One hundred seventy-four new packages made it to CRAN in October. Here are my “Top 40” selections in sixteen categories: Astronomy, Biology, Business, Computational Methods, Data, Ecology, Finance, Genomics, Mathematics, Machine Learning, Medicine, Pharma, Statistics, Time Series, Utilities, Visualization. Astronomy skylight v1.1: Provides a function to calculate sky illuminance values (in lux) for both the sun and moon. The model is a verbatim translation of the code by Janiczek and DeYoung (1987). There are vignettes for Use and Advanced Use. Biology palaeoverse v1.0.0: Provides tools to support data preparation and exploration for palaeobiological analyses including functions for data cleaning, binning (time and space), summarisation and visualisation with the goals of improving code reproducibility and accessibility and establishing standards for the palaeobiological community. See Jones et al. for details, and the contribution guide to get involved. pirouette v1.6.5: Implements a method to create a Bayesian posterior from a phylogeny that depicts the true evolutionary relationships. See Richèl et al. (2020) for background. There are several vignettes including a Tutorial, a demo, and a guide showing how to use the package in a scientific experiment. Business bupaverse v0.1.0: Facilitates loading the packages comprising the bupaverse, an integrated suite of R packages for handling and analysing business process data, developed by the Business Informatics research group at Hasselt University, Belgium. See the Getting Started Guide. Computational Methods fastWavelets v1.0.1: Provides an Rcpp implementation of the Maximal Overlap Discrete Wavelet Transform (MODWT) and the À Trous Discrete Wavelet Transform. See Quilty & Adamowski (2018) for background and README for examples. gips v1.0.0: Employs the methods described in Graczyk et al. (2022) to find the permutation symmetry group under which the covariance matrix of the data is invariant. See the vignettes Optimizers, Theory, and gips. HomomorphicEncryption v0.1.0: Implements the Brakerski-Fan-Vercauteren (2012), Brakerski-Gentry-Vaikuntanathan (2014), and Cheon-Kim-Kim-Song (2016) schema for fully homomorphic encryption. There are seven short vignettes including BFV, BGV, and CKKS. rxode2random v2.0.9: Implements parallel random number generation. See Wang et al. (2016) and Fidler et al (2019) for background and README for an example.. Data airnow v0.1.0: Provides functions to retrieve U.S. Government AirNow air quality data. See README to get started. amazonadsR v0.1.0: Provides functions to collect data on digital marketing campaigns using the Windsor.ai API. See the tutorial for an example and also look at the related new packages: bingadsR, facebookadsR, googleadsR, instagramadsR, linkedinadsR, pinterestadsR, redditadsR, snapchatadsR, ticktokadsR, twitteradsR. Pablo Sanchez was on a roll in October. congress v0.0.1: Provides functions to download and read data on United States congressional proceedings through the Congress.gov API of the Library of Congress. See README for an example. Ecology canaper v1.0.0: Provides functions to analyze the spatial distribution of biodiversity especially useful in the categorical analysis of neo- and paleo-endemism (CANAPE) as described in Mishler et al. (2014) and for statistical tests to determine the types of endemism that occur in a study area while accounting for the evolutionary relationships of species. There are vignettes on CANAPE, randomization, and parallel computing. EcoEnsemble v1.0.1: Provides functions to fit and sample from the ensemble model described in Spence et al (2018). There is an Introduction and there are two additional vignettes: ExploringPriors and SyntheticData. rTRIPLEXCWFlux v0.2.0: Encodes the carbon uptake submodule and evapotranspiration submodule of the TRIPLEX-CW-Flux model to run the simulation of carbon-water coupling. See Zhou et al. (2008) Monteith (1965) for background and the vignette for examples. stopdetection v0.1.1: Enables stop detection in time stamped trajectory by implementing the Stay Point detection algorithm originally described in Ye (2009) that uses time and distance thresholds to characterize spatial regions as stops. See the vignette for examples. Finance highOrderPortfolios v0.1.0: Implements methods to select portfolios using high order moments to characterize return distributions. See Zhou & Palomar (2021) and Wang et al. (2022) for the theory and the vignette to get started. MSTest v0.1.0: Implements hypothesis testing procedures described in Hansen (1992), Carrasco, Hu, & Ploberger (2014) and Dufour & Luger (2017) that can be used to identify the number of regimes in Markov switching models. See README for an example. Genomics metevalue v0.1.13: Implements the e-value method to correct p-values in omics data association studies. See Hebestreit & Klein (2022) and Akalin et.al (2012) for background and the vignette for an example. SCpubr v1.0.4: Implements a system that provides a streamlined way of generating publication ready plots for known Single-Cell transcriptomics data. Look here for an online reference manual. Mathematics Boov v1.0.0: Provides functions to perform the Boolean operations union, difference and intersection on volumes. Computations are done by the C++ library CGAL. See README for some examples. Also, have a look at the package MinkowskiSum. fitode v0.1.1: Provides methods and functions for fitting ordinary differential equations that use sensitivity equations to compute gradients of ODE trajectories with respect to underlying parameters. See the vignette for details. manifold v0.1.1: Implements operations for Riemannian manifolds including geodesic distance, Riemannian metric, and exponential and logarithm maps, and also incorporates a random object generator on the manifolds. See Dai, Lin, and Müller (2021) for details. Machine Learning SoftBart v1.0.1: Implements the SoftBart model of described by Linero and Yang (2018) with the optional use of a sparsity-inducing prior to allow for variable selection. The vignette contains theory and examples. tidyfit v0.5.1: Extends the tidy data environment with functions to fit and cross validate linear regression and classification algorithms on grouped data. There are several vignettes including Predicting Boston House Prices, Multinomial Classification, and Rolling Window Time Series Regression. Medicine cities v0.1.0: Provides functions to simulate clinical trials and summarize causal effects and treatment policy estimands in the presence of intercurrent events. Have a look at the demo. RCT2 v0.0.1: Implements various statistical methods for designing and analyzing two-stage randomized controlled trials using the methods developed by Imai, Jiang, and Malani (2021) and Imai, Jiang, and Malani (2022). There are vignettes on Interference and Causal Inference. Pharma DTSEA v0.0.3: Implements a novel tool to identify candidate drugs against a particular disease based on the drug target set enrichment analysis. It assumes the most effective drugs are those with a closer affinity in the protein-protein interaction network to the specified disease. See Gómez-Carballa et al. (2022) and Feng et al. (2022) for disease expression profiles, Wishart et al. (2018) and Gaulton et al. (2017) for drug target information, and Kanehisa et al. (2021) for the details of KEGG database. There is a vignette. nlmixr2lib v0.1.0: Provides tools to create model libraries for nlmixr2. Models include pharmacokinetic, pharmacodynamic, and disease models used in pharmacometrics. See the vignette Creating a model library. Statistics aIc v1.0: Implements set of tests for compositional pathologies including for coherence of correlations as suggested by Erb et al. (2020), compositional dominance of distance, compositional perturbation invariance as suggested by (Aitchison (1992) and singularity of the covariation matrix. See the vignette for details and examples. ktweedie v1.0.1: Uses Reproducing Kernel Hilbert Space methods to implement Tweedie compound Poisson gamma models with high-dimensional predictors for the analyses of zero-inflated response variables. See the vignette for examples. missoNet v1.0.0: Implements efficient procedures for fitting conditional graphical lasso models linking predictor variables to response variables or tasks, when the response data may contain missing values. See the vignette for examples. ShalpeyOutlier v0.1.0: Provides methods to use Shapley values to detect, explain, and cell wise impute multivariate outliers. See Mayrhofer and Filzmoser (2022) for details and the vignette for examples. SpatialfdaR v1.0.0: Provides functions to that implement finite element analysis methods to spatial functional data analysis. See Sangalli et al. (2013) and Bernardi et al. (2018) for background and the vignette for an example. Time Series dfms v0..1.3: Provides a user friendly and computationally efficient approach to estimate linear Gaussian dynamic factor models using Kalman filter and EM algorithm methods. See Doz et al. (2011) and Banbura & Modugno (2014) for background and the vignette for examples. Utilities ExclusionTable v1.0.0: Provides functions for creating tables of excluded observations by reporting the number before and after each subset() call together with the number of observations that have been excluded. See the vignette. shiny.tailwind v0.2.2: Allows TailwindCSS to be used in Shiny apps with just-in-time compiling including custom CSS with @apply directive, and custom tailwind configurations. See README for examples. Visualization AlphaHull3D v1.1.0: Provides functions to compute the alpha hull of a set of points (informallly: the shape formed by these points) in 3D space. See README for some visualizations, and also have a look at the related packages MeshesTools, and PolygonSoup. bangladesh v1.0.0: Provides sf objects, shape files, and functions to draw regional chorpleth maps for Bangladesh. See the vignette. ggstats v0.1.0: Provides functions to create forest plots of regression model coefficients along with new statistics to compute proportions, weighted mean and cross-tabulation statistics, as well as new geometries to add alternative background color to a plot. There are vignettes on plotting coefficients and on computing cross-tabulation, custom proportions, and weighted means. jagshelper v0.1.11: Provides tools to streamline Bayesian analyses in JAGSincluding functions for extracting output, streamlining assessment of convergence, and producing summary plots. See the vignette for examples. roughsf v1.0.0: Provides functions to draw maps, including “sketchy”, hand-drawn-like maps using the Javascript library Roughjs. See README for examples.

