearch NoSQL database built on the Java Virtual Machine. There are two vignettes: elastic introduction and search.
    • EnsemleBase - V0.7.1: Provides base classes for batch training of machine learning algorithms. These “base learners” can be combined to form ensemble predictions. The package wrappers for cross validation, error selection and more.
    • gelnet - V1.0: Implements several extensions to the elastic net regularization scheme including individual feature penalties for the L1 term and feature-feature penalties for the L2 term.
    • GenForImp - V1.0: Provides two forward imputation methods for the imputation missing data. One alternates Nearest Neighbour Imputation and Principal Component Analysis, the other uses Nearest Neighbour Imputation with the Mahalanobis distance.
    • GOplot - V1.0: Provides functions for visualizing biological data including bubble plots and circular plots. There is a vignette.
    • HistDAWass - V0.1.1: Provides functions for the statistical analysis of univariate histograms based on the L2 Wasserstein metric between distributions.
    • httr - V0.6.1: Contains tools for working with URLs and HTTP. It provides a wrapper for RCurl customised to the demands of modern web APIs. There are two vignettes: httr quickstart guide and Best practices for writing an API package a thoughtful design guide.
    • ICAFF - V1.0.1: Implements the Imperialist Competitive Algorithm useful for solving optimization problems for continuous functions.
    • Ihs - V1.0: provides the usual pdf, cdf, quantile and random sampling functions for the inverse hyperbolic sine distribution. It also provides a function for fitting this distribution from data.
    • itsadug - V0.8: Provides functions for the evaluation and visualization of Generalized Additive Mixed Models (GAMM) including model comparisons, determining regions of significance, the inspection of autocorrelational structure in residuals and visualizing complex interactions and contrasts. There is a nice vignette.
    • jagsUI - V1.3.1: Provides a set of wrappers around rjags functions to facilitate running Bayesian analyses in JAGS.
    • laketemps - V0.5.1: Lake temperature records, metadata, and climate drivers for 291 global lakes during the time period 1985-2009. Temperature observations were collected using satellite and in situ methods.
    • mountainplot - V1.0: Provides functions for drawing folded empirical cumulative distribution plots with lattice. The vignette provides examples.
    • onls - V0.1-0: Functions to implement Orthogonal Nonlinear Least-Squares Regression using Levenberg-Marquardt minimization.
    • pathological - V0.0-3: Path Manipulation Utilities for files and directories.
    • PoisBinOrd - V1.0: Functions to generate multiple count, binary and ordinal variables simultaneously given marginal characteristics and association structures.
    • ppmlasso - V1.1: Functions to fit point process models with sequences of LASSO penalties.
    • probFDA - V1.0 Contains functions for Probabilistic Fisher DIscriminant Analysis, a stochastic version of Fisher linear discriminant analysis for dimensionality reduction and classification.
    • PRROC - V1.1: Computes precision-recall and ROC curves and the area under these curves. Interpolation is done using non-linear piecewise functions. There is a vignette.
    • protoclust - V1.5: Functions to perform minimax linkage hierarchical clustering as described in Bien and Tibshirani (2011).
    • roughrf - V1.0: Implements a roughened random forests algorithm for binary classification. Have a look at the webpage.
    • RcppStreams - V0.1.0: Connects R with the Streamulus library for stream processing.
    • rebus - V0.0-5: Provides functions to build regular expressions in a human readable manner.
    • reproducer - V0.1.2: Functions and data sets to assist with reproducible research in the context of software engineering. See the webpage.
    • rglobi - V0.2.5: Provides a programmatic interface to the web service methods for the Global Biotic Interactions (GloBI) project. Find out who eats whom. There is a vignette to get started.
    • sgt - V1.1: provides the usual pdf, cdf, quantile and random sampling functions for the skewed, generalized t distribution. It also provides a function for fitting this distribution from data.
    • SurvCorr - V1.0: Estimates correlation coefficients with confidence limits for bivariate, partially censored survival times. It uses the iterative multiple imputation approach (Schemper et al Medicine 2013) and provides a scatterplot function to visualize the bivariate distribution.
     

    Updated Packages

    The following list spotlights some CRAN packages that were updated between 12/1/14 and 3/1/15. These packages are noteable either because many changes were made or because they have not been updated in quite some time.

