June 2022: “Top 40” New CRAN Packages

One hundred eighty-nine new packages made it to CRAN in June. Here are my “Top 40” selections in eleven categories: Computational Methods, Data, Ecology, Genomics, Machine Learning, Mathematics, Medicine, Statistics, Time Series, Utilities, and Visualizations.

Computational Methods

itp v1.2.0: Implements the interpolate, truncate, project root-finding algorithm developed by Oliveira & Takahashi (2021). The vignette provides an overview.

QR v0..1.3: Provides a function to perform QR factorization without pivoting to a real or complex matrix. It is based on LAPACK. See the vignette.

qsplines v1.0.0: Provides functions to create quaterion splines. See Barry & Goldman (1988) and Kochanek & Bartels (1984) for the details and look here for an example.

VMDecomp v1.0.1: Implements the variational mode decomposition and two-dimensional variational mode decomposition algorithm. See Dragomiretskiy & Zosso (2014) for background and the vignette for examples.

Data

cmch v0.2.0: Implements a wrapper around the Canadian Mortgage and Housing Corporation web interface and enables programmatic and reproducible access to a wide variety of housing data. See the vignette for examples.

EDIutils v1.0.1: Implements a client for the Environmental Data Initiative repository REST API and provides access to ecological data and metadata. There are five short vignettes: Evaluate & upload, Citation Metrics, Download Metrics, Search andaccess, and Tests.

globaltrends v0.0.12: Provides functions to access global search volumes from the Google Trends portal. This working paper outlines the package’s methodological foundations and potential applications. See the vignette to get started.

kaigiroku v0.5: Allows users to search and download data from the API for Japanese Diet proceedings. Look here for examples.

NasdaqDataLink v1.0.0: Provides functions to interact directly with the Nasdaq Data Link API and obtain data in a number of formats. Look here for API documentation and here for package information.

stortingscrape v0.1.1: Provides functions for retrieving data from the Norwegian Parliament, through the Norwegian Parliament API. See the vingette for an introduction.

Ecology

PointedSDMs v1.0.6: Provides tools to build integrated species distribution models and includes tools to run spatial cross-validation and plotting. See Issac et al. (2020) for and introduction to the methods. There is a Setophaga Example and an example for the Solitary Tinamou.

restoptr v1.0.1: Implements a flexible framework for ecological restoration planning that aims to identify priority areas for restoration efforts using optimization algorithms described in Justeau-Allaire et al. 2021. See the vignette to get started.

Genomics

scapGNN v0.1.1: Implements a single cell active pathway analysis tool based on the graph neural network algorithm described in Scarselli et al. (2009) and Kipf & Welling (2017). This may be used to construct a gene-cell association network, infer pathway activity scores from different single cell modalities data and more. See the vignette for an overview and examples.

SRTsim v0.99.2: Implements an independent, reproducible, and flexible Spatially Resolved Transcriptomics simulation framework that can be used to facilitate the development analytical methods and for a wide variety of SRT-specific analyses. See the vignette.

xQTLbiolinks v1.1.1: Implements tools to query, download, and visualize of molecular quantitative trait locus and gene expression data from public resources through the GTEx API. There is a Quick Start Guide and vignettes on Colocalization, Specivicity, and Visualization.

Machine Learning

agua v0.0.1: Enables users to specify h2o as an engine for several tidymodels modeling methods. See README for examples.

MagmaClustR V1.0.0: Implements two main algorithms, called Magma (Leroy et al. (2022) and MagmaClust (Leroy et al. (2020)), using a multi-task Gaussian processes (GP) model to perform predictions for supervised learning problems. See README for examples.

openai v0.1.0: Provides a wrapper for OpenAI API endpoints including engines, completions, edits, files, fine-tunes, embeddings and legacy searches, classifications, and answers endpoints. See README to get started.

sketching v0.1.0: Provides functions to construct sketches of data via random subspace embeddings. See Lee & Ng (2022) for the theory and the vignette for examples.

webmorphR v0..1.1: Provides functions to create reproducible image stimuli, specialised for face images with psychomorph or webmorph templates. See README to get started.

