New R Packages on R Views

March 2019: "Top 40" New CRAN Packages

Fri, 26 Apr 2019 00:00:00 +0000

By my count, two hundred and thirty-three packages stuck to CRAN last month. I have tried to capture something of the diversity of the offerings by selecting packages in ten categories: Computational Methods, Data, Machine Learning, Medicine, Science, Shiny, Statistics, Time Series, Utilities, and Visualization. The Shiny category contains packages that expand on Shiny capabilities, not just packages that implement a Shiny application. It is not clear whether this is going to be a new cottage industry or not.

Computational Methods

DistributionOptimization v1.2.1: Fits Gaussian mixtures by applying Genetic algorithms from the GA package using Gaussian Mixture Logic stems from AdaptGauss.

latte v0.2.1: Implements connections to LattE for counting lattice points and integration inside convex polytopes, and 4ti2 for algebraic, geometric, and combinatorial problems on linear spaces and front-end tools facilitating their use in the ‘R’ ecosystem. Look here for an example.

nlrx v0.2.0: Provides tools to set up, run, and analyze NetLogo model simulations in R. There is a Getting Started Guide, vignettes for Advanced Configuration, and Examples.

nvctr v0.1.1: Implements the n-vector approach to calculating geographical positions using an ellipsoidal model of the Earth. This package is a translation of the FFi Matlab library from FFI described in Gade (2010). The vignette provides examples.

Data

EHRtemporalVariability v1.0: Provides functions to delineate reference changes over time in Electronic Health Records through the projection and visualization of dissimilarities among data temporal batches, and explore results through data temporal heat maps, information geometric temporal (IGT) plots, and a Shiny app. The vignette shows how to use the package.

kayadata v0.4.0: Provides data for Kaya identity variables (population, gross domestic product, primary energy consumption, and energy-related CO2 emissions), and includes utility functions for exploring and plotting fuel mix for a given country or region. See the vignette for examples.

newsanchor v0.1.0: Implements an interface to gather news from the News API. A personal API key is required. The vignette shows how to scrape New York Times online articles.

raustats v0.1.0: Provides functions for downloading Australian economic statistics from the Australian Bureau of Statistics and Reserve Bank of Australia websites. The vignette shows how to use the package.

Machine Learning

akmedoids v0.1.2: Advances a set of R-functions for longitudinal clustering of long-term trajectories, and determines the optimal solution based on the Caliński-Harabasz criterion ( Caliński and Harabasz (1974) ). The vignette works through an extended example.

shapper v0.1.0: Implements a wrapper for the Python shap library that provides SHapley Additive exPlanations (SHAP) for the variables that influence particular observations in machine learning models. There are vignettes for classification and regression.

sparkxgb v0.1.0: Implements a sparklyr extension that provides an interface for XGBoost on Apache Spark. See the README for a brief overview.

xgb2sql v0.1.2: Enables in-database scoring of XGBoost models built in R, by translating trained model objects into SQL query. See Chen & Guestrin (2016) for details on XGBoost, and the vignette for an overview of the package.

Medicine

ctrdata v0.18: Provides functions for querying, retrieving, and analyzing protocol- and results-related information on clinical trials from two public registers, the European Union Clinical Trials Register and ClinicalTrials.gov. There is a Getting Started Guide and a vignette with examples.

pubtatordb v0.1.3: Provides functions to download PubTator (National Center for Biotechnology Information) annotations, and then create and query a local version of the database. There is a vignette.

tacmagic v0.2.1: Provides functions to facilitate the analysis of positron emission tomography (PET) time activity curve (TAC) data. See Logan et al. (1996) and Aizenstein et al. (2008) for use cases, and the vignette for a detailed overview.

Science

bulletcp v1.0.0: Provides functions to automatically detect groove locations via a Bayesian changepoint detection method, to be used in the data pre-processing step of forensic bullet matching algorithms. See Stephens (1994) for reference, the vignette for the theory, and Mejia et al. in the most recent issue of Significance for the big picture.

earthtide v0.0.5: Ports the Fortran ETERNA 3.4 program by H.G. Wenzel for calculating synthetic Earth tides using the Hartmann and Wenzel (1994) or Kudryavtsev (2004) tidal catalogs. See the vignette for an introduction.

steps v0.2.1: Implements functions to simulate population dynamics across space and time. The Eastern Grey Kangeroo vignette offers an extended example.

Shiny

periscope v0.4.1: Implements an enterprise-targeted, scalable and UI-standardized shiny framework. There are vignettes for a downloadFile module, downloadablePlot module, downloadableTable module, and the creation of a framework-based application.

reactlog v1.0.0: Provides visual insight into that black box of shiny reactivity by constructing a directed dependency graph of the application’s reactive state at any point in a reactive recording. See the vignette for an introduction.

reactlog highlight filter from Carson Sievert on Vimeo.

shinyhttr v1.0.0: Modifies the progress() function from the httr package to let it send output to progressBar() function from the shinyWidgets package.

Statistics

CoopGame v0.2.1: Provides a comprehensive set of tools for cooperative game theory with transferable utility, enabling users to create special families of cooperative games, such as bankruptcy games, cost-sharing games, and weighted-voting games. The vignette offers theory and examples.

discfrail v0.1: Provides functions for fitting Cox proportional hazards models for grouped time-to-event data, where the shared group-specific frailties have a discrete non-parametric distribution. See Gasperoni et. al (2018). The vignette shows the math.

fastglm v0.1.1: Provides functions to fit generalized linear models efficiently using RcppEigen. The iteratively reweighted least squares implementation utilizes the step-halving approach of Marschner (2011). There is a vignette.

hettx v0.1.1: Implements methods developed by Ding, Feller, and Miratrix (2016), and Ding, Feller, and Miratrix (2018) for testing whether there is unexplained variation in treatment effects across observations, and for characterizing the extent of the explained and unexplained variation in treatment effects. There are vignettes on heterogeneous treatment effects and systematic fariation estimation.

mcmcabn v0.1: Implements a structural MCMC sampler for Directed Acyclic Graphs (DAGs). It supports the new edge reversal move from Grzegorczyk and Husmeier (2008) and the Markov blanket resampling from Su and Borsuk (2016), and three priors: a prior controlling for structure complexity from Koivisto and Sood (2004), an uninformative prior, and a user-defined prior. The vignette provides an overview of the package.

networkABC v0.5-3: Implements a new multi-level approximation Bayesian computation (ABC) algorithm to decipher network data and assess the strength of the inferred links between network’s actors. The vignette provides an example.

retrodesign v0.1.0: Provides tools for working with Type S (Sign) and Type M (Magnitude) errors, as proposed in Gelman and Tuerlinckx (2000) and Gelman & Carlin (2014), using the closed forms solutions for the probability of a Type S/M error from Lu, Qiu, and Deng (2018). The vignette shows how to use Type S and M errors in hypothesis testing.

senssobol v0.1.1: Enables users to compute, bootstrap, and plot up to third-order Sobol indices using the estimators by Saltelli et al. (2010) and Jansen (1999), and calculate the approximation error in the computation of Sobol first and total indices using the algorithm of Khorashadi Zadeh et al. (2017). The vignette provides an overview.

