Top 40 New Packages on R Views

April 2023: "Top 40" New CRAN Packages

Thu, 25 May 2023 00:00:00 +0000

One hundred fifty-six new packages made it to CRAN in April. Here are my “Top 40” selections in twelve categories: Computational Methods, Data, Ecology, Economics, Genomics, Machine Learning, Mathematics, Medicine, Science, Statistics, Utilities, and Visualization.

Computational Methods

clarabel v0.4.1: Implements Clarabel, a versatile interior point solver that solves linear programs, quadratic programs, second-order cone programs, and problems with exponential and power cone constraints. See the vignette.

condor v1.0.0: Provides functions to access the Condor high performance computing environment. Files are first uploaded to a submitter machine and the resulting job is then passed on to Condor. Look here for the code.

GPUmatrix v0.1.0: Extends R to use GPUs for matrix computations. See the vignette.

hydroMOPSO v0.1-3: Implements a state-of-the-art Multi-Objective Particle Swarm Optimiser (MOPSO), based on the algorithm developed by Lin et al. (2018) with improvements described by Marinao-Rivas & Zambrano-Bigiarini (2020) which can be used for global optimization of non-smooth and non-linear R functions and other models that need to be run from the system console, e.g. SWAT+.

Data

dataverifyr v0.1.5: Provides a thin wrapper around dplyr, data.table, arrow, and DBI to allow users to define rules which can be used to verify a given dataset. See README to get started.

neotoma2 v1.0.0: Provides functions to access and manipulate data in the Neotoma Paleoecology Database. See the vignette.

rpaleoclim v1.0.0: Implements an interface to PaleoClim, a set of free, high resolution paleoclimate surfaces covering the whole globe that includes data on surface temperature, precipitation and the standard bioclimatic variables commonly used in ecological modelling. See Brown et al. (2019) for background and the vignette.

zctaCrosswalk v2.0.0: Contains the US Census Bureau’s 2020 ZCTA to County Relationship File, as well as convenience functions to translate between States, Counties and ZIP Code Tabulation Areas (ZCTAs). See the Introduction and the vignettes Workflow with tidycensus, and Developer Notes.

Ecology

EWSmethods v1.1.2: Implements methods for forecasting tipping points at the community level that include rolling and expanding window approaches to assessing abundance based early warning signals, non-equilibrium resilience measures, and machine learning. See Dakos et al. (2012), Deb et al. (2022), and Drake and Griffen (2010) for background and the vignette for an introduction.

fqacalc v1.0.0: Provides functions for calculating Floristic Quality Assessment (FQA) metrics using regional FQA databases that have been approved or approved with reservations as ecological planning models by the U.S. Army Corps of Engineers (USACE). For information on FQA see Spyreas (2019). There is an Introduction.

Economics

clptheory v0.1.0: Provides functions to compute the uniform rate of profit, the vector of price of production and the vector of labor values, and also compute measures of deviation between relative prices of production and relative values. See Basu and Moraltis (2023) for background and README for an introduction.

Genomics

BREADR v1.0.1: Implements a method for estimating degrees of relatedness for extreme low-coverage genotype data and includes functions to quantify and visualize the level of confidence in the estimated degrees of relatedness. See Rohrlach et al. (2023) for package details and README for examples.

crosshap v1.2.2: Implements a local haplotyping visualization toolbox to capture major patterns of co-inheritance between clusters of linked variants, while connecting findings to phenotypic and demographic traits across individuals. See Marsh et al. (2022) for a detailed example and README for an introduction.

DAISIEprep v0.3.2: Extracts colonization and branching times of island species for analysis with the DAISIE package. There is a Tutorial and there are vignettes on Performance and Sensitivity.

Machine Learning

CCMMR v0.1: Implements the convex clustering through majorization-minimization algorithm described in Touw, Groenen, and Terada (2022) to minimize the convex clustering loss function. See README for examples.

rcccd v0.3.2: Provides functions to fit class cover catch digraph classification models. Methods are explained in Priebe et al. (2001), Priebe et al. (2003), and Manukyan and Ceyhan (2016). README contains some description.

TheOpenAir v0.1.0: Implements a wrapper using the OpenAI API as a back end to integrate ChatGPTinto diverse data-related tasks, such as data cleansing and automating analytics scripts. See README to get started.

Mathematics

cyclotomic v1.1.0: Implements algorithms from the GAP project to work with cyclotomic numbers: complex numbers that can be thought of as the rational numbers extended with the roots of unity. They have applications in number theory, algebraic geometry, algebraic number theory, coding theory, in the theory of graphs and combinatorics, and in the theory of modular functions and modular curves. See README for examples.

markovmix v0.1.1: Provides functions to fit a mixture of Markov chains of higher orders from multiple sequences along with various utility functions to derive transition patterns, transition probabilities per component and component priors. See README for examples.

Medicine

DiDforBigData v1.0: Provides a big-data-friendly and memory-efficient difference-in-differences estimator for staggered (and non-staggered) treatment contexts. See the Get Started Guide the vignettes Background, Examples, and Theory.

predictNNB v0.1.0: Provides tools to estimate when and where a model-guided treatment strategy may outperform a treat-all or treat-none approach using Monte Carlo simulation and evaluation of the Net Monetary Benefit. See Parsons et al. (2023) for details, the Introduction, and the vignettes on creating functions, summarising results, and detailed example.

predRupdate v0.1.0: Provides functions to evaluate the predictive performance of existing clinical prediction model given a new dataset. See Su et al. (2018), Debray et al. (2014), and Martin et al. (2018) for background and the vignettes Introduction and Technical Background.

SPARRAfairness v0.0.0.1: Provides functions to analyse the behavior and performance of the Scottish Patients At Risk of admission and Re-Admission risk score which estimates yearly risk of emergency hospital admission using electronic health records for most of the Scottish population. Analysis focuses on differential performance over demographically-defined groups. See the vignette.

Science

kronos v1.0.0: Implements a framework to analyse circadian or otherwise rhythmic data using the familiar R linear modelling syntax, while taking care of the trigonometry under the hood. Look here for examples.

mpmsim v1.0.0: Provides functions to to simulate matrix population models with particular characteristics based on aspects of life history such as mortality trajectories and fertility trajectories, and allows the exploration of sampling error due to small sample size. See the vignettes on robustness, sampling error & propagation, and PCA.

Statistics

BGFD v0.1: Implements the probability density function, cumulative distribution function, quantile function, random numbers, survival function, hazard rate function, and maximum likelihood estimates for the family of Bell-G and Complementary Bell-G distributions. See Fayomi et al. (2022), Alanzi et al.(2023), and Algarni (2022) for details.

D3mirt v1.0.3: Provides functions for identifying, estimating, and plotting descriptive multidimensional item response theory models, restricted to 3D and dichotomous or polytomous data that fit the two-parameter logistic model or the graded response model. See the vignette for an extensive introduction.

funStatTest v1.0.2: Implements two sample comparison procedures based on median-based statistical tests for functional data, described in Smida et al. (2022), Chakraborty and Chaudhuri (2015), Horvath et al. (2013, and Cuevas et al. (2004). See the vignette for examples.

lessSEM v1.4.16: Provides regularized structural equation modeling (regularized SEM) with non-smooth penalty functions (e.g., lasso) building on lavaan. There are nine vignettes including: lessSEM, The Structural Equation Model, and Mixed Penalties.

panelhetero v1.0.0: Provides tools for estimating the degree of heterogeneity across cross-sectional units in the panel data analysis using the methods developed by Okui and Yanagi (2019) and Okui and Yanagi (2020). See the vignette.

tdsa v1.0-1: Provides functions to perform time-dependent sensitivity analysis by calculating time-dependent state and parameter sensitivities for both continuous- and discrete-time deterministic models. See Ng et al. (in review) for background and the vignette to get started.

Utilities

crew.cluster v0.1.0: Extends the mirai-powered crew package with worker launcher plugins for traditional high-performance computing systems to enable statisticians and data scientists to asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. Look here to get started.

duke v0.0.1: Provides functions to generate visualizations with Duke’s official suite of colors in a color blind friendly way. There is an Overview and four additional vignettes including one on the theme_duke() function.

grateful v0.2.0: Facilitates the citation of R packages used in analysis projects by providing functions to scan projects for packages used and produces documents with citations in the preferred bibliography format. Functions may be used within rarkdownor quarto documents. See README for examples.

hightR v0.3.0: Implements the HIGHT block cipher encryption algorithm developed to provide confidentiality in low power consumption computing environments such Radio-Frequency Identification and Ubiquitous Sensor Network. Look here for more information.

myCRAN v1.0: Provides functions to plot the daily and cumulative number of downloads of R packages, obtaining daily and cumulative counts in one run. See the vignette.

woodendesc v0.1.0: Provides functions to simplify obtaining available packages, their version codes and dependencies from any R repository. Uses extensive caching for repeated queries. See READMEfor examples.