Two hundred and six new packages stuck to CRAN in March. Here are my "Top 40" selections in thirteen categories: Computational Methods, Data, Finance, Game Theory, Genomics, Machine Learning, Medicine, Networks, Science, Statistics, Time Series, Utilities, and Visualization. Provides functions to perform 2D Delaunay triangulation, constrained or unconstrained, with the help of the CDT C library. Look here for a list of algorithms. Offers tools for downloading and extracting data from the Copernicus Agrometeorological indicators from 1979 to present derived from reanalysis (AgERAS) dataset.

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. . 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.. . 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.

MKclass v0.3: Implements performance measures and scores for statistical classification including accuracy, sensitivity, specificity, recall, similarity coefficients, AUC, GINI index, Brier score and more. It calculates optimal cut-offs and decisions stumps according to (Iba and Langley (1991) follows Lemeshow and Hosmer and Hosmer et al. (1997) for goodness of fit tests and Porta (2014) for epidemiological risk measures. See the vignette to get started.

One hundred fifty-two packages made it to CRAN in December. Here are my "Top 40" picks in ten categories: Data, Genomics, Machine Learning, Mathematics, Medicine, Science, Statistics, Time Series, Utilities, and Visualization. Look here for more information as well as the vignette. Loads and creates spatial data, including layers and tools that are relevant to the activities of the Commission for the Conservation of Antarctic Marine Living Resources ( CCAMLR). Have a look at the vignette.

Provides tools to create and manipulate probability distributions using S3. Generics random(), pdf(), cdf(), and quantile() provide replacements for base R's r/d/p/q style functions. The documentation for each distribution contains detailed mathematical notes. There are several vignettes: Intro to hypothesis testing, One-sample sign tests, One-sample T confidence interval, One-sample T-tests, Z confidence interval for a mean, One-sample Z-tests for a proportion, One-sample Z-tests, Paired tests, and Two-sample Z-tests.

There are several vignettes: 1.