Time Series

DTSg v:0.1.2: Provides a class for working with time series data based on data.table and R6 with reference semantics. There are vignettes for Basic and Advanced usage.

RJDemetra v0.1.2: Implements an interface to JDemetra+, the seasonal adjustment software officially recommended to the members of the European Statistical System (ESS) and the European System of Central Banks.

runstats v1.0.1: Provides methods for quickly computing time series sample statistics, including: (1) mean, (2) standard deviation, and (3) variance over a fixed-length window of time-series, (4) correlation, (5) covariance, and (6) Euclidean distance (L2 norm) between short-time pattern and time-series. See the vignette for examples.

Utilities

aweek v0.2.0: Converts dates to arbitrary week definitions. The vignette provides examples.

credentials v1.1: Provides tools for managing SSH and git credentials. See the vignette for details.

cyphr v1.0.1: Implements wrappers using low-level support from sodium and OpenSSL to facilitate using encryption for data analysis. There is an Introduction and a vignette on Data Encryption.

encryptr v0.1.2: Provides functions to encrypt data frame or tibble columns using strong RSA encryption. See README for examples.

lenses v0.0.3: Provides tools for creating and using lenses to simplify data manipulation. Lenses are composable getter/setter pairs for working with data in a purely functional way, which were inspired by the Haskell library lens ( Kmett (2012) ). For a comprehensive history of lenses, see the lens wiki and look here for examples.

yum v0.0.1: Provides functions to facilitate extracting information in YAML fragments from one or multiple files, optionally structuring the information in a data.tree. See the README file.

Visualization

ggasym v0.1.1: Provides functions for asymmetric matrix plotting with ggplot2. See the vignette for examples.

predict3d v:0.1.0: Provides functions for 2- and 3-dimensional plots for multiple regression models using packages ggplot2 and rgl. It supports linear models (lm), generalized linear models (glm), and local polynomial regression fittings (loess). There is a vignette.

February 2019: “Top 40” New CRAN Packages

Tue, 26 Mar 2019 00:00:00 +0000

One hundred and fifty-one new packages arrived at CRAN in February. Here are my “Top 40” picks organized into eight categories: Bioinformatics, Data, Machine Learning, Medicine, Statistics, Time Series, Utilities and Visualization.

Bioinfomatics

Cascade v1.7: Implements a modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. See Jung et al. (2014) for details, along with a Package Introduction and a vignette on re-analysis.

Result of reverse engineering a TH1 network

countfitteR v1.0: Implements functions and a Shiny app for the automatized evaluation of distribution models for count data with an eye towards use in DNA analyses. The vignette provides an overview.

Data

noaaoceans v0.1.0: Provides tools to access the National Oceanic and Atmospheric Administration (NOAA) API. See the vignette for details.

guardianapi v0.1.0: Provides functions to access to The Guardian’s open API, containing all articles published in ‘The Guardian’ from 1999 to the present. The vignette shows how to use the package.

RobinHood v:1.0.1: Implements an interface to the RobinHood investing platform, including the ability to access account data, retrieve investment statistics and quotes, place and cancel orders, and more.

stlcsb v0.1.2: Provides functions working with data from The Citizens’ Service Bureau of the City of St. Louis including downloading data, categorizing problem requests, cleaning and subsetting CSB data, and projecting the data using the x and y coordinates. See the vignette.

Machine Learning

bigMap v2.1.0: Implements an unsupervised clustering protocol for large scale structured data, based on a low dimensional representation of the data. See Garriga and Bartumeus (2018) and the vignette for details.

fastNaiveBayes v1.0.1: Provides an extremely fast implementation of a Naive Bayes classifier that is largely based on the paper Schneider (2003). See the vignette for an introduction.

gama v1.0.3: Implements a genetic, evolutionary approach to performing hard partitional clustering. For details see Scrucca (2013), Charrad et al. (2014), and Tsagris and Papadakis (2018). The vignette shows how to use the package.

leiden v0.2.3: Uses reticulate to implement the Python leidenalg clustering algorithm for partitioning graphs in to communities in R. See the Python repository and Traag et al (2018) for details. There is also a vignette.

r.blip v1.1: Provides functions to learn Bayesian networks from datasets containing thousands of variables, and includes algorithms for (1) parent set identification (Scanagatta (2015)), (2) general structure optimization (Scanagatta (2018)), (3) bounded tree width structure optimization (Scanagatta (2016)), and (4) structure learning on incomplete data sets (Scanagatta (2018)).

RTML v0.9: Implements efficient solvers for 10 regularized multi-task learning algorithms applicable for regression, classification, joint feature selection, task clustering, low-rank learning, sparse learning and network incorporation. The details are described Cao and Schwarz (2018). There is a Tutorial.

Spectrum v0.4: Implements a fast, adaptive spectral clustering algorithm for single and multi-view data. The vignette provides an introduction.

SAR v1.0.0: Provides both a stand-alone and Azure Cloud implementation of the Smart Adaptive Recommendations (SAR) algorithm for personalized recommendations. Look here for a description of the SAR algorithm.

tfdeploy v0.6.0: Provides tools to deploy TensorFlow models across several services. There is a vignette of Deploying TensorFlow Models and another for using Saved Models.

tfio v0.4.0: Provides an interface to TensorFlow IO. There is a brief Introduction.

stabm v1.0.0: Implements several measures for the assessment of the stability of feature selection. See Bommert et al. (2017).

tidystopwords 0.9.0: Provides functions to generate stopword lists in 53 languages, in a way consistent across all the languages supported. There is a vignette.

Medicine

ClinReport v0.9.1.11: Provides functions to create formatted statistical tables in Microsoft Word documents that meet clinical standards. There is a vignette for Getting Started, a vignette for Modifying Outputs, and another for Graphic Outputs.

safetyGraphics v0.7.3: Implements a framework for evaluation of clinical trial safety through a Shiny application or standalone htmlwidget charts. See the User Guide.

Statistics

dosearch v1.0.2: Implements a method to identify causal effects from arbitrary observational and experimental probability distributions via do-calculus and standard probability manipulations, using a search-based algorithm that handles selection bias (Bareinboim and Tian (2015)), transportability (Bareinboim and Pearl (2014)), missing data (Mohan et al. (2013)), and arbitrary combinations of these. There is an informative Introduction

geosample v0.2.1: Provides functions for constructing sampling designs. For details, see Chipeta et al. (2016) and the vignette.

interactions v1.0.0: Provides a suite of functions for conducting and interpreting the analysis of statistical interaction in regression models, and includes visualization of two- and three-way interactions. There is a vignette for Exploring Interactions and another for Plotting Interactions.

IrregLong v0.1.1: Provides functions to analyze longitudinal data for which the times of observation are random variables that are potentially associated with the outcome process, and includes inverse-intensity weighting methods (Lin et al. (2004)) and multiple outputation (Pullenayegum (2016)). Look here for an overview.

missCompare v1.0.1: Implements a pipeline to test and compare various missing data imputation algorithms on simulated and real data. There is a Tutorial.

OutlierDetection v0.1.0: Implements various methods to detect outliers including: model-based (Barnett (1978)), distance-based (Hautamaki et al. (2004)), dispersion-based (Jin et al. (2001)), depth-based (Johnson et al. (1998)), and density-based (Ester et al. (1996)).

plsr v0.0.1: Provides functions for the partial least squares analysis of the relation between two high-dimensional data sets. See McIntosh & Lobaugh (2004) and the vignette for more information.

pliable v1.1: Fits a pliable lasso model. For details see Tibshirani and Friedman (2018) and the package vignette.