Visualization

fxl v1.6.3: Provides functions to prepare and design single case design figures that are typically prepared in spreadsheet software. See the vignette for theory and examples.

ggragged v0.1.0: Extends ggplot2 facets to panel layouts arranged in a grid with ragged edges with rows and columns of potentially varying lengths. These may be useful in representing nested or partially crossed relationships between faceting variables. See README for examples.

nndiagram v1.0.0: Generates LaTeX code for drawing well-formatted neural network diagrams with TikZ. Users define the number of neurons on each layer, neuron connections to keep or omit, layers considered to be oversized, and neurons to draw with lighter color. See README for instructions.

PlotTools v0.2.0: Provides functions to manipulate irregular polygons and annotate plots with legends for continuous variables and color spectra using the base graphics plotting tools. See README for an example.

January 2023: "Top 40" New CRAN Packages

Tue, 28 Feb 2023 00:00:00 +0000

One hundred sixty-five new packages made it to CRAN in January. Here are my “Top 40” selections in thirteen categories: Actuarial Statistics, Archaeology, Computational Methods, Ecology, Genomics, Mathematics, Medicine, Machine Learning, Science, Statistics, Time Series, Utilities, Visualization.

Actuarial Statistics

actuaRE v0.1.3: Provides functions to fit random effects models using either the hierarchical credibility model alone or combined with a glm or with a Tweedie generalized linear mixed model. See Campo & Antonio (2023) for background and the vignette for an example.

Archaeology

archeoViz v0.2.2: Implements a shiny application for the visualisation, interactive exploration, and web communication of archaeological excavation data. It includes interactive 3D and 2D visualisations, th generation of cross sections and maps, basic spatial analysis methods, and excavation timeline visualisations. There is a short vignette in English and French.

shoredate v1.0.0: Provides tools for shoreline dating Stone Age sites located on the Norwegian Skagerrak coast using methods presented in Roalkvam (2023). See the vignette.

Computational Methods

em v1.0.0: Implements a generic Expectation-Maximization (EM) algorithm within a maximum likelihood framework based on Dempster, Laird, and Rubin (1977). See the vignette for some theory and examples.

ROptimus v3.0.0: Implements a general-purpose optimisation engine that supports Monte Carlo optimisation with the Metropolis criterion and acceptance ratio replica exchange Monte Carlo optimization. See the foundational papers Metropolis et al. (1953), Hastings (1970), Kirkpatrick et al. (1983) and Černý (1985) for background.

Data

CopernicusMarine v0.0.6: Provides functions to import data on the ocean’s physical and biogeochemical state from EU Copernicus Marine Service Information. See README to get started.

itol.toolkit v1.1.0: Provides helper functions to access the Interactive Tree of Life including functions to edit and annotate trees interactively. See the vignette to get started.

rdracor v0.7.2: Provides an interface to the Drama Corpora Project (DraCor) API.

usdoj v1.0.0: Provides functions to fetch data from the U.S Department of Justice API such as press releases, blog entries, and speeches. Look here for notes on data structure.

Ecology

pastclim v1.2.3: Implements methods to extract and manipulate palaeoclimate reconstructions for ecological and anthropological analyses as described in Leonardi et al. (2022). See the Overview and the vignettes available datasets and custom dataset.

PERK v0.0.9.2: Implements a shiny web application to predict and visualize concentrations of pharmaceuticals in the aqueous environment. See Jagadeesan et al. (2022) and the vignette for a walk through.

Gemomics

autoGO v0.9.1: Implements a framework to enable automated, high quality gene ontology enrichment analysis visualizations and a wrapper for differential expression analysis using the DESeq2 package described in Love et al. (2014). See the vignette.

phylter v0.9.6: Provides functions to detect and remove outliers in phylogenomics datasets that build on the Distatis approach described in Abdi et al. (2005). See the vignette.

poolHelper v1.0.0: Provides functions to simulate pooled sequencing data under a variety of conditions, and also evaluate the average absolute difference between allele frequencies computed from genotypes and those computed from pooled data. See Carvalho et al. (2022) for the details and the vignette for an introduction to the package.

Machine Learning

BT v0.3: Implements adaptive boosting trees for Poisson distributed response variables, using log-link function. See Trufin & Denuit (2021), Denuit et al. (2019), and Hainaut & Trufin (2022) for background, and the vignette for an example.

chatgpt v0.1.5: Implements a ChatGPT coding assistant for the RStudio IDE.

evreg v1.0.1: Implements a evidential neural network for the regression model recently introduced in Denoeux (2023) in which prediction uncertainty is quantified by Gaussian random fuzzy numbers as introduced in Denoeux (2023). See the vignette.

FuzzyDBScan v0.0.3: Provides an interface to the Fuzzy DBScan clustering algorithm described in Ienco and Bordogna (2018). See README for an example.

Mathematics

rgudhi v0.1.0: Implements and interface to the C++ library, GHUDI for topological data analysis (TDA) and offers state-of-the-art data structures and algorithms to construct simplicial complexes and compute persistent homology.

Medicine

injurytools v1.0.1: Provides standardized routines and utilities to simplify the data analysis of sports injuries in order to identify and describe the magnitude of sports injury problems and determine the potential risk factors. See the vignettes estimate-epi-measures, prepare-injury-data. and visualize-injury-data.

simIDM v0.0.5: Provides functions to simulate oncology trials using an illness - death model. See Meller, Beyersmann and Rufibach (2019) for background and the vignettes Getting Started and Power and Type 1 Error Correlations.

Science

gravmagsubs v1.0.1: Provides functions to compute the gravitational and magnetic anomalies generated by 3-D vertical rectangular prisms at specific observation points using the method of Plouff (1976). See the vignette.

QurvE v1.0: Implements three methods for solving high-throughput analysis of growth curves and fluorescence data: linear regression, growth model fitting, and smooth spline fits. A shiny application provides access to all features without requiring any programming knowledge. There is a User Manual and there are vignettes on Flouresence Curve Evaluation and Growth Curve Evaluation.

Statistics

BCClong v1.0.0: Implements a Bayesian consensus clustering (BCC) model for multiple longitudinal features via a generalized linear mixed model that allows simultaneous clustering of mixed-type (e.g., continuous, discrete and categorical) longitudinal features. There are vignettes for continuous and mixed type data.

clarify v0.1.2: Provides functions to perform simulation-based inference as an alternative to the delta method for obtaining valid confidence intervals and p-values for regression post-estimation quantities such as average marginal effects and predictions at representative values. The methodology is described in King et al. (2000). See the vignette for examples.

emplikAUC v0.3: Provides functions to test hypotheses and construct confidence intervals for AUC (Area Under receiver operating characteristic curve) and pAUC (partial area under ROC curve) using the method described in Zhao, Ding & Zhou .

jtdm v0.1-0: Implements The Joint Trait Distribution Model in a Bayesian framework using conjugate priors to compute joint probabilities and multivariate confidence intervals. See the vignette.

mbreaks v1.0.0: Functions provide comprehensive treatments for estimating, inferring, testing and selecting linear regression models with structural breaks. See Bai & Perron (1998) for background and the vignette examples.

sdmTMB v0.3.0: Implements spatial and spatiotemporal predictive-process GLMMs (Generalized Linear Mixed Effect Models) using TMB, INLA, and the SPDE (Stochastic Partial Differential Equation) approximation to Gaussian random fields. See Anderson et al. (2022) for background and the vignette for examples.

snapKrig v0.0.1: Provides functions for geostatistical modeling and kriging with gridded data using spatially separable covariance Kronecker covariance functions. See Koch, Lele, Lewis (2020) for descriptions of the computational methods and the vignette for examples.

Time Series

fnets v0.1.2: Implements methods for network estimation and forecasting of high-dimensional time series exhibiting strong serial and cross-sectional correlations under a factor-adjusted vector autoregressive model. See Barigozzi et al. (2022) for the methodology and Owens et al. (2023) for details of the package.

MSinference v0.0.9: Provides functions to perform multiscale analysis of a nonparametric regression or nonparametric regressions with time series errors. See Khismatullina and Vogt (2020), Khismatullina and Vogt (2022) and Khismatullina and Vogt (2023) for the theory and examples, and the vignette to get started.

Utilities

datetimeoffset v 0.2.1: Provides support for a number of datetime string standards including ISO 8601 and pdfmark and also datetimes with UTC offsets and possibly heterogeneous time zones with up to nanosecond precision. See the package Introduction.

mathml v0.5: Provides functions to translate R expressions to MathML or MathJax so that they can be rendered in rmarkdown documents and shiny applications. See the vignette

options v0.0.1: Provides a simple mechanisms for defining and interpreting package options, including helper functions for interpreting environment variables, global options, defining default values and more. See the vignettes environment variables and options.

parquetize v0.5.3: Provides functions to convertcsv, RData, rds, RSQLite, json, ndjson, SAS, SPSS and other files to the Parquet columnar storage format. See the vignette.

scenes v0.1.0: Provides functions to facilitate switching between shiny UIs depending on the information that is to be passed to the request object. See the vignettes Creating new actions and Changing scenes.

shiny.fluent v0.3.0: Provides shiny components based on the Fluent UI JavaScript library. There are several small vignettes including a Tutorial on creating a full dashboard with shiny and Fluent.