    • AER - V1.2.3: Is the companion package for the book "Applied Econometrics with R" by Christian Kleiber and Achim Zeileis. It contains almost 100 data sets.
    • bio3d - V2.2-2: Provides functions for biological structure analysis. This update includes new facilities for sub-optimal path analysis of biomolecular correlation networks, new vignette detailing PDB structure manipulation and much more.
    • devEMF - V2.0: Provides functions to output graphics in EMF (enhanced metafile) format.
    • EnsembleCV - V0.7.1: Extends the base classes and methods of the EnsembleBase package and provides efficient methods for writing estimation objects to disk.
    • granovaGG - V1.3: Provides functions to visualize ANOVA results using ggplot2. This update, the first in two years, now uses ggplot2 V0.92’s theming system.
    • lcmm - V1.7.2: Allows the estimation of extended mixed models using latent classes and latent processes has been updated with a new function, predictlink, replaces link.confint.
    • rNOMADS - V2.2.2: Provides an interface to NOAA’s model archive and distribution system NOMADS. It allows R users to get to weather data.
    • RODBC - V1.3-11: This package which provides an interface to ODBC databases has had two updates recently, the first since November of 2013.
    • pwr - V1.1-2: Provides functions for basic power calculations using effect sizes and notations from Cohen (1988). This is the first update since 2009.
    • VineCopula - V1.4: Provides tools for bivariate exploratory data analysis, copula selection and construction and contains a number of new updates over the previous version which was released about 8 month ago.
     

    GitHub Packages

    This section highlights some R packages that are only available on GitHub. For a more complete view of what’s trending on GitHub, check here.

    • AnomalyDetection - Provides functions to detect anomalies in the presence of seasonality and an underlying trend.
    • CausalImpact - Provides functions for causal inference using Bayesian structural time series models.
    • covr - Tracks test coverage by augmenting a package’s function definitions with counting calls. There is a vignette.
    • distcomp - Enables collaborative, distributed computing without having to explicitly share data. The package, the web services environment built on opencpu and shiny technology and the algorithms are described in a paper by Narasimhan et al. There is also a brief summary here.
    • iotools - Provides a collection of highly efficient, chunk-wise functions for processing I/O streams on Hadoop.
    • plyrmr - Enables R users to perform data manipulation operations as found in packages such as plyr and reshape2 on very large data sets stored in Hadoop.
    • quickcheck - Provides support for randomized software testing for R. Have a look at the tutorial.
    • rcrunchbase - Provides an R client for the Crunchbase API, there is a getting started vignette and a blog post.
    • slidify - Lets you generate HTML5 slides from R markdown.
    • SparkR - An R frontend for Spark.

     

    logo.jpg Revolution R Open 8.0.1 Beta

    By default, Revolution R Open 8.0.1 Beta uses a fixed CRAN repository snapshot taken on December 1, 2014.

    The following list spotlights some of the new and updated CRAN packages that were released between 10/1/14 to 11/30/14. These packages and more are available for use with Revolution R Open.

     

    New Packages

    • anim.plots - V0.1: provides simple animated versions of basic R plots including plot, barplot, contour, hist and more. Two vignettes are provided.

    • BayesTree - V0.3-1.2: provides an implementation of Bayesian Additive Regression Trees (BART)

    • bglm - V1.0: Metropolis Hastings based Bayesian estimation of glm models following Gamerman (1997)

    • broom - V0.3.4: provides functions to convert R objects into “Tidy” data frames. There are four vignettes including Introduction to broom and Tidy bootstrapping.

    • checkpoint - V0.3.3: A step towards solving the reproducibility problem by allowing you to install packages as they existed on CRAN on a specific date as if you had a CRAN time machine.

    • cqrReg - V1.0: implements quantile regression (QR) and composite quantile regression (CQR) with adaptive Lasso penality.

    • curl - V0.3: provides a connection interface to Libcurl. The curl() function provides drop-in replacement for vase url() with better performance and support for http.2.0,ssl.

    • db.r - V0.1.0: uses OOP style objects to visualize tables and columns from a database. db.r dynamically loads database schemas, executes queries and manages credentials.

    • EBglmnet - V3.4: provides Empirical Bayesian Lasso (EBlasso) and Elastic Net (EBEN) methods for generalized linear models.

    • enigma - V0.1.0: An R client to access the enigma API. Enigma holds many public data sets from governments, universities, companies and other organizations.

    • EnsemblePCReg - V0.6: extends the base classes and methods of EnsembleBase for principle components regression based integration of base learners.

    • EnsemblePenReg - V0.6: extends the base classes and methods of EnsembleBase for penalized regression (Ridge and Lasso) It enables writing estimation objects to disk.

    • ggRandomForests - V1.0.0: designed to be used with the randomForestsSRC package, ggRandomForests contains tools for creating and plotting structures to visually understand random forest models.

    • HiDimDA - V0.2-2: provides functions for linear discriminant analysis in high dimensions based on reliable covariance estimators for datasets with many more variables than observations.

    • highfrequency - V0.4: provides functions to manage, clean and match high frequency trades and quotes, calculate liquidity measures, forecast volatility, investigate noise and more.

    • lucid - V1.0: allows users to print vectors and data frame of floating point numbers using non-scientific notation optimized for people. The vignette is Lucid printing.