PointFore v0.2.0: Provides functions to estimate specification models for the state-dependent level of an optimal quantile/expectile forecast along with Wald Tests and a test of overidentifying restrictions. There is a Tutorial and vignettes on the GDP Greenbook and Preciptation examples.

segmenTier v0.1.2: Implements a dynamic programming solution to segmentation based on maximization of arbitrary similarity measures within segments, based on the theory described in Machne et al. (2017). The vignette provides an Introduction.

TextForecast v0.1.1: Provides functions for regression analysis and forecasting using textual data, which are based on Lima (2018). The vignette shows how to use the package.

Time Series

Rlgt v0.1-2: Provides functions to use rstan to fit several Global Trend models for time series forecasting that are Bayesian generalizations and extensions of some Exponential Smoothing models. There is an Intorduction to global trend time series forecasting and an Introduction to the package.

tsfeatures v1.0.0: Implements methods for extracting various features from time series data as described in Hyndman et al. (2013) , Kang et al.(2017) and Fulcher et al. (2013). The vignette contains examples.

Utilities

pak v0.1.2: Streamlines and improves package installation. See README.

qs v0.14.1: Provides functions for quickly writing and reading any R object to and from disk. See the vignette for use and timings.

ropendata v0.1.0: Provides functions to collect cyber-security data and make it available via the Open Data portal. Look at README for information on using the package.

rosr v0.0.5: Provides methods to create reproducible academic projects with integrated academic elements, including datasets, references, codes, images, manuscripts, dissertations, slides and so on.

ShinyEventLogger v0.1.1: Implements a logging framework for complex Shiny apps. The vignette shows how to start logging.

Visualization

gratia v0.2-8: Provides graceful ggplot-based graphics and utility functions for working with generalized additive models (GAMs) fitted using the mgcv package. Look here for examples.

jskm v0.3.1: Provides the function jskm() to create publication quality Kaplan-Meier plots with at-risk tables below, and svyjskm() to plot a weighted Kaplan-Meier estimator.

January 2019: “Top 40” New CRAN Packages

Mon, 25 Feb 2019 00:00:00 +0000

One hundred and fifty-three new packages made it to CRAN in January. Here are my “Top 40” picks in eight categories: Computational Methods, Data, Machine Learning, Medicine, Science, Statistics, Utilities, and Visualization.

Computational Methods

cPCG v1.0: Provides a function to solve systems of linear equations using a (preconditioned) conjugate gradient algorithm. The vignette shows how to use the package.

RcppDynProg v0.1.1: Implements dynamic programming using Rcpp. Look here for examples.

Data

cimir v0.1-0: Provides functions to connect to the California Irrigation Management Information System (CIMIS) Web API. See the Quick Start for details.

ecmwfr v1.1.0: Provides a programmatic interface to the European Centre for Medium-Range Weather Forecasts’ public and restricted dataset web services ECMWF, as well as Copernicus’s Climate Data Store CDS, allowing users to download weather forecasts and climate data. There are vignettes for both CDS and ECMWFR.

germanpolls v0.2: Provides functions to extract data from Wahlen.de.

nhdR v0.5.1: Provides tools for working with the National Hydrography Dataset, with functions for querying, downloading, and networking both the NHD and NHDPlus datasets. There are vignettes for Creating Simple Maps and Quering Flow Information, as well as an example.

snotelr v1.0.1: Provides a programmatic interface to the SNOTEL snow data. See the vignette for information.

wdpar v0.0.2: Provides an interface to the World Database on Protected Areas (WDPA). Data is obtained from Protected Planet. See the README for information.

Machine Learning

analysisPipelines v1.0.0: Implements an R interface that enables data scientists to compose inter-operable pipelines between R, Spark, and Python for data manipulation, exploratory analysis, modeling, and reporting. There are vignettes for Python Functions, R data frames, Spark data frames, Interoperable Pipelines, Meta-pipelines, Streaming Analysis Pipelines, and Using Pipelines with Spark.

bender v0.1.1: Implements an R client for Bender Hyperparameters optimizer.

FiRE v1.0: Implements an algorithm to find outliers and rare entities in voluminous datasets. Look here for information.

foto v1.0.0: Implements the Fourier Transform Textural Ordination method, which uses a principal component analysis on radially averaged, two-dimensional Fourier spectra to characterize image texture. See the vignette for details.

RcppHNSW v0.1.0: Provides bindings to the Hnswlib C++ library for Approximate Nearest Neighbors.

ruimtehol v0.1.2: Wraps the StarSpace library, allowing users to calculate word, sentence, article, document, webpage, link, and entity embeddings. The techniques are explained in detail in Wu et al. (2017). See the vignette for more information.

zoomgrid v1.0.0: Implements a grid search algorithm with zoom to help solve difficult optimization problems where there are many local optima inside the domain of the target function. Look here for information.

Medicine

bayesCT v0.99.0: Provides functions to simulate and analyze Bayesian adaptive clinical trials, incorporating historical data and allowing for early stopping. There is an Introduction, and vignettes for Binomial and Normal outcomes.

BioMedR v1.1.1: Provides tools for calculating 293 chemical descriptors and 14 kinds of chemical fingerprints, 9920 protein descriptors based on protein sequences, more than 6000 DNA/RNA descriptors from nucleotide sequences, and six types of interaction descriptors. There is a very informative vignette.

dr4pl v1.1.8: Models the relationship between dose levels and responses in a pharmacological experiment using the 4 Parameter Logistic model, and provides bounds that prevent parameter estimates from diverging. See Gadagkar and Call (2015) and Ritz et al. (2015) for background information, and the vignette for examples.

GMMAT v1.0.3: Provides functions to perform association tests using generalized linear mixed models (GLMMs) in genome-wide association studies (GWAS) and sequencing association studies. See Chen et al. (2016) and Chen et al. (2019) for background information, and the vignette for an introduction to the package.

Science

ethnobotanyR v0.1.4: Implements functions to calculate common quantitative ethnobotany indices to assess the cultural significance. See Tardio and Pardo-de-Santayana (2008) for background information, and the vignette for information on the package.

wsyn v1.0.0: Implements tools for a wavelet-based approach to analyzing spatial synchrony, principally in ecological data. The vignette gives the details.

Statistics

apcf v0.1.2: Implements the adapted pair correlation function, which transfers the concept of the pair correlation function from point patterns to patterns of objects of finite size and irregular shape. This is a re-implementation of the method suggested by Nuske et al. (2009). See the vignette for details.

concurve v1.0.1: Provides functions to compute confidence (compatibility/consonance) intervals for various statistical tests, along with their corresponding P-values and S-values. Consonance functions allow modelers to determine what effect sizes are compatible with the test model at various compatibility levels. For details, see Poole (1987), Schweder and Hjort (2002), Singh, Xie, and Strawderman (2007), and Amrhein, Trafimow and Greenland (2018). See the vignette for examples.