Visualization

ggplate v0.0.1: Provides functions to create simple plots of biological culture plates as well as microplates which can plot both continuous and discrete values. See README for examples.

plotRCS v0.1.3: Extends ggplot2 to draw restricted cubic spline curves from a logistic regression model or a Cox proportional hazards regression model using the method described in Harrell (2015). Look here for examples.

viscomp v1.0.0: Implements several visualization tools for exploring the behavior of the components in a network meta-analysis of multi-component interventions including heat plots of the two-by-two component combinations, leave one component combination out scatter plot, violin plots for specific component combination effects, and density plots for components effects. See the vignette for examples.

November 2022: "Top 40" New CRAN Packages

Tue, 03 Jan 2023 00:00:00 +0000

One hundred sixty-seven new packages made it to CRAN in November: Here are my “Top 40” selections in fourteen categories: Climate Modeling: Computational Methods, Data, Ecology, Epidemiology, Genomics, Machine Learning, Mathematics, Networks, Pharma, Statistics, Time Series, Utilities, and Visualization.

Climate Modeling

gtfs2emis v0.1.0: Implements a bottom up model to estimate the emission levels of public transport systems based on General Transit Feed Specification data. Functions estimate several pollutants at high spatial and temporal resolutions. See Viera et al for background. There is a Getting Started Guide, and vignettes on Emission Factors and Preparing Data.

Computational Methods

jmatrix v1.1: A mainly instrumental package that allows other packages with cores written in C++ to read, write and manipulate matrices in a binary format to mitigate memory issues. See the vignette.

lazyNumbers v1.2.1: Implements lazy numbers, a new number type whose arithmetic is exact, contrary to ordinary floating-point arithmetic. The lazy numbers are implemented in C++ with the CGAL library. See README for examples.

miesmuschel v0.0.2: Provides optimization algorithms and functions that can be used to manually construct specialized optimization loops including the mixed integer evolution strategy as described in Li et al. (2013) and the multi-objective optimization algorithms NSGA-II described in Deb et al. (2002). See README for examples.

mlr3mbo v0.1.1: Implements a flexible approach to Bayesian optimization that includes both ready-to-use optimization algorithms as well as fundamental building blocks to construct custom algorithms. See Jones et al. (1998), Knowles (2006), and Ponweiser et al. (2008) for examples of ready to use optimization algorithms and the vignette for examples.

Data

googletraffic v0.1.1: Allows users to create geographically referenced traffic data from the Google Maps JavaScript API. Look here for information to get started.

IPEDS v0.1.1: Implements an interface to the US Post-Secondary Institution Statistics for 2020 which contains information on post-secondary institutions, students, faculty, demographics, financial aid, educational and recreational offerings, and completions. See the vignette.

npi v0.2.0: Provides access the US National Provider Identifier Registry API which contains administrative data linked to a specific individual or organizational healthcare providers. There is an Introduction and a vignette on Advanced Use.

rfars v0.2.0: Implements an interface to the US Fatality Analysis Reporting System. See the vignettes Crash Sequences and Rural Roads.

tidyDisasters v0.1.1: Provides a queryable data set that unites information from three complementary resources: Belgium’s Centre for Research on the Epidemiology of Disasters EMDAT, the US National Consortium for the Study of Terrorism GTD, and the US Federal Emergency Management Agency FEMA. There is a brief User Guide.

Ecology

et.nwfva v0.1.1: Implements a forest management tool developed by the Northwest German Forest Research Institute (NW-FVA) for the five main commercial tree species oak, beech, spruce, Douglas-fir and pine for northwestern Germany. See Albert et al (2022) for background and the vignettes: Beispiele, Nutzerhinweise zum Geleit, and Vergleich der Interpolationsmethoden.

mmodely v0.2.2: Provides functions to perform multivariate modeling of evolved traits, with special attention to understanding the interplay of the multi-factorial determinants of their origins in complex ecological settings. See Stephens (2007), Gruebner (2011), and Garamszegi (2011) for background, and the examples on primate vision and vocal communications.

webSDM v1.1-1: Implements the method of Poggiato et al. (2022) for working with tropic Species Distribution Models. There is an Introduction and there are vignettes on Composit variables, Differences between SDM and Trophic SDM.

Epidemiology

exDE v1.0.0: Provides tools to set up modular ordinary and delay differential equation models for mosquito-borne pathogens, focusing on malaria. See Wu et al. (2022) for a description on the methods implemented. There are ten vignettes including Basic Copmetition Aquatic Mosquito Model and SIP Human Model.

Genomics

idopNetwork v0.1.1: Implements a cartographic tool to chart spatial microbial interaction networks. See Kim et al. (2008) and Wang et al. (2011) for information on functional clustering, Chen et al. (2019) and Cao et al. (2022) for background on the model, and the vignette for examples.

tip v0.1.0: Provides functions to cluster data without specifying the number of clusters using the Table Invitation Prior (TIP) introduced by Harrison et al. (2022). There are vignettes on matrix clustering with CONSTANT and MNIW, Tensor clustering CONSTANT, iris NIW, and usarrests NIW.

scistreer v1.0.1: Enables fast maximum-likelihood phylogeny inference from noisy single-cell data using the ScisTree algorithm described in Wu (2019) making the method applicable to massive single-cell datasets (>10,000 cells). Look here for an example.

Machine Learning

tidyclust v0.1.1: Implements a common interface to specifying clustering models, in the same style as parsnip. Creates unified interface across different functions and computational engines. See README for examples.

VSOLassoBag v0.99.0: Implements an integrated Wrapped LASSO ensemble learning strategy to help select efficient, stable, and high confidential variables from omics-based data. Functions integrate and vote on variables generated from multiple LASSO models to determine the optimal candidates. See Luo et al. (2020) for details and the vignette for examples.

Mathematics

tensorFun v0.1.1: Provides basic functions to handle higher-order tensor data. See Kolda and Bader (2009) for background on tensor decompositions, Bau and Ng (2021) for information on missing values, and the vignette for a short introduction.

TransTGGM V1.0.0: Implements a transfer learning framework for tensor Gaussian graphical models, which takes full advantage of informative auxiliary domains even when non-informative auxiliary domains are present. See Ren, Zhen, and Wang for background and the vignette.

Networks

nett 1.0.0: Provides multiple methods for fitting, model selection and goodness-of-fit testing in degree-corrected stochastic blocks models. Implements the methods in Amini et al.(2013), Bickel and Sarkar (2015), Lei (2016), Wang and Bickel (2017) and more. There are vignettes Community Detection, Visualization, Explore Comm, and dcsbm testing.

Pharma

DrugSim2DR v0.1.0: Implements a tool to predict drug functional similarity for drug repurposing. See the vignette.

parttime v0.1.0: Provides classes for embedding partial missingness as a central part of datetime classes allowing for more ergonomic use of datetimes for challenging datetime computation, including calculations of overlapping date ranges, imputations, and more. See README for examples.

Statistics

GAGAs v0.5.1: Implements the Global Adaptive Generative Adjustment Algorithm for generalized liner models used for improving the computational efficiency in the high-dimensional data analysis. See Wang et al. (2022) for the theory.

kfino v1.0.0: Implements method for detecting outliers with a Kalman filter on impulsed noised outliers and prediction on cleaned data. See Cloez et al. (2022) for the details and the vignettes on outlier detection and outlier detection with parallelization.

pwrss v0.2.0: Implements power and sample size calculations for a number of one, two and three sample tests. See the vignette for examples.

spatstat.models v3.0-2: A member of the spatstat family of packages, it provides multiple functions for exploratory data analysis and nonparametric analysis of spatial data, mainly spatial point patterns. See spatstat.org for documentation.

vMF v0.0.1: Provides functions for fast sampling from von Mises-Fisher distribution using the method proposed in Wood (1994). See the vignette.

Time Series

ardl.nardl v1.2.2: Implements linear and nonlinear autoregressive distributed lag (ARDL & NARDL) models and the corresponding error correction models and includes a test for long-run and short-run asymmetry and the Pesaran, Shin & Smith (2001) bounds test for level relationships.

Utilities

cookies v0.2.0: Provides tools for working with cookies in shiny apps, in part by wrapping the js-cookie JavaScript library. See README for an example.

formatdown v0.1.1: Provides a small set of tools for formatting tasks when creating documents in rmarkdown or quarto. See the vignette.

hellorust v1.0.0: Implements tools to use Rust code in R without hacks or frameworks. Includes basic examples of importing cargo dependencies, spawning threads and passing numbers or strings from Rust to R. Look here and here for for documentation.

prismjs v1.1.0: Implements a server-side rendering in R using Prism, a lightweight, extensible syntax highlighter, built with modern web standards in mind such that no JavaScript library is required in the resulting HTML documents. Look here for examples.

rjtools v1.0.9: Provides tools to create an R Journal rmarkdown template article, that will generate HTML and PDF versions of your paper. There are vignettes rjtools-template, Check, Create article, and Format details.

