Sometimes it appears to me that the invisible hand economists speak of guides the market for new R packages. Eight of the 129 new packages that stuck to CRAN in December fall under Computational Methods, a category I have only recently begun using. All of them made it into the list below of my “Top 40” picks. One day, I would like to go back and reexamine the categories I have been using to see if package developers really do respond to some idea that is “in the air” or whether the variation in categories is just one more of my many hidden biases.
alphashape3d v1.3: Provides functions to compute the alpha-shape (a generalization of the convex hull) of a finite set of points in the three-dimensional space.
deGradInfer v1.0.0: Implements efficient Bayesian parameter inference for systems of ordinary differential equations based on adaptive gradient matching. See Dondelinger et al. (2013) and Macdonald (2017). The vignette provides examples.
FixedPoint v0.1: Provides algorithms for finding fixed-point vectors, including iterative procedures for non-linear integral equations Anderson (1965), epsilon extrapolation methods Wynn (1962), and minimal polynomial methods Cabay & Jackson (1976). The vignette provides a very nice introduction to the subject.
grapherator v1.0.0: Aimed at research in single- and multi-objective combinatorial optimization, the package provides functions for step-wise generation of weighted graphs. There are vignettes on Graph Generation, Custom Generators and using pipes.
sparseEigen v0.1.0: Provides methods to compute sparse eigenvectors of a matrix with running time two to three orders of magnitude lower than existing methods. The methods are based on the paper by (Benidis et al. (2016). The vignette includes performance benchmarks.
TukeyRegion v0.1.2: Provides fast computation of Tukey regions, polytopes in the Euclidean space giving upper-level sets of the Tukey depth function for given data. For details, see Liu, Mosler, and Mozharovskyi (2017).
mlbgameday v0.0.1: Implements methods for multi-core processing of Gameday data from Major League Baseball Advanced Media (http://gd2.mlb.com/components/game/mlb/). There are vignettes on Database Connedtions, Parallel Processing, Plotting Pitches, and Searching Games.
afCEC v1.0.2: Implements active function cross-entropy clustering partitions the n-dimensional data into the clusters by finding the parameters of the mixed generalized multivariate normal distribution, that optimally approximates the scattering of the data in the n-dimensional space. For details see P. Spurek et al (2017).
dissever v0.2-2: Enables spatial down-scaling of coarse-grid mapping to fine-grid mapping using predictive covariates and a model fitted using the ‘caret’ package. The original dissever algorithm was published by Malone et al. (2012) and extended by Roudier et al. (2017). There is a short tutorial.
tfestimators v1.5: Implements an interface to
TensorFlow Estimators, a high-level API that provides implementations of many different model types, including linear models and deep neural networks. There is an Introduction and vignettes on Custom Estimators, the Dataset API, Basic Components, Feature Columns, Input Functions, Parsing Utilites, Run Hooks, and TensorBoard Visualization.
ePCR v0.9.9-4: Provides the top-performing ensemble-based Penalized Cox Regression (ePCR) framework developed during the DREAM 9.5 mCRPC Prostate Cancer Challenge. See Guinney J et al. (2017) for details.
simRVPedigree v0.1.0: Provides routines to simulate and manipulate pedigrees ascertained to contain multiple family members affected by a rare disease. See Nieuwoudt et al. (2017) for the science and the vignette to get started.
theseus v0.1.0: Provides analysis and visualization tools for the interpretation of microbial community composition data, especially those originating from amplicon sequencing. The vignette describes how to use the package.
ForecastComb v1.1: Provides geometric and regression-based forecast combination methods under a unified user interface for the packages ForecastCombinations and GeomComb. For details see Hsiao C, Wan SK (2014), Hansen BE (2007), [Elliott G, Gargano A, Timmermann A (2013)](doi:10.1016/j.jeconom.2013.04.017] and Clemen RT (1989).
hesim v0.1.0: Provides functions to develop and analyze health-economic simulation models, including random sampling functions for probabilistic sensitivity analyses Claxton et al. (2005), individual patient simulations Brennan et al. (2006), cost-effectiveness analysis Basu and Meltzer (2007), and Ioannidis and Garber (2011). The vignette provides an overview.
PUlasso v2.1: Implements an efficient algorithm for solving the Positive and Unlabeled problem in low- or high-dimensional settings with lasso or group lasso penalty. See Hyebin 7 Raskutti (2017) for details and the vignette for an introduction.
recurse v1.0.1: Computes revisitation metrics for trajectory data, such as the number of revisitations for each location as well as the time spent for that visit and the time since the previous visit. The vignette works through a case study of using the package to analyze revisitations in animal movement data.
samplesizeCMH v0.0.0: Provides functions to calculate the power and sample size for Cochran-Mantel-Haenszel tests, and for working with probability, odds, relative risk, and odds ratio values. There is an Introduction to the Cochran-Mantal-Haenszel Test, and vignettes on Power Calculations and Sample Size Calculations.
ZOIP v0.1: Implements the ZOIP (Zeros Ones Inflated Proportional), proportional data distribution inflated with zeros and/or ones. See Jørgensen and Barndorff-Nielsen (1991), Ferrari and Cribari-Neto (2004), and Rigby and Stasinopoulos (2005) for details, and the vignette for a summary.
OSTSC v0.0.1: Provides functions for oversampling imbalanced univariate time series classification data using integrated Enhanced Structure Preserving Oversampling (ESPO) and Adaptive Synthetic (ADASYN) methods. The vignette describes the method and provides examples.
swatches v0.5.0: Provides functions to read and inspect Adobe Color (ACO), Adobe Swatch Exchange (ASE), GIMP Palette (GPL), OpenOffice palette (SOC) files, and KDE Palette (colors) files.
BioCircos.png v0.2.2: Implements interactive Circos-like visualizations of genomic data, to map information such as genetic variants, genomic fusions, and aberrations to a circular genome. The vignette shows how to use the package.