IMaGES v0.1: Provides functions to implement Independent Multiple-sample Greedy Equivalence Search (IMaGES), a causal inference algorithm for creating aggregate graphs and structural equation modeling data for one or more datasets. See Ramsey et. al (2010) for background information. There is a vignette.

metamer v0.1.0: Provides functions to create data with identical statistics (metamers) using an iterative algorithm proposed by Matejka & Fitzmaurice (2017). See README for help with the package.

mimi v0.1.0: Implements functions to estimate main effects and interactions in mixed data sets with missing values. Estimation is done through a convex program where main effects are assumed sparse and the interactions low-rank. See Geneviève et al. (2018).

pcLasso v1.1: Implements a method for fitting the entire regularization path of the principal components lasso for linear and logistic regression models. See Tay, Friedman, and Tibshirani (2014) for details and the vignette for an Introduction.

qrandom v1.1: Implements an API to the ANU Quantum Random Number Generator, provided by the Australian National University, that generates true random numbers in real-time by measuring the quantum fluctuations of the vacuum. The quantum Random Number Generator is based on the papers by Symul et al. (2011) and Haw, et al. (2015). Look here for live random numbers.

rstap v1.0.3: Provides tools for estimating spatial temporal aggregated predictor models with stan. See the vignette for an introduction.

ROCit v1.1.1: Provides functions to calculate and visualize performance measures for binary classifiers. The vignette describes the details.

surveysd v1.0.0: Provides functions to calculate point estimates and their standard errors in complex household surveys using bootstrap replicates. A comprehensive description of the methodology can be found here.

Utilities

askpass v1.1: Provides safe password entry for R, Git, and SSH. Look here for help.

logger v0.1: Provides a flexible and extensible way of formatting and delivering log messages with low overhead. There is an Introduction and vignettes on The Anatomy of a Log Request, Format Customization, Migration, Benchmarks, Logging, and Extensions.

pagedown v0.1: Implements tools to use the paged media properties in CSS and the JavaScript library paged.js to split the content of an HTML document into discrete pages. See the README for details.

rmd v0.1.4: Provides functions to manage multiple R Markdown packages. Look here for information.

tor v1.1.1: Provides functions to enable users to import multiple files at the same time. See the README for details.

vitae v0.1.0: Provides templates and functions to simplify the production and maintenance of curricula vitae. There is an Introduction and a vignette for creating templates.

Visualization

gganimate v1.0.1: Implements a ggplot2-compatible grammar for creating animations. The vignette will get you started.

RIdeogram v0.1.1: Implement tools to draw SVG (Scalable Vector Graphics) graphics to visualize and map genome-wide data in ideograms. See the vignette for information.

voronniTreeMap v0.2.0: Provides functions to create Voronni tree maps using the d3.js framework. Look here for examples.

December 2018: “Top 40” New CRAN Packages

Wed, 30 Jan 2019 00:00:00 +0000

By my count, 157 new packages stuck to CRAN in December. Below are my “Top 40” picks in ten categories: Computational Methods, Data, Finance, Machine Learning, Medicine, Science, Statistics, Time Series, Utilities and Visualization. This is the first time I have used the Medicine category. I am pleased that a few packages that appear to have clinical use made the cut. Also noteworthy in this month’s selection are the inclusion of four packages from the Microsoft Azure team (stuffing 41 packages into the “Top 40”), and some eclectic, but fascinating packages in the Science section.

Computational Methods

ar.matrix v0.1.0: Provides functions that use precision matrices and Choleski factorization to simulates auto-regressive data. The README offers examples.

mvp v1.0-2: Provides functions for the fast symbolic manipulation polynomials. See the vignette and this R Journal paper for details on how to create this image of the Rosenbrock function.

pomdp v0.9.1: Provides an interface to pomdp-solve, a solver for Partially Observable Markov Decision Processes (POMDP). See the vignette for examples.

Data

dbparser v1.0.0: Provides a tool for parsing the DrugBank XML database. The vignette shows how to get started.

rdhs v0.6.1: Implements a client querying the DHS API to download and manipulate survey datasets and metadata. There are introductions to using rdhs and the rdhs client, an extended example about Anemia prevalence, and vignettes on Country Codes, Interacting with the geojson API results, and Testing.

Finance

optionstrat v1.0.0: Implements the Black-Scholes-Merton option pricing model to calculate key option analytics and graphical analysis of various option strategies. See the vignette.

riskParityPortfolio v0.1.1: Provides functions to design risk parity portfolios for financial investment. In addition to the vanilla formulation, where the risk contributions are perfectly equalized, many other formulations are considered that allow for box constraints and short selling. The package is based on the papers: Feng and Palomar (2015), Spinu (2013), and Griveau-Billion et al.(2013). See the vignette for an example.

Machine Learning

BTM v0.2: Provides functions to find Biterm topics in collections of short texts. In contrast to topic models, which analyze word-document co-occurrence, biterms consist of two words co-occurring in the same short text window.

ParBayesianOptimization v0.0.1: Provides a framework for optimizing Bayesian hyperparameters according to the methods described in Snoek et al. (2012). There are vignettes on standard and advanced features.

Medicine

LUCIDus v0.9.0: Implements the LUCID method to jointly estimate latent unknown clusters/subgroups with integrated data. See the vignette for details.

metaRMST v1.0.0: Provides functions that use individual patient-level data to produce a multivariate meta-analysis of randomized controlled trials with the difference in restricted mean survival times ( RMSTD ).

webddx v0.1.0: Implements a differential-diagnosis generating tool. Given a list of symptoms, the function query_fz queries the FindZebra website and returns a differential-diagnosis list.

Science

bioRad v0.4.0: Provides functions to extract, visualize, and summarize aerial movements of birds and insects from weather radar data. There is an Introduction and a vignette on Exercises.

pmd v0.1.1: Implements the paired mass distance analysis proposed in Yu, Olkowicz and Pawliszyn (2018) for gas/liquid chromatography–mass spectrometry. See the vignette for an introduction.

tabula v1.0.0: Provides functions to examine archaeological count data and includes several measures of diversity. There are vignettes on Diversity Measures, Matrix Classes, and Matrix Seriation. This last vignette includes an example reproducing the results of Peeples and Schachner (2012).

traitdataform v0.5.2: Provides functions to assist with handling ecological trait data and applying the Ecological Trait-Data Standard terminology described in Schneider et al. (2018).

waterquality v0.2.2: Implements over 45 algorithms to develop water quality indices from satellite reflectance imagery. The vignette introduces the package.

Statistics

areal v0.1.2: Implements areal weighted interpolation with support for multiple variables in a workflow that is compatible with the tidyverse and sf frameworks. There are vignettes on Areal Interpolation, Wieghted Areal Interpoaltion, and Preparing Data for Interpolation.

FLAME v1.0.0: Implements the Fast Large-scale Almost Matching Exactly algorithm of Roy et al. (2017) for causal inference. Look at the README to get started.

mistr v0.0.1: Offers a computational framework for mixture distributions with a focus on composite models. There is an Introduction and a vignette on Extensions.

mlergm v0.1: Provides functions to estimate exponential-family random graph models for multilevel network data, assuming the multilevel structure is observed. There is a Tutorial.