Visualization

funkyheatmap v0.1.0: Provides functions for generating heatmap-like visualizations for benchmark data frames, which can be fine-tuned with annotations for columns and rows. See Saelens et al. (2019) for background and the vignettes Recreating the dynbenchmark figures and Demo with mtcars for examples.

ggbrain v0.8.0: Implements a ggplot2-consistent approach to generating 2D displays of volumetric brain imaging data from multiple NIfTI images. There is an Introduction and there are vignettes on Aesthetic refinement and Annotations and labels.

ggpcp v0.2.0: Provides a Grammar of Graphics implementation of parallel coordinate plots that incorporates categorical variables into the plots in a principled manner. Look here for examples.

ggredist v0.0.2: Provides ggplot2 extensions for political map making based on simple features and includes palettes and scales for red to blue color mapping and for discrete maps. See README for an example.

ggsector v1.6.6: Implements functions that use grid and ggplot2 to plot sectors, draw complex heat maps and interact with Seurat to plot gene expression percentages. See the vignette.

sherlock v0.5.1: Provides graphical displays and statistical tools for structured problem solving and diagnosis with functions that are especially useful for applying the process of elimination as a problem diagnosis technique. See Hartsborne (2020) for background and README for examples.

October 2022: "Top 40" New CRAN Packages

Mon, 28 Nov 2022 00:00:00 +0000

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.

May 2022: "Top 40" New CRAN Packages

Tue, 28 Jun 2022 00:00:00 +0000

One hundred seventy-nine new packages made it to CRAN in May. Here are my “Top 40” picks in twelve categories: Computational Methods, Data, Ecology, Epidemiology, Finance, Machine Learning, Networks, Science, Statistics, Time Series, Utilities, and Visualization.

Computational Methods

graDiEnt v1.0.1: Implements the derivative-free, optim-style Stochastic Quasi-Gradient Differential Evolution optimization algorithm published in Sala, Baldanzini, and Pierini (2018) that uses population members to build stochastic gradient estimates. See README for an example.

rxode2 V2.0.7: Provides facilities for running simulations from ordinary differential equation models, such as pharmacometrics and other compartmental models, but requires both C and Fortran compilers. See the vignette for an example.

ScaleSpikeSlab v1.0: Provides a scalable Gibbs sampling implementation for high dimensional Bayesian regression with the continuous spike-and-slab prior described in Biswas, Mackey & Meng (2022). See README for an example.

Data

bluebike v0.0.3: Provides functions that facilitate importing and working with the Boston Blue Bike Data Set including functions to compute trip distances and map the locations of stations within a given radius. See the vignette for examples.

eurodata v1.4.2: Implements an interface to Eurostat’s Bulk Download Facility with fast data.table based import of data, labels, and metadata along with data search and data description and comparison functions. See README to get started.

gbifdh v0.1.2: Implements a high performance interface to the Global Biodiversity Information Facility that supports large-scale analyses using SQL or dplyr operations on complete tables. See the vignette for examples.

getwiki v0.9.0: Implements a simple wrapper for Wikipedia data to retrieve text in a tidy format that can be used for Natural Language Processing. See the vignette.

Ecology

FIESTA v3.4.1: Implements an estimation tool for analysts that work with sample-based inventory data from the U.S. Department of Agriculture, Forest Service, Forest Inventory and Analysis Program. There are nine vignettes including manuals for Module Estimates and Population Data, and Small Area Estimators and Spatial Tools.

soiltestcorr v2.1.2: Provides functions designed to assist users on the correlation analysis of crop yield and soil test values including functions to estimate crop response patterns to soil nutrient availability and critical soil test values using various approaches. See Correndo et al. (2017), Cate & Nelson (1971), Anderson & Nelson (1975), Bullock & Bullock (1994) and Melsted & Peck (1977) for background. There are seven vignettes including an Introduction and Quadratic-plateau response.

sspm v0.9.1: Implement a gam-based spatial surplus production model, aimed at modeling northern shrimp population in Atlantic Canada but potentially to any stock in any location. There is a vignette on Package and Workflow design and another that provides an example with simulated data.

Epidemiology

EpiInvert v0.1.1: Inverts a renewal equation to estimate time-varying reproduction numbers and restored incidence curves with festive days and weekly biases corrected as described in Alvarez et al. (2021) and Alvarez et al. (2022). See README for examples.

linelist v0.0.1: Provides tools to help storing and handling case line list data by adding a tagging system to classical data.frame objects to identify key epidemiological data. See the vignette for examples.

Finance

markets v1.0.3: Provides functions to estimate markets in equilibrium and disequilibrium based on full information maximum likelihood techniques given in Maddala and Nelson (1974) and implemented using the analytic derivative expressions calculated in Karapanagiotis (2020). There is an Overview providing theory and code and vignettes on Model initializion details, Market-clearing assessment, and Use cases.

portvine v1.01: Provides portfolio level risk estimates including value at Risk and Expected Shortfall following the approach described in Sommer (2022) by modeling each asset with an ARMA-GARCH model and then modeling their cross dependency via a Vine Copula in a rolling window fashion. See the vignette to get started.

usincometaxes v0.4.0: Implements a wrapper to the NBER’s TAXSIM 35 tax simulator. TAXSIM 35 to calculate federal and state income taxes. There are vignettes on Uploading Data, Input Columns, Output Columns, and Calculating Taxes.

Genomics

MixviR v3.3.5: Implements tools for exploring DNA and amino acid variation and inferring the presence of target lineages from microbial high-throughput genomic DNA samples that potentially contain mixtures of variants/lineages. MixviR was originally created to help analyze environmental SARS-CoV-2/Covid-19 samples from environmental sources such as waste water or dust, but can be applied to any microbial group. See DePristo et al. (2011) and Danecek et al. (2021) for background, and the vignette for examples.

simer v0.9.0.0: Implements a data simulator including genotype, phenotype, pedigree, selection and reproduction for animals and plants and provides data for genomic gelection, genome-wide association, and breeding studies. See Kao and Zeng (2002) and Ripley (1987) for background. Look here for extensive documentation.

Machine Learning

fastTopics v0.6-135: Implements fast, scalable optimization algorithms for fitting topic models and non-negative matrix factorization for count data. The methods exploit the special relationship between the multinomial topic model (probabilistic latent semantic indexing) and Poisson non-negative matrix factorization. See the vignettes: Relationship between NMF and topic modeling and Topic mideling vs. clustering.

metrica v1.2.3: Provides functions to evaluate prediction performance of point-forecast models accounting for different aspects of the agreement between predicted and observed values including error metrics, model efficiencies, indices of agreement, goodness of fit, concordance correlation, and error decomposition, and plots the visualized agreement. See the vignettes on Available Metrics and Model Assessment.

SparseVFC v0.1.0: Implements The sparse vector field consensus algorithm described in Ma et al. (2013) for robust vector field learning. See the vignette.

Networks

Rwclust v0.0.1: Implements the random walk clustering algorithm for weighted graphs as found in Harel and Koren (2001). See the vignette.

Science

EvoPhylo v0.1: Provides functions to support automated morphological character partitioning for phylogenetic analyses, and analyses of macroevolutionary parameter outputs. See Simões and Pierce (2021) for background. There is a vignette on Theoretical Background, and there are others on Character Partitioning, FBD parameters, and Evolutionary Rates.

sits v1.0.0: Provides an end-to-end toolkit for land use and land cover classification using big Earth observation data, based on machine learning methods applied to satellite image data cubes, as described in Simoes et al (2021). Builds regular data cubes from collections in AWS, Microsoft Planetary Computer, Brazil Data Cube, and Digital Earth Africa using the STAC protocol and the gdalcubes package. An eBook provides extensive documentation.

Statistics

biosensors.usc v1.0: Provides a framework for using distributional representations of biosensor data such as ECG, medical imaging or fMRI data in various statistical modeling tasks: regression models, hypothesis testing, cluster analysis, visualization, and descriptive analysis. See Matabuena et al. (2021) for background and the vignette for an introduction.

CopSens v0.1.0: Implements the copula-based sensitivity analysis method for observational causal inference discussed in Zheng et al. (2022). See README for examples.

GeoModels v1.0.1: Provides functions to analyze Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data and simulate random fields using likelihood methods. See Bevilacqua and Gaetan (2015) and Vallejos et al. (2020) for background, and look here for examples.

nlmixr2 v2.0.6: Fit and compare nonlinear mixed-effects models with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics using differential equations solved by compiled C code provided in the rxode2 package. See Almquist et al. (2015) and Wang et al. (2015) for background, and the vignette for examples.

stdmod v0..1.7.1: Provides functions for computing a standardized moderation effect in moderated regression and forming its confidence interval by nonparametric bootstrapping as proposed in Cheung et al. (2002). There are six vignettes including a Quick Start Guide and a vignette on Standardized Moderation.