Mathematics

GeneralizedWendland v0.5-2: Implements the fully parameterized generalized Wendland covariance function for use in Gaussian process models, as well as multiple methods for approximating it via covariance interpolation. The available methods are linear interpolation, polynomial interpolation, and cubic spline interpolation. See Bevilacqua et al. (2022) and the vignette for examples.

jacobi v2.0.0: Evaluates Jacobi theta functions and related functions including the Weierstrass elliptic function, the Weierstrass sigma function, the Weierstrass zeta function, the Klein j-function, the Dedekind eta function, the lambda modular function, Jacobi elliptic functions, Neville theta functions, and the Eisenstein series for real and complex variables. Look here for some images.

Medicine

clinicalsignificance v1.0.0: Implements the clinical significance algorithm proposed by Jacobson et al. (1984) to determine if an intervention has a meaningful practical effect. There is a Getting Started Guide and vignettes on Cutoffs and Plots.

PlatformDesign v1.0.1: Provides functions to calculate design parameters for an optimal two-period, multi-arm platform design allowing pre-planned deferred arms to be added during the trial. See Dunnett (1955) for background and the vignette for some theory and examples.

Statistics

bayesassurance v0.1.0: Provides functions to compute Bayesian assurance under various settings characterized by different assumptions and objectives, including precision-based conditions, credible intervals, and goal functions. See Pan & Banerjee (2021) for the theory. There are vignettes for using closed form solutions, the conjugate linear model, and precision based conditions.

DSSP v0.1.1: Provides functions to draw samples from the direct sampling spatial prior model as described in White, Sun, & Speckman (2019). See the vignette for examples.

edibble v0.1.0: Implements a system to facilitate designing comparative experiments using the grammar of experimental designs. See the edibble-book for documentation.

mixgb v0.1.0: Implements a method for multiple imputation using XGBoost, bootstrapping and predictive mean matching as described in Deng and Lumley (2021). There is an Introduction and a vignette on Imputing new data with a saved imputer.

outerbase v0.1.0: Implements in new method for high-dimensional regression using outer product models. See Plumlee (2014) and Plumlee et al. (2021) for background. There is a Getting started guide, a Base walkthrough, and vignettes on Learning from data and Speeding up inference.

PFIM v5.0: Provides functions to evaluate or optimize designs for nonlinear mixed effects models using the Fisher Information matrix. See Malle & Baccar D (1997) and Retout et al. (2007) for background and the vignettes Design evaluation and optimixation (01), Design evaluation and optimixation (02), and Library of models for examples.

VirtualPop v1.0.2: Provides functions to generate lifespans and fertility histories in continuous time using individual-level state transition (multi-state) models and data. See the vignettes on Simulation of life histories, Sampling from waiting time distributions, Simulation of individual fertility careers, and Validation.

Time Series

kssa v0.0.1: Implements the known sub-sequence algorithm described in Benavides et al. (2022), which helps to automatically identify and validate the best method for missing data imputation in a time series. Look here for examples.

ts2net v0.1.0: Implements methods to transform time series into networks, a technique which may be useful for complex systems modeling, time series data mining, or time series analysis using networks. For an introduction to the topic and descriptions of the methods see Mitchell (2006), Silva & Zhao (2016), and Silva et al. (2021). See README to get started.

Utilities

cppchedkR Allows users to run Cppcheck on C/C++ files as an R command or an RStudio addin. See README. .

gtExtras v0.4.1: Provides additional functions for creating tables with gt. See README for examples.

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Visualization

ggpie v0.2.2: Provides functions for creating pie, donut and rose pie plots with ggplot2. See the vignette.

ggtrace v0.2.0: Provides ggplot2 geoms that allow groups of data points to be outlined or highlighted for emphasis. See the vignettes Trace lines and Trace points.

Morphoscape v1.0.0: Implements adaptive landscape methods first described by Polly et al. (2016) for the integration, analysis and visualization of biological trait data on a phenotypic morphospace which are typically defined by shape metrics. See the vignette.

r3js v0.0.1: Provides R and JavaScript functions to allow WebGL-based 3D plotting using the three.js library. See the vignettes: Getting Started, Creating a plot from scratch, and Grouping plot elements.

rgl2gltf v1.0.0: Provides functions to work with glTF files which are used to describe 3D models. See the vignette for examples..

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shapviz v0.2.0: Provides functions to visualize SHapley Additive exPlanations (SHAP), such as waterfall plots, force plots, various types of importance plots, and dependence plots. See Lundberg & Lee (2017) for background and the vignette for examples.