MTLR v0.1.0: Implements the Multi-Task Logistic Regression (MTLR) proposed by Yu et al. (2011). See the vignette.

mulitRDPG v1.0.1: Provides functions to fit the Multiple Random Dot Product Graph Model and performs a test for whether two networks come from the same distribution. See Nielsen and Witten (2018) for details.

ocp v0.1.0: Implements the Bayesian online changepoint detection method of Adams and MacKay (2007) for univariate or multivariate data. Gaussian and Poisson probability models are implemented. The vignette provides an introduction.

probably v0.0.1: Provides tools for post-processing class probability estimates. See the vignettes Where does probability fit in? and Equivocal Zones.

smurf v1.0.0: Implements the SMuRF algorithm of Devriendt et al. (2018) to fit generalized linear models (GLMs) with multiple types of predictors via regularized maximum likelihood. See the package Introduction.

subtee v0.3-4: Provides functions for naive and adjusted treatment effect estimation for subgroups. Proposes model averaging Bornkamp et al. (2016) and bagging Rosenkranz (2016) to address the problem of selection bias in treatment effect estimation for subgroups. There is a Introduction and vignettes for the plot and subbuild functions.

xspliner v0.0.2: Provides functions to assist model building using surrogate black-box models to train interpretable spline based, additive models. There are vignettes on Basic Theory and Usage, Automation, Classification, Use Cases, Graphics, Extra Information, and the xspliner Environment.

Time Series

mfbvar v0.4.0: Provides functions for estimating mixed-frequency Bayesian vector autoregressive (VAR) models with Minnesota or steady-state priors as those used by Schorfheide and Song (2015), or by Ankargren, Unosson and Yang (2018). Look at the GitHub page for an example.

NTS v1.0.0: Provides functions to simulate, estimate, predict, and identify models for nonlinear time series.

Utilities

AzureContainers v1.0.0: Implements an interface to container functionality in Microsoft’s Azure cloud that enables users to manage the the Azure Container Instance, Azure Container Registry, and Azure Kubernetes Service. There are vignettes on Plumber model deployment and Machine Learning server model deployment.

AzureRMR v1.0.0: Implements lightweight interface to the Azure Resource Manager REST API. The package exposes classes and methods for OAuth authentication and working with subscriptions and resource group. There is an Introduction and a vignette on Extending AzureRMR.

AzureStor v1.0.0: Provides tools to manage storage in Microsoft’s Azure cloud. See the Introduction.

AzureVM v1.0.0: Implements tools for working with virtual machines and clusters of virtual machines in Microsoft’s Azure cloud. See the Introduction.

cliapp v0.1.0: Provides functions that facilitate creating rich command line applications with colors, headings, lists, alerts, progress bars, and custom CSS-based themes. See the README for examples.

projects v0.1.0: Provides a project infrastructure with a focus on manuscript creation. See the README for the conceptual framework and an introduction to the package.

remedy v0.1.0: Implements an RStudio Addin offering shortcuts for writing in Markdown.

solartime v0.0.1: Provides functions for computing sun position and times of sunrise and sunset. The vignette offers an overview.

Visualization

easyalluvial v0.1.8: Provides functions to simplify Alluvial plots for visualizing categorical data over multiple dimensions as flows. See Rosvall and Bergstrom (2010). See the README for details.

spatialwidget v0.2: Provides functions for converting R objects, such as simple features, into structures suitable for use in htmlwidgets mapping libraries. See the vignette for details.

transformr v0.1.1: Provides an extensive framework for manipulating the shapes of polygons and paths and can be seen as the spatial brother to the tweenr package. See the README for details.

Feb 2018: "Top 40" New Package Picks

Thu, 29 Mar 2018 00:00:00 +0000

Here are my picks for the “Top 40” packages of the 171 new packages that made it to CRAN (and stuck) in February, organized into the following categories: Computational Methods, Data, Finance, Science, Statistics, Time Series, and Utilities.

Computational Methods

adnuts v1.0.0: Provides an implementation of the no-U-turn (NUTS) algorithm by Hoffman and Gelman (2014) for ADMB and TMB models. The vignette will get you started.

CholWishart v0.9.2: Provides functions to sample from the Cholesky factorization of a Wishart random variable, the inverse Wishart distribution and the Cholesky factorization of an inverse Wishart random variable. See the vignette for details.

particles v0.2.1: Provides functions to simulate particle movement in 2D space using the ideas behind the ‘d3-force’ JavaScript particles library. It implements all forces defined in d3-force, as well as others such as vector fields, traps, and attractors. The vignette explains how to use the package.

rosqp v0.1.0: Provides bindings to the OSQP solver, which can solve sparse convex quadratic programming problems with optional equality and inequality constraints.

SolveLS v1.0: Implements methods including Jacobi, Gauss-Seidel, Successive Over-Relaxation, SSOR and non-stationary, Krylov subspace methods. See this book for details.

Data

Cluster.OBeu v1.2.1: Provides functions to estimate and return the needed parameters for visualizations designed for OpenBudgets data. There is a vignette for Using Cluster.OBeu with OpenCPU and one for Cluster analysis.

photobiologySun v0.4.0: Contains data for extraterrestrial solar spectral irradiance and ground-level solar spectral irradiance and irradiance. See Aphalo P. J. (2015) and the User Guide for more information.

SympluR v0.3.0: Provides functions to analyze data from the Healthcare Social Graph via access to the Symplur API. Look here for related research articles.

totalcensus v0.3.0: Allows users to download summary files from the Census Bureau and extract data - in particular, high resolution data at block, block group, and tract level - from decennial census and American Community Survey 1-year and 5-year estimates.

Finance

estudy2 v0.8.4: Implements event study models, including rate-of-return estimation and classical models. Tests include those proposed by [Brown and Warner (1980)](doi:10.¹⁰¹⁶⁄₀₃₀₄-405X(80)90002-1], [Brown and Warner (1985)](doi:10.¹⁰¹⁶⁄₀₃₀₄-405X(85)90042-X], [Boehmer et al. (1991)](doi:10.¹⁰¹⁶⁄₀₃₀₄-405X(91)90032-F>] and more. The vignette provides an introduction.

Machine Learning

DALEX v0.1.1: Provides various explainers that help to understand the link between input variables and model output in machine learning models. See this website for explanations.

forestControl v0.1.1: Allows approximate false positive rate control in selection frequency for random forest using the methods described by Konukoglu and Ganz (2015).

kmed v0.0.1: Implements the distance-based k-medoids clustering algorithm from Park and Jun (2009). Cluster validation applies bootstrap procedure producing a heatmap with a flexible reordering matrix algorithm. There is a vignette.

lolR v1.0.1: Implements optimal low-rank projection algorithms to obtain a lower-dimensional representation of data before applying supervised learning techniques in situations where the dimensionality exceeds the sample size. There are several vignettes including: Class Condidtional PCA, Low-Rank Canonical Correlation Analysis, and HDLSS Simulations.

projpred v0.7.0: Provides functions to perform projection predictive feature selection for generalized linear models; see, for example, Piironen and Vehtari (2017). The package is compatible with rstanarm. There is a Quick Start Guide.

RGF v1.0.1: Implements a wrapper for the python package Regularized Greedy Forest. It also includes a multi-core implementation called FastRGF.