Time Series

forceR v1.0.15: Initially written and optimized to deal with insect bite force measurements, the functions in this package can be used to clean and analyze any time series. They provide a workflow to load, plot and crop data, correct amplifier and baseline drifts, identify individual peak shapes, rescale (normalize) peak curves, and find best polynomial fits to describe and analyze force curve shapes. See the vignette for examples.

ZINARp v0.1.0: Provides functions for simulation, exploratory data analysis and Bayesian analysis of p-order integer-valued autoregressive, INAR(p), and zero-inflated p-order integer-valued autoregressive, ZINAR(p), processes, as described in Garay et al. (2020).

Utilities

async v0.2.1: Provides functions for writing sequential-looking code that pauses and resumes similarly to generator and async constructs from Python or JavaScript. Objects produced are compatible with the iterators and promises packages. See the vignette for an example.

chronicler v0.2.0: Provides tools to decorate a function so that it returns its along with a log detailing when the function was run, what were its inputs, what were the errors (if the function failed to run) and other useful information. See the vignettes: A non-mathematician’s introduction to monads, The Maybe monad, and A real world example.

jpgrid v0.2.0: Provides functions to generate Japanese grid square codes from longitude, latitude and geometries. See README for examples.

partialised v0.1.0: Provides a partialised class that extends the partialising function of purrr by making it easier to change the arguments. This is similar to the function-like object in `Julia’. See README for an example.

shinybrowser v1.0.0: Provides information about shiny app users including browser name and version, device type (mobile or desktop), operating system and version, and browser dimensions. See README for more information.

webshot2 v0.1.0: Takes screenshots of web pages, including Shiny applications and R Markdown documents using a headless Chrome or Chromium browser as the browser back-end. See README for examples.

Visualization

accrualPlotv1.0.1: Implements accrual plots for clinical trials. See the vignette.

ggbraid v0.2.2: Implements stat_braid(), that extends the functionality of geom_ribbon() to correctly fill the area between two alternating lines (or steps) with two different colors, and geom_braid(). Three vignettes, US Supreme Court, NBA Finals Game, and Average Daily Temperatures provide examples.

ggisotonic v0.1.2: Provides stat_isotonic() to add weighted univariate isotonic regression curves. See README for an example.

UpSetVP v1.0.0: Uses the ideas of variance partitioning and hierarchical partitioning as described in Lai et al. (2022) to visualize the unique, common, or individual contribution of each predictor (or matrix of predictors) towards explaining variation. Look here for examples.

April: "Top 40" New CRAN Packages

Mon, 30 May 2022 00:00:00 +0000

Computational Methods

hmer v1.0.1: Provides objects and functions for Bayes Linear emulation and history matching, including functions for automated training of emulators, diagnostic functions to ensure suitability, and a variety of methods for generating waves of points. There is a vignette Demo of the package, an Emulation and History matching Handbook, and vignettes on Examples, and Stochastic Emulation.

rminqa v0.1.1: Implements a wrapper for the C++ function bobyqa to perform derivative-free optimization algorithms in R.

rolog v0.9.4: Embeds SWI-Prolog, so that R can send deterministic and non-deterministic queries to Prolog. See README for examples.

torchopt v0..1.1: Implements optimizers for the torch deep learning that are not among the optimizers offered in torch. These include:adabelief by Zhuang et al (2020), adabound by Luo et al.(2019), adamw by Loshchilov & Hutter (2019), madgrad by Defazio and Jelassi (2021), nadam by Dozat (2019), qhadam by Ma and Yarats (2019), radam by Liu et al. (2019), swats by Shekar and Sochee (2018), and yogi by Zaheer et al.(2019)

villager v1.1.1: Provides a set of base classes with core functionality to allow users to create and run Agent Based Models. There are vignettes on Extending Agents and Extending Resources.

Data

baseballr v1.2.0: Provides numerous utilities for acquiring and analyzing baseball data from online sources such as Baseball Reference, FanGraphs, and the MLB Stats API. See the Getting Started Guide and the vignettes NCAA Scraping and Plotting Statcast data.

toRvik v1.0.2: Provides a suite of functions to quickly scrape and tidy advanced metrics, detailed player and game statistics, team and coach histories, and more from Barttorvik. See the vignette.

ustfd v0.1.0: Lets users make requests from the US Treasury Fiscal Data API endpoints. See README for an example.

valet v0.9.0: Implements a client for the recently updated Bank of Canada Valet API. See README for examples.

Ecology

OBIC v2.0.1: Provides functions to calculate the Open Boden Index method used in the Netherlands to evaluate the quality of soils of agricultural fields and evaluate the sustainability of the current agricultural practices. There are vignettes on the Open soil index, Score aggregation, and Workability.

timbeR v2.0.1: Provides functions to estimate wood volumes, for example, number of logs, diameters along the stem and heights at which certain diameters occur. See Weiskittel, A. (2021) for background and the vignette for an introduction.

Finance

AssetAllocation v1.0.0: Provides functions to implement customizable asset allocation strategies and automatically download data from Yahoo Finance. See the vignette.

multilateral v1.0.0: Implements multilateral price index calculations focused on time product dummy regression and GEKS variations, and allows for extension of the methods through automatic window splicing. See Krsinich (2016) for information on window splicing and the vignette for examples.

Machine Learning

clusterHD Provides tools for clustering high dimensional data as described in Raymaekers and Zamar (2020) and Raymaekers and Zamar (2020).

tglkmeans v0.3.4: Efficiently implements the Kmeans algorithm. See Arthur and Vassilvitskii (2007) and Ostrovsky et al. (2013) for background and the vignette to get started.

Mathematics

hilbert v0.2.1: Provides utilities for encoding and decoding coordinates to and from Hilbert curves based on the iterative encoding implementation described in Chen et al. (2006). See the vignette to get started.

gellipsoid v0.7.2: provides functions to represent degenerate and unbounded generalized geometric ellipsoids together with methods for linear and duality transformations, and for plotting. The ideas are described in Friendly, Monette & Fox (2013). See README for examples.

Medicine

crossnma v1.0.1: Provides functions for cross-design and cross-format Network Meta-Analysis Regression as described in Hamza et al. 2022. See the vignette.

exact.n v1.0.0: Allows the user to determine minimum sample sizes that achieve target size and power at a specified alternative. See Lloyd & Ripamonti (2021) for the theory and README for examples.

stoppingrules v0.1.1: Provides functions for creating, displaying, and evaluating stopping rules for safety monitoring in clinical studies including stopping rule methods described in Goldman (1987), Geller et al. (2003), Ivanova, Qaqish, & Schell (2005), and Kulldorff et al. (2011). See README for an example.

Networks

incidentally v0.9.0: Provides functions to generate random incidence matrices and bipartite graphs under different constraints or using different generative models. See the vignette.

networkscaleup v0.1-1: Provides a variety of network scale-up models to analyze aggregated relational data, including models from Laga et al. (2021) Zheng et al. (2006), Killworth et al. (1998), and Killworth et al. (1998). See the vignette.

pald v0.0.1: Implements the partitioned local depths algorithm described in Berenhaut, Moore, & Melvin (2022) which may be helpful in determining both local and global structure in data. Look here to get started.

Statistics

bmstdr v0.1.4: Provides functions to fit, validate, and compares a number of Bayesian models for spatial and space-time point referenced and areal unit data. See the vignette for theory and examples.

cubble v0.1.0: Implements a spatiotemperal data object in a relational data structure to separate the recording of time variant and invariant variables. See the vignettes: aggregation, design, cubble, import, and matching.

incubate v1.1.8: Fits parametric models to time-to-event data that show an initial incubation period, i.e., a variable phase where the hazard is zero. The delayed Weibull distribution serves as the foundational data model. Look here for an example.

pspatreg v1.0.2: Provides functions to estimate and analyze spatial and spatio-temporal semiparametric models including spatial or spatio-temporal non-parametric trends, parametric and non-parametric covariates with a possible spatial lag for the dependent variable, and temporal correlation in the noise. See Basile et al. (2014), Rodriguez-Alvarez et al. (2015), and especially Minguez et al. (2020) for background. There is an Introduction, and vignettes on Cross-sectional data and Spatial panel data.

sfdep v0.1.0: Provides and interface to spdep to integrate sf objects and the tidyverse. There are vignettes on The Basics, Conditional Permutations, and spdep and pysal.

smile v1.0.4.1: Provides functions to estimate, predict, and interpolate areal data. For estimation and prediction, areal data are assumed to be an average of an underlying continuous spatial process as in Moraga et al. (2017), Johnson et al. (2020), and Wilson and Wakefield (2020). There are vignettes on Fitting Models, Areal Interpolation, Converting to spm, Spatial Covariance, and Method.

SpatialPOP v0.1.0: Provides functions to generate a spatial population from a spatially varying regression model under the assumption that observations are collected from a uniform two-dimensional grid with unit distance between any two neighboring points. See Chao et al. (2018) for method details and the vignette for an example.

Time Series

lite v1.0.0: Performs likelihood-based inference for stationary time series extremes following the approach of Fawcett and Walshaw (2012). Marginal extreme value inferences are adjusted for cluster dependence using the methodology of Chandler and Bate (2007). See the vignette.

spooky v1.1.0: Uses the Discrete Fast Fourier Transformation to extrapolate time features beyond their boundaries. Look here for examples and references.