    • MAVIS - V1.0: implements a Shiny application for interactive meta-analysis. It provides support for both fixed and random effects models.

    • meteoForecast - V0.43: provides access to several numerical weather prediction services in both raster and time series formats.

    • OptionPricing - V0.1: provides efficient Monte Carlo Algorithms for the price and sensitivities of Asian and European Options using Geometric Brownian Motion.

    • orderedLasso - V1.7: implements the ordered Lasso and time-lag regression. The Ordered Lasso fits a linear model and imposes an order constraint on the coefficients. For details, see the paper by Suo and Tibshirani.

    • ore - V1.0.4: An R interface to the Oniguruma regular expressions library which is an alternative to R base regex capabilities. Advantages of ore include regexs are first-class objects, substitutions can be functions, consistent names.

    • plotROC - V1.2: provides functions for generating interactive ROC curve plots and for comparing multiple curves on the same plot. There is an associated Shiny App and a vignette.

    • RccpAnnoy - V0.0.3: provides an R interface to the C++ Annoy library relying on the Rcpp and BH packages. The Annoy library for Approximate Nearest Neighbors has been written for efficient memory usage as well as the ability to load from / save to disk.

    • rclinicaltrials - V1.4: allows users to download aggregate clinical trial information and results from ClinicalTrials.gov. The vignette shows how to get started.

    • rcrossref - V0.2.0: provides an R client for various CrossRep APIs and enables getting citations in various formats. Comes with two vignettes Crossref and Crossref Filters.

    • rex - V0.2: A friendly, human-readable interface for constructing regular expressions with two nice vignettes: Server Log Parsing and URL Validation.

    • rfUtilities - V1.0: provides utilities for random forest model selection including class balance correction, significance tests, cross validation and probability partial plots.

    • ropensecretsapi : V1.0.1: provides an interface to the OpenSecrets.org, the website tracking money in US politics and its influence on public policy.

    • RSQLServer - V1.1: RSQLServer wraps the jTDS project’s JDBC 3.0 SQL Server driver and extends the RJDBC classes and DBI methods.

    • statar - V0.1.2: Based on datatable and inspired by Stata and Julia string and expression interpolation, statar contains functions to clean and summarize variables, join tables using SQL syntax and manipulate data sets with panel structure.

    • TDboost - V1.0: A fully nonparametric Tweedie model using the gradient boosting. It is capable of fitting a flexible nonlinear model and capturing interactions among predictors

    • tufterhandout - V 1.2: Provides a custom template and output formats to produce Tufte-style handouts in html formats. To be used with rmarkdown. Vignette available .

    • tumblR - V1.0: tumblr is a microblogging platform and social networking website. tumblr provides an interface to the tumblr web API .

     

    Updated Packages

    • caret - V6.0-37: caret is a major tool for machine learning algorithms in R. This appears to be a minor upgrade.

    • effects - 3.0-2: provides graphical and tabular effects displays for various linear models. The new update enables computing the variance covariance matrix of the coefficient estimates.

    • fBasics - V3011.87: implements basic functions for investigating financial returns. It was last updated in May of 2013.

    • fPortfoilo - V3011.81:provides an environment for teaching Financial Engineering and Computational Finance that contains many functions to analyze and optimize portfolios. This is the first upgrade since 2011.

    • Hmisc - V3.14-6: Some minor changes have been made to this venerable, very popular package containing tools for data analysis, graphics, sample size calculations and much more. This is the seventh upgrade this year.

    • miceadds - V1.0: contains auxiliary functions for multiple imputation which complement other R imputation functions. Main features include plausible value imputation and Partial Least Squares imputation. The new version adds functions for the mice algorithm.

    • mlr - V2.2: provides an interface to a large number of classification and regression techniques. In this update the web tutorial has been improved, ordered factors are supported and many other improvements have been made.

    • randtests - V1.0: The exact distribution of the Bartels Rank Test Statistic, a plot option to the runs test and enhanced documentation have been added to this first stable version of this package which provides non parametric randomness tests for numeric sequences.

    • rFerns - V1.1.0: implements the random ferns classifier of Ozuysal et. al. The package has been updated to reflect publication of Kursa’s paper in the JSS.

    • rmongodb - V1.8.0: Some significant changes have been made to this interface to the mongoDB database. mongo.bson.from.list and mongo.bson.to.list (rewritten from scratch) now correctly handles arrays. The new version solves many issues from github and stackoverflow.

    • rngwell19937 - V0.6-0: implements a long period random number generator WELL19937a by F. Panneton, P. L'Ecuyer and M. Matsumoto. This first update since 2012 contains corrected and improved documentation.

    • RSQLite - V1.0.0: embeds the SQLite database engine in R. The previous update was in May of 2013.

    • quandl- V 2.4.0: allows R users to connect to the Quandl API. The previous upgrade was in April of this year.