Science

cRegulome v0.1.1: Provides functions to build a SQLite database file of pre-calculated transcription factor/microRNA-gene correlations (co-expression) incancer from the Cistrome and miRCancerdb databases. There is an Introduction and a Case Study.

CENFA v0.1.0: Provides tools for climate- and ecological-niche factor analysis of spatial data, including methods for visualization of spatial variability of species sensitivity, exposure, and vulnerability to climate change. See Hirzel et al. (2002) and Basille et al. (2008). The vignette introduces the package.

detectRUNS v0.9.5: Provides functions to detect runs of homozygosity and of heterozygosity in diploid genomes using the sliding windows ( Purcell et al (2007) ) and consecutive runs ( Marras et al (2015) ) methods. The vignette provides an overview.

Statistics

cosa v1.1.0: Implements generalized constrained optimal sample allocation framework for two-group multilevel regression discontinuity studies and multilevel randomized trials with continuous outcomes. There is a short Tutorial.

DirectEffects v0.1: Provides functions to estimate the controlled direct effect of treatment fixing a potential mediator to a specific value. Implements the sequential g-estimation estimator described in Vansteelandt (2009) and Acharya et al. (2016). The vignette introduces the package.

dnr v0.3.2: Provides functions to fit temporal lag models to dynamic networks built on top of exponential random graph models (ERGM) framework. The vignette describes the method.

geozoning v1.0.0: Provides a zoning method and a numerical criterion for assessing zoning quality. There are vignettes on Geozoning Structures and Simulated Data.

GpGp v0.1.0: Provides functions for Gaussian process predictions and conditional simulations, along with covariance functions for spatial and spatial-temporal data on Euclidean domains and spheres. The original approximation is due to Vecchia (1988), and the reordering and grouping methods are from Guinness (2018). The vignette contains an example using wind speed.

idealstan v0.2.7: Offers item-response theory (IRT) ideal-point scaling/dimension reduction methods that incorporate additional response categories and missing/censored values. Full and approximate Bayesian inference is done via the Stan engine. There is an Introduction and a vignette on Evaluating Models.

kdensity v1.0.0: Provides methods for univariate non-parametric density estimation with parametric starts and asymmetric kernels. See Chen (2000), Chen (1999), and Jones & Henderson (2007). There is a Tutorial.

NetLogoR v0.3.2: Provides functions to create agent-based models in R following the NetLogo framework. See Wilensky (1999). The NetLogo models Ants and Wolf-Sheep-Predation have been translated in R. See the Programming Guide and Data Dictionary.

riskyr v0.1.0: Provides functions to express risk-related information in terms of probabilities or frequencies to make the teaching and training of risk literacy more transparent. There is a User Guide and Quick Start Primer, along with vignettes on Data Formats, the Confusion Matrix and Metrics, and Functional Perspectives.

rsimsum v0.3.0: Provides functions to summarize results from simulation studies and compute Monte Carlo standard errors of commonly used summary statistics. This package is modeled on the simsum user-written command in Stata. There is an Introduction and vignettes on Visualization, Simulating a simulation study, and rsimsum and the tidyverse.

SimCorrMix v0.1.0: Provides functions to generate continuous (normal, non-normal, or mixture distributions), binary, ordinal, and count (regular or zero-inflated, Poisson or Negative Binomial) variables with a specified correlation matrix, or one continuous variable with a mixture distribution. This package can be used to simulate data sets that mimic real-world clinical or genetic data sets (i.e., plasmodes, as in Vaughan et al. (2009). There are vignettes on Continuous Mixture Distributions, Expected Cumulants and Correlations for Continuous Mixture Variables, Comparison of Correlation Methods, Variable Types, and Overall Workflow for Generation of Correlated Data

tree.bins v0.1.0: Allows users to recategorize the factors variables through a decision tree method derived from the rpart() function of the rpart package. For details, see Hastie et al (2009) and the vignette.

Time Series

segclust2d v0.1.0: Provides two methods for segmentation and joint segmentation/clustering of bivariate time-series. The segmentation method is a bivariate extension of Lavielle’s method available in adehabitatLT Lavielle (1999) and Lavielle (2005). The segmentation/clustering method is an extension of Picard et al (2007). The vignette contains several examples.

tstools v0.3.6: Provides functions to plot official statistics time series with automatic legends, highlight windows, stacked bar chars with positive and negative contributions, and other options. It includes a fast, data.table backed time series I/O that allows the user to export / import long format, wide format, and transposed wide format data to various file types. See the vignette for details.

Utilities

codemetar v0.1.5: Provides utilities to generate, parse, and modify codemeta.json files automatically for R packages, as defined in the Codemeta Project. There is an Introduction to the Codemeta Project, and vignettes on Translating Between Data Formats, Validating JSON-LD, and Examples.

knitrProgressBar v1.1.0: Provides a progress bar similar to dplyr that can write progress out to a variety of locations, including stdout(), stderr(), or from file(). There is an Example and a vignette for setting up.

msgpack v1.0: Implements a fast, C-based encoder and streaming decoder for the messagepack data format.

pmatch v0.1.3: Implements type constructions and pattern matching. See the README for details.

shinyalert v1.0: Provides functions to create pretty popup messages (modals) in Shiny that may contain text, images, OK/Cancel buttons, an input to get a response from the user, and many more customizable options.

trackr v0.7.5: Provides functions to automatically annotate R-based artifacts with relevant descriptive and provenance-related notes, and provides a back-end-agnostic storage and discoverability system for organizing, retrieving, and interrogating such artifacts. There is an Introduction and a vignette on Extending trackr.

Jan 2018: "Top 40" New Package Picks

Thu, 22 Feb 2018 00:00:00 +0000

Here are my “Top 40” picks from the two hundred or so new packages that stuck to CRAN in January, listed under seven categories: Data, Data Science, Science, Statistics, Time Series, Utilities and Visualizations (I say “stuck to” because I counted at least six packages that were accepted onto CRAN in January but removed within the month. Having packages quickly removed from CRAN is a phenomenon I have observed in recent months.)

While looking over the packages that I have listed under Data and Science, it struck me that in addition to being the world’s largest repository of statistical knowledge, CRAN is becoming a repository for practical, hard-won scientific knowledge.

Data

cancensus v0.1.7: Provides an interface to Canadian census and geographic data using the CensusMapper API. There is an Introduction and a vignette for Making maps.

elevatr v0.1.4: Provides access to several services offering elevation data, and returns the data either as a SpatialPointsDataFrame from point elevation services or as a raster object from raster elevation services. Currently, the package supports access to the Mapzen Elevation Service, Mapzen Terrain Service, Amazon Web Services Terrain Tiles, and the USGS Elevation Point Query Service. The vignette shows how to use the package.

fabricatr v0.2.0: Provides functions to simulate hierarchical and correlated data. There are several vignettes including a Getting Started guide and an Advanced Features guide, as well as introductions to Resampling and Generating Discrete Random Variables.

getTBinR v0.5.2: Facilitates easy import of analysis-ready World Health Organisation Tuberculosis data, and provides plotting functions for exploratory data analysis. There is a vignette.

homologene v1.1.68: Provides a wrapper for the homologene database by the National Center for Biotechnology Information, which allows searching for gene homologs across species.

photobiologyFilters v0.4.4: Is a data-only package with spectral ‘transmittance’ data for frequently used filters and materials, including plastic sheets and films, optical glass and ordinary glass, and some labware. It complements the photobiology package. See this website and the vignette for details.

tfdatasets v1.5: Provides an interface to TensorFlow Datasets, a high-level library for building complex input pipelines from simple, re-usable pieces.

washdata v0.1.2: Provides access to the urban water and sanitation survey data set collected by Water and Sanitation for the Urban Poor (WSUP), with technical support from Valid International. There is a vignette.