Utilities

chromote v0.1.0: Implements the Chrome DevTools Protocol for controlling a headless Chrome web browser. Look here for examples.

chkptstanr v0.1.1: Implements a framework to checkpoint Bayesian models fit with Stan and brms. The MCMC sampler can be stopped and then restarted where it left off. There is a vignette for brms and another for Stan.

ivs v0.1.0: Implements a new interval vector class for generic interval manipulations including locating various kinds of relationships between two interval vectors, merging overlaps within a single interval vector, splitting an interval vector on its overlapping endpoints, and applying set theoretical operations on interval vectors. The package was inspired by Allen (1983). See the vignette for an introduction.

listr v0.0.2: Pools for common operations on lists such as selecting and merging data stored in lists which can be used with pipes. See the vignette.

shinyGizmo v0.1: Provides UI components and input widgets for Shiny applications to apply non-standard operations and address performance issues. See README for examples.

shinytest2 v0.1.0: Provides automated unit testing of Shiny applications through a headless Chromium browser. There is a Getting Started Guide and seven additional vignettes including Testing in depth, Robust testing, and Monkey testing.

thaipdf v0.1.2: Provides R Markdown templates and aLaTeX preamble to create PDFs from R Markdown documents in the Thai language. See the vignette for examples.

Visualization

ggtrendline v1.0.3: Enhances ggplot2 with tools to add a trendline with a confidence interval for linear or nonlinear regression models and show the equation. See Ritz and Streibig (2008) and Greenwell and Schubert Kabban (2014) for background and look here for examples.

May 2020: "Top 40" New CRAN Packages

Wed, 24 Jun 2020 00:00:00 +0000

One hundred eighty-four new packages stuck to CRAN in May. The following are my “Top 40” picks in eleven categories: Data, Finance, Genomics, Marketing, Machine Learning, Medicine, Science, Statistics, Time Series, Utilities, and Visualization.

Data

covid19nytimes v0.1.3: Provides accesses the NY Times Covid-19 county-level data for the US that is also available here. There is a vignette.

geodata v0.1.0: Contains small spatial datasets used to teach basic spatial analysis concepts. Datasets are based on of the GeoDa software workbook and data site.

GermaParl v1.4.2: Provides access to the GermaParl corpus of parliamentary debates of the German Bundestag maintained by the PolMine Project. The vignette introduces the corpus and package.

nhlapi v0.1.2: Retrieves and processes the data exposed by the open NHL API, including information on players, teams, games, tournaments, drafts, standings, schedules and other endpoints. There are vignettes on a Low-level API, Retrieving Player Data, and Retireving Team Data.

polAr v0.1.3: Implements a toolbox for the analysis of political and electoral data from Argentina. There are vignettes on Computing, Data Access, and Displaying Results.

rKolada v0.1.3: Provides methods for downloading and processing data and metadata from Kolada, the official Swedish regions and municipalities database. There is an Introduction and a Quick Start Guide.

Finance

strand v0.1.3: Provides a framework for performing discrete (share-level) simulations of investment strategies. Simulated portfolios optimize exposure to an input signal subject to constraints such as position size and factor exposure. The vignette on Backtesting with strand is nicely done.

TwitterAutomatedTrading v0.1.0: Provides access to the MetaTrader 5 platform that enables users to carry out automated trading using sentiment indexes computed from twitter and/or stockwits. See Godeiro (2018) for background, and the vignette for how to use the package.

Genomics

immunarch v0.6.5: Provides a framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires that includes data loading, analysis and visualization for bulk and single-cell AIRR (Adaptive Immune Receptor Repertoire) data. There is an Introduction and a vignette on Working with Data.

SubtypeDrug v0.1.0: Implements a tool to prioritize cancer subtype-specific drugs by integrating genetic perturbation, drug action, biological pathway, and cancer subtype. See Han et al. (2019) for background and the vignette for details on the package.

TransPhylo v1.4.4: Provides functions to reconstruct infectious disease transmission using genomic data. See Didelot et. al (2014) and Didelot et. al (2017) for background. See the Introduction and the vignettes: Inference of transmission tree from a dated phylogeny, Simultaneous Inference of Multiple Transmission Trees and Simulation of outbreak data.

Marketing

CLVTools v0.5.0: Implements various probabilistic latent customer attrition models for non-contractual settings (e.g., retail business) with and without time-invariant and time-varying covariates. See Schmittlein et al. (1987) and Fader et al. (2005) for background and the vignette to get started.

grizbayr v1.2.2: Provides functions to implement Bayesian A / B and Bandit marketing tests. See Stucchio (2015) for background and the vignette to get started.

Machine Learning

applicable v0.0.1.1: Provides functions that measure the amount of extrapolation new samples can have from the training set which are based on the concept of applicability domains. See Netzeva et al (2005). There are vignettes for binary and continuous data.

piRF v0.1.0: Implements multiple state-of-the-art prediction interval methodologies for random forests including quantile regression intervals, out-of-bag intervals, bag-of-observations intervals, one-step boosted random forest intervals, bias-corrected intervals, high-density intervals, and split-conformal intervals. Look here for an example.

rules v0.0.2: Provides bindings that allow prediction rule ensembles, C5.0 rules, and Cubist to be used with the parsnip package.

Medicine

AdhereRViz v0.1.0: Implements a Shiny based GUI to the AdhereR package to allow users to access different data sources, explore patterns of medication, and compute various measures of adherence. See the vignette for details.

MrSGUIDE v0.1.1: provides functions to facilitate subgroup analysis for single and multiple responses in both randomized trials and observational studies based on the GUIDE algorithm. See the Vignette.

Science

ldsr v0.0.2: Provides functions to reconstruct streamflow and climate information using linear dynamical systems. See Nguyen and Galelli (2018) for background and the vignette for examples.

rties v5.0.0: Provides tools for investigating temporal processes in bivariate (e.g., dyadic) systems. The theoretical background can be found in Butler (2011) and Butler & Barnard (2019). There is an Overview, and vignettes on Intertia Coordination, Data Preparation, and System Varibles.

Statistics

Compack v0.1.0: Implements regression methodologies with compositional covariates, including sparse log-contrast regression with compositional covariates proposed by Lin et al. (2014), and sparse log-contrast regression with functional compositional predictors proposed by Sun et al. (2020). There is a vignette.

ghypernet v1.0.0: Provides functions for model fitting and selection of generalized hypergeometric ensembles of random graphs (gHypEG). The package is based on the research by Casiraghi and collaborators. For example, see Casiraghi et al. (2016), Casiraghi (2017) and Casiraghi and Nanumyan (2018). There is an Introduction, a short Tutorial, and a vignette on Finding Significant Links.

motifcluster v0.1.0: Provides tools for spectral clustering of weighted directed networks using motif adjacency matrices. These methods, which perform well on large and sparse networks, are based on the methodology described in Underwood et al. (2020). See the vignette.

regmedint v0.1.0: Implements the regression-based causal mediation analysis with a treatment-mediator interaction term, as originally implemented in the SAS macro described in Valeri and VanderWeele (2013) and Valeri and VanderWeele (2015). There is an Introduction, and vignettes on Implementing Formulas, Bootstrapping, and Multiple Imputation.

Time Series

DeCAFS v3.1.5: Provides functions to detect abrupt changes in time series with local fluctuations as a random walk process and autocorrelated noise as an AR(1) process. See Romano et al. (2020) for the theory.

Rdrw v1.0.1: Provides functions to fit and simulate a univariate or multivariate damped random walk process (also known as an Ornstein-Uhlenbeck process or a continuous-time autoregressive model of the first order) which is suitable for analyzing time series data with irregularly-spaced observation times and heteroscedastic measurement errors. See Hu and Tak (2020) for background.

statespacer v0.1.0: Provides functions for estimating time series using the state space method. For background see JSS Vol 41. The package has an Introduction, a Dictionary for the model object and vignettes on Fitting and ARIMA Model, an Example and on Specifying a new model component.

Utilities

almanac v0.1.1: Provides tools for implementing recurrence rules, i.e. functions for defining recurring events. There is an Introduction and vignettes on Adjusting and Shifting Dates, iCalendar Specification, and Quarterly Rules.

gdiff v0.2-1: Provides functions for performing graphical difference testing. Look here for more information.

i2dash v0.2.1: Provides functions for creating web-based dashboards. See the vignette.

pkgndep v1.0.0: Provides functions to check and visualize the “heaviness” of R packages. See the vignette.

presser v1.0.0: Implements the httpbin.org web service and functions to test web clients without using the internet.

stringfish v0.12.1: Implements a framework for performing string and sequence operations using the alt-rep system to speed up the computation of common string operations. See the vignette.

worcs Implements the Workflow for Open Reproducible Code in Science, WORCS. There is an Introduction, and vignettes on citing, git_cloud, and setup.

