October 2022: “Top 40” New CRAN Packages
This article is originally published at https://rviews.rstudio.com/
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.
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.
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.
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.
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.
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:
twitteradsR. Pablo Sanchez was on a roll in October.
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.
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.
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.
Boov v1.0.0: Provides functions to perform the Boolean operations union, difference and intersection on volumes. Computations are done by the
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.
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.
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.
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.
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.
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.
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.
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
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.
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