Data Science

CRPClustering v1.0: Provides a clustering method using the Chinese restaurant process Pitman (1995) that does not need to decide the number of clusters in advance. Also provides functions to calculate the ambiguity of clusters as entropy Yngvason (1999). The vignette shows how to use the package.

kerasformula v0.1.1: Provides a high-level interface for keras neural nets. See the vignette for details.

multiROC v1.0.0: Provides tools to solve problems with multiple classes by computing the areas under ROC curve via micro- and macro-averaging. The methodology is described in Van Asch (2013) and Pedregosa et al. (2011). See the vignette for a quick tour.

reinforcelearn v0.1.0: Implements reinforcement learning environments and algorithms. as described in Sutton & Barto (1998). There are vignettes for Agents and Environments.

stranger v0.3.2: Provides a framework for unsupervised anomalies detection There is a Vignette for the Impatient, and vignettes for Methods and Anomalies manual selection.

tidypredict v0.1.0: Provides functions to parse a fitted ‘R’ model object, and return a SQL query. There are vignettes for GLM and Random Forest models.

Science

annovarR v1.0.0: Provides unctions and database resources to offer an integrated framework to annotate genetic variants from genome and transcriptome data. The wrapper functions unify the interface of many published annotation tools, such as VEP, ANNOVAR, vcfanno, and AnnotationDbi. There is an Introduction and a vignette on Databases.

pubh v0.1.7: Offers a toolbox for making R functions and capabilities more accessible to students and professionals from Epidemiology and Public Health related disciplines. There is an Introduction and a Regression Example.

trajr v1.0.0: Provides a toolbox to assist with statistical analysis of two-dimensional animal trajectories. The vignette provides several examples.

Statistics

dalmatian v0.3.0: Automates fitting a double GLM in JAGS. There is a vignette on weighted regression and a two-part example using the Pied Flycatcher Data: Part 1 and Part 2.

dirichletprocess v0.2.0: Enables the creation of Dirichlet process objects that can be used as infinite mixture models. Examples include density estimation, Poisson process intensity inference, hierarchical modelling, and clustering. See Teh, Y. W. (2011) and the vignette for details.

detpack v1.0.1: Enables density estimation for possibly large data sets and conditional/unconditional random number generation with distribution element trees. For details on distribution element trees, see Meyer (2016), Meyer (2017), and Meyer (2017).

gnorm v1.0.0: Provides functions for obtaining generalized normal/exponential power distribution probabilities, quantiles, densities, and random deviates. See the vignette for details.

IROmiss v1.0.1: Provides a general algorithm, the Imputation Regularized Optimization (IRO) algorithm, for high-dimensional missing data problems. See Liang et al. (2018) for details.

KRIG v0.1.0: Provides functions for Kriging models and various methods for spatial statistics, including multivariate sensitivity analysis using reproducing kernel Hilbert spaces and computation of Sobol indexes. There are vignettes on Ordinary Kriging, Simple Kriging, Universal Kriging, and a worked example.

natural v0.9.0: Implements two error variance estimation methods in high-dimensional linear models. See Yu, Bien (2017) and the vignette.

OpVar v1.0: Provides functions for modeling operational (value-at-)risk, including loss frequencies and loss severities with plain, mixed (Frigessi et al. (2012)) or spliced distributions using Maximum Likelihood estimation and Bayesian approaches (Ergashev et al. (2013)). The vignette shows some examples.

netrankr v0.2.0: Implements methods for centrality-related analyses of networks, focusing on index-free assessment of centrality via partial rankings obtained by neighborhood-inclusion or positional dominance. See Schoch (2018). There are vignettes for benchmarks, centrality indices, indirect relations, neighborhood inclusion, partial centrality, positional dominance, probabilistic centrality, uniquely ranked graphs, and a use case.

palmtree v0.9.0: Implements the PALM tree algorithm, an extension to the MOB algorithm (implemented in the partykit package), where some parameters are fixed across all groups. See Seibold et al. (2016) for details.

PMCMRplus v1.0.0: Provides functions to calculate many different types of pairwise multiple comparisons tests. See the vignette for charts listing the tests covered.

seminr v0.4.0: Implements a domain-specific language for building PLS structural equation models, allowing for the latest estimation methods for Consistent PLS as per Dijkstra & Henseler (2015), adjusted interactions as per Henseler & Chin (2010), and bootstrapping utilizing parallel processing as per Hair et al. (2017). There is a vignette.

Time Series

santaR v1.0: Provides a graphical, automated pipeline for the analysis of short time series that has been designed to accommodate asynchronous time sampling, inter-individual variability, noisy measurements and large numbers of variables. There is a Getting Started Guide and vignettes on advanced command line functions, automated command line functions, plotting options, preparing input, selecting degrees of freedom, the theoretical background, and the GUI.

TSrepr v1.0.0: Provides methods for representations (e.g., dimensionality reduction, preprocessing, feature extraction) of time series. There is an Introduction to the Framework, a vignettes on representations, and a Use Case.

TSstudio v0.1.1: Provides a set of interactive visualization tools for time series analysis supporting ts, mts, zoo and xts objects including visualization functions for forecasting model performance (forecasted vs. actual), time series interactive plots (single and multiple series), and seasonality plots. The vignette shows the features available.

Utilities

arrangements v1.0.2: Provides fast generators and iterators for permutations, combinations and partitions, allowing users to generate arrangements in a memory-efficient manner. Benchmarks may be found here.

fs v1.1.0: Implements a cross-platform interface to file system operations, built on top of the libuv C library. See README for details.

googlePolylines v0.4.0: Provides functions to encode simple feature (sf) objects and coordinates using the Google polyline encoding algorithm. The vignette introduces the package.

prrd v0.2.0: Provides functions to queue reverse depends for a given package, such that multiple workers can run the tests in parallel. Look here or in the README for functionality details.

rquery v0.3.1: Implements a query generator based on Edgar F. Codd’s relational algebra and operator names, which is aimed at enhancing the experience using ‘SQL’ at big-data scale. There is a vignette on the Assignment Partitioner and one on Query Generation.

tsibble v0.1.3: Provides a tbl_ts class, the tsibble, to store and manage temporal-context data in a data-centric format. There is an Introduction.

Visualizations

breakDown v0.1.3: Implements break-down plots which show the contribution of every variable present in the model. Vignettes cover linear models, GLMs, and ranger models.

sigmaNet v1.0.3: Offers functions to create interactive graph visualizations using Sigma.js. The vignette shows how to get started.

June 2017 New Package Picks

Wed, 26 Jul 2017 00:00:00 +0000

Two hundred and thirty-eight new packages were added to CRAN in June. Below are my picks for the “Top 40”, organized into six categories: Biostatistics, Data, Machine Learning, Miscellaneous, Statistics and Utilities. Some packages, including geofacet and secret, already seem to be gaining traction.