Visualization

ggpacman v0.1.0: Reproduces the game Pac-Man using ggplot2 and gganimate. Look here for more information.

iNZightTS v1.5.2: Provides tools for working with time series data, including functions for drawing, decomposing, and forecasting, comparing multiple series, and fitting both additive and multiplicative models. Look here for more information.

prismadiagramR v1.0.0: Provides functions to create PRISMA diagrams used to track the identification, screening, eligibility, and inclusion of studies in a systematic review. See the vignette.

sketcher v0.1.3: Implements image processing effects that convert a photo into a line drawing image. See Tsuda (2020) for background and look here for examples.

upsetjs v1.3.1: Provides an htmlwidget wrapper for the JavaScript UpSet.js library. There is an Introduction, and vignettes on Coloring, Combination Modes, and Venn and Euler Diagrams.

xaringanthemer v0.3.0: Provides functions to create custom CSS themes. There is and Overview, and vignettes on ggplot2 Themes, and Template Variables.

April 2020: "Top 40" New CRAN Packages

Thu, 28 May 2020 00:00:00 +0000

One hundred forty-eight new packages made it to CRAN in April. Here are my “Top 40” picks in nine categories: Computational Methods, Data, Machine Learning, Medicine, Science, Statistics, Time Series, Utilities, and Visualization.

Computational Methods

JuliaConnectoR v0.6.0: Allows users to import Julia packages and functions in such a way that they can be called directly as as R functions.

RcppBigIntAlgos: v0.2.2: Implements the multiple polynomial quadratic sieve (MPQS) algorithm for factoring large integers and a vectorized factoring function that returns the complete factorization of an integer. See Pomerance (1984) and Silverman (1987) for background and this Microsoft post for an explanation.

smoothedLasso v1.0: Implements the smoothed LASSO regression using the method of Nesterov (2005).

Data

daqape v0.3.0: Provides a variety of methods to identify data quality issues in process-oriented data. There is an Introduction.

DSOpal v1.1.0: is the DataShield implementation of Opal, the data integration application for biobanks by OBiBa, open source software for epidemiology.

epuR v0.1: Provides functions to collect data from the the economic policy uncertainty website. See the vignette.

hystReet v0.0.1: Implements an API wrapper for the Hystreet project which provides pedestrian counts for various cities in Germany. See the vignette to get started.

rGEDI v0.1.7: Provides a set of tools for downloading, reading, visualizing and processing GEDI Level1B, Level2A and Level2B data. see the vignette to get started.

Machine Learning

catsim v0.2.1: Computes structural similarity metrics for binary and categorical 2D and 3D images including Cohen’s kappa, Rand index, adjusted Rand index, Jaccard index, Dice index, normalized mutual information, or adjusted mutual information. See Thompson & Maitra (2020) for background and the vignette for an introduction.

klic v1.0.2: Implements a kernel learning integrative clustering algorithm which allows combining multiple kernels, each representing a different measure of the similarity between a set of observations. There is an Introduction.

MIDASwrappeR V0.5.1: Provides a wrapper for the C++ implementation of the MIDAS algorithm described in Bhatia et al. (2020) for graph like data. See the Introduction.

VUROCS v1.0: Calculates the volume under the ROC surface and its (co)variance for ordered multi-class ROC analysis as well as certain bivariate ordinal measures of association.

WeightSVM v1.7-4: Provides functions for subject/instance weighted support vector machines (SVM). It uses a modified version of libsvm and is compatible with e1071 package. Look here for some background.

Medicine

covid19.analytics v1.1: Provides functions to load and analyze COVID-19 data from the Johns Hopkins University CSSE data repository. It includes functions to visualize cases for specific geographical locations, generate interactive visualizations and produce a SIR model. See the vignette for an introduction.

covid19france Provides functions to import, clean and update French COVID-19 data from opencovid19-fr.

interactionR v0.1.1: Produces a publication-ready table that includes all effect estimates necessary for full reporting effect modification and interaction analysis as recommended by Knol & Vanderweele (2012), estimates confidence interval additive interaction measures using the delta method Hosmer & Lemeshow (1992), the variance recovery method Zou (2008), or percentile bootstrapping Assmann et al. (1996).

RCT v1.0.2: Provides tools to facilitate the process of designing and evaluating randomized control trials, including methods to handle misfits, power calculations, balance regressions, and more. For background see Athey et al. (2017). The vignette describes how to use the package.

Science

rasterdiv: Provides functions to calculate indices of diversity on numerical matrices based on information theory. The rationale behind the package is described in Rocchini et al. (2017). See the vignette for an extended example.

SSHAARP v1.0.0: Processes amino acid alignments from the IPD-IMGT/HLA database to identify user-defined amino acid residue motifs shared across HLA alleles, calculate the frequencies of those motifs, and generate global frequency heat maps that illustrate the distribution of each user-defined map around the globe. See the vignette for an introduction.

Statistics

BayesSampling v1.0.0: Provides functions for applying the Bayes Linear approach to finite populations with the simple random sampling, stratified simple random sampling designs, and to the ratio estimator. See Gonçalves et al. (2014) for background and the vignettes: BLE_Ratio, BLE_Reg, BLE_SRS, BLE_SSRS, and BayesSampling.

cort v0.3.1: Provides S4 classes and methods to fit several copula models including empirical checkerboard copula Cuberos et. al (2019) and the Copula Recursive Tree algorithm proposed by Laverny et. al (2020). There are vignettes on the Empirical Checkerboard Copula, the Copula Recursive Tree, the Empirical Checkerboard Copula with known margins, and the convex mixture of m-randomized checkerboards.

ExpertChoice v0.2.0: Implements tools for designing efficient discrete choice experiments. See Street et. al (2005) for some background. There is an Practical Introduction and a vignette with some theory.

genscore v1.0.2: Implements the generalized score matching estimator from Yu et al. (2019) for non-negative graphical models with truncated distributions, and the estimator of Lin et al. (2016) for untruncated Gaussian graphical models. See the vignette.

hmma v1.0.0: Provides functions to fit Bayesian asymmetric hidden Markov models. HMM-As are similar to regular HMMs, See Bueno et al. (2017) for background and the vignette for and introduction.

lmeInfo v0.1.1: Provides analytic derivatives and information matrices for fitted linear mixed effects models and generalized least squares models estimated using lme() and gls() as well as functions for estimating the sampling variance-covariance of variance component parameters and standardized mean difference effect sizes. See Pustejovsky et al. (2014) and the vignette.

metapower v0.1.0: Implements a tool for computing meta-analytic statistical power for main effects, tests of homogeneity, and categorical moderator models. Have a look at Pigott (2012), Hedges & Pigott (2004), or Borenstein et al. (2009) for background and the vignett to get started.

sasLM v0.1.3: Implements the SAS procedures for linear models: GLM, REG, ANOVA. The sasLM functions produce the same results as the corresponding SAS procedures for nested and complex models.

sdglinkage 0.1.0: Provides a tool for synthetic data generation that can be used for linkage method development. There is an Overview and vignettes on Real and Synthetic Identifiers, Gold Standard File and Linkage Files, Synthetic Data Generation and Evaluation.

starm v0.1.0: Estimates the coefficients of the two-time centered autologistic regression model described in Gegout-Petit et al. (2019). The vignette describes the theory.

Time Series

ConsReg v0.1.0: Provides functions to fit regression and generalized linear models with autoregressive moving-average (ARMA) errors for time series data. There is a vignette.

simITS v0.1.1: Implements the method of Miratrix (2020) to create prediction intervals for post-policy outcomes in interrupted time series. It provides methods to fit ITS models with lagged outcomes and variables to account for temporal dependencies and then to simulate a set of plausible counterfactual post-policy series to compare to the observed post-policy series. See the vignette.

Utilities

dreamerr v1.1.0: Implements tools to facilitate package development by providing a flexible way to check the arguments passed to functions. See the vignette for details.

flair v0.0.2: Facilitates formatting and highlighting of R source code in a R Markdown based presentation. The vignette shows how.

J4R v1.0.7: Makes it possible to create Java objects and to execute Java methods from the R environment. The JVM is handled by a gateway server which relies on the Java library j4r.jar.

waldo v0.1.0: Provides functions to compare complex R objects and reveal the key differences. It was designed primarily for use in testing packages.

Visualization

anglr v0.6.0: Extends rgl conversion and visualization functions to mesh3d to give direct access to generic 3D tools and provide a full suite of mesh-creation and 3D plotting functions. See the vignette

brickr v0.3.4: Uses tidyverse functions to generate digital LEGO models and convert image files into 2D and 3D LEGO mosaics. There are vignettes for building mosaics and for generating models from mosaics, programs, tables, and by piece type.

survCurve v1.0: Provides functions to enhance plots created with the survival and mstate packages. See the vignette for examples.

textplot v0.1.2: Provides functions to visualize complex relations in texts by displaying text co-occurrence networks, text correlation networks, dependency relationships and text clustering. The vignette provides examples.

