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.
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.
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)
ropercenter v0.1.0: Provides registered users with programmatic, reproducible access to data sets from The Roper Center for Public Opinion Research, which maintains the largest archive of public opinion data in existence. The vignette shows how to get started.
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.
margins v0.3.0: Ports Stata’s
marginscommand for calculating marginal (or partial) effects. There is an introduction, a vignette on the Technical Implementation Details, and a comparison with the Stata Command.
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).
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.
pivottabler v0.1.0: Allows users to create complex pivot tables and pivot tables with irregular layouts in R. There are multiple vignettes, including an introduction, a styling guide, a Shiny example and explanations of calculations and data groups.
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.
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