Biostatistics

BIGL v1.0.1: Implements response surface methods for drug synergy analysis, including generalized and classical Loewe formulations and the Highest Single Agent methodology. There are vignettes on Methodology and Synergy Analysis.

colorpatch v0.1.2: Provides functions to show color patches for encoding fold changes (e.g., log ratios) and confidence values within a diagram; especially useful for rendering gene expression data and other types of differential experiments. See the vignette.

eesim v0.1.0: Provides functions to create simulated time series of environmental exposures (e.g., temperature, air pollution) and health outcomes for use in power analysis and simulation studies in environmental epidemiology. The vignette gives an overview of the package.

personalized v0.0.2: Provides functions for fitting and validating subgroup identification and personalized medicine models under the general subgroup identification framework of Chen et al. The vignette provides a brief tutorial.

tidygenomics v0.1.0: Provides method to deal with genomic intervals the “tidy way”. The vignette explains how they work.

Data

alfred v0.1.1: Provides direct access to the ALFRED and FRED databases. The vignette gives a brief example.

CityWaterBalance v0.1.0: Provides functions to retrieve data and estimate unmeasured flows of water through an urban network. Data for US cities can be gathered via web services using this package and dependencies. See the vignette for an introduction to the package.

censusapi v0.2.0: Provides a wrapper for the U.S. Census Bureau APIs that returns data frames of census data and metadata. Available data sets include the Decennial Census, American Community Survey, Small Area Health Insurance Estimates, Small Area Income and Poverty Estimates, and Population Estimates and Projections. There is a brief vignette.

dataverse v0.2.0: Provides access to Dataverse version 4 APIs, enabling data search, retrieval, and deposit. There are four vignettes: Introduction, Search and Discovery, Retrieval and Data Archiving.

data.world v1.1.1: Provides high-level tools for working with data.world data sets. There is a Quickstart Guide and a vignette for writing Queries.

SimMultiCorrData v0.1.0: Provides functions to generate continuous, binary, ordinal, and count variables with a specified correlation matrix that can be used to simulate data sets that mimic real-world situations (e.g., clinical data sets, plasmodes). There are several vignettes including an Overall Workflow for Data Simulation and a Comparison to Other Packages.

tidycensus v0.1.2: Provides an integrated R interface to the decennial US Census and American Community Survey APIs, and the US Census Bureau’s geographic boundary files.

ukbtools v0.9.0: Provides tools to work with UK Biobank datasets. The vignette shows how to get started.

wpp2017 v1.0-1: Provides and interface to data sets from the United Nation’s World Population Prospects 2017.

Machine Learning

cld3 v1.0: Provides an interface to Google’s experimental Compact Language Detector 3 algorithm, a neural network model for language identification that is the successor of cld2.

datafsm v0.2.0: Implements a method that automatically generates models of dynamic decision-making that both have strong predictive power and are interpretable in human terms. The vignette provides an example.

diceR v0.1.0: Provides functions for cluster analysis using an ensemble clustering framework. The vignette shows some examples.

glmertree v0.1-1: Implements recursive partitioning based on (generalized) linear mixed models (GLMMs) combining lmer() and glmer() from lme4 and lmtree() and glmtree() from partykit. The vignette shows an example.

greta v0.2.0: Lets users write statistical models in R and fit them by MCMC on CPUs and GPUs, using Google TensorFlow. There is a website, a Getting Started Guide, and vignettes providing Examples andTechnical Details.

penaltyLearning v2017.07.11: Implements algorithms from Learning Sparse Penalties for Change-point Detection using Max Margin Interval Regression. There is a vignette.

SentimentAnalysis v1.2-0: Implements functions to perform sentiment analysis of textual data using various existing dictionaries, such as Harvard IV, or finance-specific dictionaries, and create customized dictionaries. The vignette provides an introduction.

Miscellaneous

convexjlr v0.5.1: Provides a high-level wrapper for Julia package Convex.jl, which makes it easy to describe and solve convex optimization problems. There is a very nice vignette that shows how to optimize the parameters for several machine learning models.

interp v1.0-29: Implements bivariate data interpolation on both regular and irregular grids using either linear methods or splines.

pkggraph v0.2.0: Allows users to interactively explore and plot package dependencies for CRAN.

parallelDist v0.1.1: Provides a parallelized alternative to R’s native dist function to calculate distance matrices for continuous, binary, and multi-dimensional input matrices with support for a broad variety of distance functions from the stats, prox and dtw R packages. The vignette offers some results on performance.

Stats

anchoredDistR v1.0.3: Supplements the MAD# software that implements the Method of Anchored Distributions for inferring geostatistical parameters. There is a vignette.

bssm v01.1-1: Efficient methods for Bayesian inference of state space models via particle Markov chain Monte Carlo and importance sampling type corrected Markov chain Monte Carlo. There is a vignette on Bayesian Inference of State Space Models and an example of a Logistic Growth Model.

factorMerger v0.3.1 Provides a set of tools to support results of post-hoc testing and enable to extract hierarchical structure of factors. There is an Introduction and vignettes on Cox Regression Factor Merging and Multidimensional Gaussian Merging.

MittagLeffleR v0.1.0: Provides density, distribution, and quantile functions as well as random variate generation for the Mittag-Leffler distribution based on the algorithm by Garrappa. There are short vignettes for the math, distribution functions and random variate generation.

walker v0.2.0: Provides functions for building dynamic Bayesian regression models where the regression coefficients can vary over time as random walks. The vignette shows some examples.

Utilities

charlatan v0.1.0: Provides functions to make fake data, including addresses, person names, dates, times, colors, coordinates, currencies, DOIs, jobs, phone numbers, ‘DNA’ sequences, doubles and integers from distributions and within a range. The Introduction will get you started.

colordistances v0.8.0: Provides functions to load and display images, selectively mask specified background colors, bin pixels by color, quantitatively measure color similarity among images,and cluster images by object color similarity. There is an Introduction and vignettes on Pixel Binning Methods and Color Distance Metrics.

dbplyr v1.1.0: Implements a dplyr back end for databases that allows working with remote database tables as if they are in-memory data frames. There is an Introduction, a vignette for Adding a new DBI backend and one for SQL translation.

geofacet v0.1.5: Provides geofaciting functionality (the ability to arrange a sequence of plots for different geographical entities into a grid that preserves some geographical orientation) for ggplot2. There is a Package Reference vignette and an Introduction. The package is already getting some traction. This is a user submission:

ggformula v0.4.0: Provides a formula interface to ggplot2. There is a vignette explaining how it works.

gqlr v0.0.1: Provides an implementation of the GraphQL query language created by Facebook for describing data requirements on complex application data models. gqlr should be useful for integrating R computations into production applications that use GraphQL.

later v0.3: Allows users to execute arbitrary R or C functions some time after the current time, after the R execution stack has emptied. The vignette shows how to use later from C++.

secret v1.0.0: Allows sharing sensitive information like passwords, API keys, etc., in R packages, using public key cryptography. There is a vignette.

sessioninfo v1.0.0: Provides functions to query and print information about the current R session. It is similar to utils::sessionInfo(), but includes more information.

webglobe v1.0.2: Provides functions to display geospatial data on an interactive 3D globe. There is a vignette