March '17 New Package Picks

by Joseph Rickert

Two hundred and sixteen new packages were added to CRAN in March. The following are my picks for the Top Forty, organized into five categories: Bioscience, Data, Data Science, Statistics and Utilities.

Bioscience

  • BioInstaller v0.0.3: Provides tools to install and download massive bioinformatics analysis software and database, such as NGS analysis tools with its required database or/and reference genome.

  • DSAIDE v0.4.0: Provides a collection of Shiny Apps that allow users to simulate and explore infectious disease transmission. The vignette will get you started.

  • treespace v1.0.0: Provides tools for the exploration of distributions of phylogenetic trees. This package includes a Shiny interface which can be started from R. There are vignettes for Dengue trees, Transmission trees, and for exploring landscapes of phylogenetic trees. The following plot from the vignette shows clusters of similar trees.

library(treespace)
data(woodmiceTrees)
wm.res <- treespace(woodmiceTrees,nf=3)
wm.groves <- findGroves(wm.res, nclust=6)
plotGrovesD3(wm.groves)

Data

Data Science

  • anomalyDetection v0.1.1: Implements procedures to aid in detecting network log anomalies. The vignette provides examples.

  • kerasR v0.4.1: Provides an interface to the Keras Deep Learning Library, which provides specifications for describing dense neural networks, convolution neural networks (CNN), and recurrent neural networks (RNN) running on top of either TensorFlow or Theano. The vignette contains examples.

  • modeval v0.1.2: Allows users to easily compare multiple classifications models built with caret functions for small data sets. The vignette provides examples.

  • supc v0.1: Implements the self-updating process clustering algorithms proposed in Shiu and Chen. The vignette contains examples.

  • tensorflow v0.7: Provides an interface to TensorFlow, an open-source software library for numerical computation using data flow graphs.

Statistics

  • frailtyEM v0.5.4: Contains functions for fitting shared frailty models with a semi-parametric baseline hazard using the Expectation-Maximization algorithm. The vignette explains the math.

  • FRK v0.1.1: Provides functions to build, fit and predict spatial random effects, fixed rank kriging models with large datasets. The vignette introduces the theory and shows some examples.

  • hmi v0.6-3: Allows users to build single-level and multilevel imputation models using functions provided, or functions from the mice and MCMCglmm packages. There is a vignette.

  • margins v0.3.0: Ports Stata’s margins command for calculating marginal (or partial) effects. There is an introduction, a vignette on the Technical Implementation Details, and a comparison with the Stata Command.

  • mlrMBO v1.0.0: Provides a toolbox for Bayesian, model-based optimization. There is an introduction and vignettes for Mixed Space Optimization, Noisy Optimization, and Parallelization.

  • MonteCarlo v1.0.0: Simplifies Monte Carlo simulation studies by providing functions that automatically set up loops to run over parameter grids, parallelize the computations, and generate output in LaTeX tables. The vignette shows how to use it.

  • RankingProject v0.1.1: Provides functions to generate plots and tables for comparing independently sampled populations. There is an introduction and a vignette that reproduces the figures from “A Primer on Visualizations for Comparing Populations, Including the Issue of Overlapping Confidence Intervals” by Wright, Klein, and Wieczorek (2017, The American Statistician, in press).

  • rjmcmc v0.2.2: Provides functions to perform reversible-jump MCMC with the restriction introduced by Barker & Link. The vignette shows how to calculate posterior probabilities from the MCMC output.

Utilities

  • canvasXpress v1.5.2: Enables creation of visualizations using CanvasXpress, a stand-alone JavaScript library for reproducible research. The vignette shows how to get started.

  • collapsibleTree v0.1.4: Provides functions to build interactive Reingold-Tilford tree diagrams created using D3.js, where every node can be expanded and collapsed by clicking on it. There are some examples on the GitHub site.

library(Polychrome)
pal2 <- alphabet.colors(26)
rancurves(pal2)

  • RApiDatetime v0.0.3: Provides a C-level API to allow packages to access C-level R date and datetime code.

  • Rcssplot v0.2.0.0: Provides tools to style plots with cascading style sheets. The vignette shows how.

  • reticulate v0.7: Implements an R interface to Python modules, classes, and functions. When calling into Python, R data types are automatically converted to their equivalent Python types. When values are returned from Python to R, they are converted back to R types. There is an overview and a vignette describing arrays in R and Python

  • shinyWidgets v0.2.0: Provides custom input widgets for Shiny apps. See the README for examples.

  • shinyjqui v0.1.0: An extension to shiny that brings interactions and animation effects from the jQuery UI library. There is an introduction and a vignette with examples.

  • valaddin v0.1.0: Provides tools to transform functions into functions with input validation checks, in a manner suitable for both programmatic and interactive use. The vignette shows how.

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