September 2017 New Package Picks

Wed, 25 Oct 2017 00:00:00 +0000

There were so many interesting ideas among the 222 new packages that made it to CRAN in September that I found it exceptionally difficult to decide on the “Top 40” packages. In the end, I only managed to limit my selection to 40 by avoiding all packages that I would normally classify under “Data”: packages that are primarily intended to provide access to some data source. I hope to make up for this by providing a list of data packages sometime soon.

Below are my picks for September’s Top 40 in six categories: Computational Methods, Machine Learning, Science, Statistics, Utilities, and Visualizations.

Computational Methods

DES v1.0.0: Implements an event-oriented approach to Discrete Event Simulation. There is a tutorial.

JuliaCall 0.9.3: Implements an interface to Julia. The vignette illustrates basic usage.

Rlinsolve v0.1.1: Implements iterative solvers for sparse linear systems of equations, including basic stationary iterative solvers using Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods and non-stationary, Krylov subspace methods. There is a vignette to get started. Detailed descriptions may be found in the SIAM book.

sdpt3r v0.1: Implements the SDPT3 method of Toh, Todd, and Tutuncu to solve Semi-Definite Linear Programming problems. There are several vignettes illustrating the use of the package in various applications, including D-Optimal Experimental Design and Distance Weighted Discrimination.

VeryLargeIntegers v0.1.4: Provides tools to work with arbitrarily large integers without loss of precision.

Machine Learning

bnclassify v0.3.3: Implements algorithms for learning discrete Bayesian network classifiers from data, including a number of those described in Bielza & Larranaga. There is an Introduction and vignettes giving Runtime Information and additional Technical Information.

DMRnet v0.1.0: Provides model selection algorithms for regression and classification, where the predictors can be numerical and categorical and the number of regressors exceeds the number of observations. See the papers by Maj-Kańska et al. and Pokarowski and Mielniczuk for the mathematical details.

ELMSurv v0.4: Implements an Extreme Learning Machine for Survival Analysis. Look here for details and here to get started.

fastrtext v0.2.1: Provides an interface to Facebook’s fastText library for text representation and classification. There is a List of Commands and vignettes on Supervised and Unsupervised learning.

FSelectorRcpp v0.1.8: provides an Rcpp-based implementation of FSelector entropy-based feature selection algorithms based on an Multi-Interval Discretization with a sparse matrix support. There are vignettes on Getting Started and Benchmarks.

googleLanguageR v0.1.0: Provides an interface to Google Cloud machine-learning APIs for text and speech tasks. Call the Cloud Translation API for detection and translation of text, the Natural Language API to analyse text for sentiment, entities or syntax, and the Cloud Speech API to transcribe sound files to text. There is an Introduction and vignettes for the NLP, Speech, and Translation APIs.

leabRa v0.1.0: Implements the Leabra (local, error-driven and associative, biologically realistic algorithm) that allows for the construction of artificial neural networks that are biologically realistic, and balances supervised and unsupervised learning within a single framework. See the vignette to get started and look here for details.

lime v0.3.0: Is a port of the Python package, which attempts to explain the outcome of black-box models by fitting local models around the points of interest. Look here for details. There is a vignette to get you started.

slowraker v0.1.0: Implements the RAKE algorithm, which can be used to extract keywords from documents without any training data. There is a Getting Started vignette and a list of FAQs.

udpipe v0.1.1: Provides a natural-language-processing toolkit for tokenization, parts-of-speech tagging, lemmatization, and dependency parsing of raw text. For details, see this paper and the vignettes on Annotating Text and Model Building.

Science

afpt v1.0.0: Implements the aerodynamic power model described in Klein Heerenbrink et al., and allows estimation and modelling of flight costs in vertebrate animal flight. There are vignettes on Basic Usage, the underlying Aerodynamic Model, and Multiple Birds.

soundgen v1.1.O: Tools for sound synthesis and acoustic analysis. There are vignettes on Acoustic Analysis and Sound Generation.

Statistics

cr17 v0.1.0: Provides tools for analyzing competing-risks models, including testing differences between groups (Gray and Fine and Gray) and visualizations of survival and cumulative incidence curves. The vignette gives examples.

EAinference v0.2.1: Provides estimator augmentation methods for statistical inference on high-dimensional data, as described in Zho and Zhou and Min. The vignette describes how to use the package.

fdAnova v0.1.0: Provides functions to perform analysis of variance testing procedures for univariate and multivariate functional data. See Cuesta-Albertos and Febrero-Bande. There is a comprehensive vignette.

geex v1.0.3: Provides a general, flexible framework for estimating parameters and empirical sandwich variance estimator from a set of unbiased estimating equations. See M-estimation as in Stefanski & Boos. There is an Introduction, as well as vignettes on M-estimation, Custom root solvers, Parameter Estimation, Software Design, and more.

mosaicModel v0.3.0: Provides functions for evaluating, displaying, and interpreting statistical models with the goal of abstracting the operations on models from the particular architecture of the model. The vignette shows how to use the package.

odr v0.3.2: Provides methods for calculating the optimal sample allocation that minimizes variance of treatment effects in a multilevel randomized trial under fixed budget and cost structure, and for performing power analyses with and without accommodating costs and budget. There is a vignette.

mvord v0.1.0: Provides a flexible framework for fitting multivariate ordinal regression models with composite likelihood methods. The vignette gives the details.

OultiersO3 v0.2.1: Provides methods for identifying potential outliers for all combinations of a dataset’s variables. The vignette shows how to use the package.

powerlmm v0.1.0: Implements both analytical and simulation methods to calculate power for two- and three-level multilevel longitudinal studies with missing data. The analytical calculations extends the method described in Galbraith et al. to three-level models. There are tutorials on Model Evaluation via Monte Carclo Simulation, Two-level Longitudinal Power Analysis, Three-level Longitudinal Power Analysis, and a vignette on the Details of Power Calculations.

randnet v0.1: Facilitates model-selection and parameter-tuning procedures for a class of random network models. Model selection can be done by a general cross-validation framework called ECV, NCV, a likelihood ratio method, and spectral methods.

threshr v1.0.0: Provides functions for the selection of thresholds for use in extreme value models, based mainly on the methodology in Northrop, Attalides and Jonathan. There is a vignette.

tscount v1.4.0: Implements likelihood-based methods for model fitting and assessment, prediction, and intervention analysis of count time series following generalized linear models. The vignette provides the details.

Utilities

basictabler v0.1.0: Provides functions to create tables from data frames and matrices, manipulate tables row-by-row, column-by-column or cell-by-cell, and then publish them using HTML, HTML widgets or Excel. There is an Introduction and vignettes on Working with Cells, Outputs, Styling, Formatting, Shiny, and Excel.

bigstatsr v0.2.2: Uses file-backed matrices to provide scalable statistical tools.

keyring v1.0.0: Provides a platform-independent API to access the operating system’s credential store. It currently supports: Keychain on macOS, The Credential Store on Windows, the Secret Service API on Linux, and a simple, platform-independent store implemented with environment variables.

pinp v0.0.2: Offers a PNAS-like style for rmarkdown derived from the Proceedings of the National Academy of Sciences of the United States of America. The vignette shows how to get started.

re2r v0.2.0: Provides an interface to Google’s deterministic finite-automaton-based regular expression engine that is very fast at matching large amounts of text. There is an Introduction and a vignette on Syntax.

spiderbar v0.2.0: Provides a wrapper for the rep-cpp C++ library for processing robots.txt files in accordance with the The Robots Exclusion Protocol, a set of standards for allowing or excluding robot/spider crawling of different areas of site content. Look in the README for an example of how to use the package.

tibbletime v0.0.2: Is an extension of the tibble package that allows for the creation of time-aware tibbles. Some immediate advantages include: the ability to perform time-based subsetting on tibbles, quickly summarising and aggregating results by time periods, and calling functions similar in spirit to the map family from purrr on time-based tibbles. There is an Introduction and vignettes on Time-based Filtering, Changing Periodicity, and Rolling Calculaions.

Visualizations

egg v0.2.0: Provides miscellaneous functions to customize ggplot2 plots, including high-level functions to post-process layouts and allow alignment between plot panels, as well as setting panel sizes to fixed values. There is an Overview and a vignette for laying out multiple plots on a page.

ggridges v0.4.1: Extends ggplot2 to enable ridgeline plots, which are a way of visualizing changes in distributions over time or space. There is an introduction and a gallery of examples.

linemap v0.1.0: Provides functions to create maps from lines. The README file shows examples.

August 2017 New Package Picks

Fri, 29 Sep 2017 00:00:00 +0000

August was a relatively slow month for new R packages; “only” 180 new packages stuck to CRAN. Here are my “Top 40” picks organized into seven categories: Data, Machine Learning, Miscellaneous, Science, Statistics, Utilities and Visualizations. Although they have been written for specialized audiences, I have included the three “Science” packages because, in my layman’s opinion, they not only seem to be useful, but they are each documented well enough to give an interested person some idea of what they do.

Data

edgarWebR v0.1.1: Provides methods to access and parse live filing information from the U.S. Securities and Exchange Commission, including company and fund filings, along with all associated metadata. See the vignette for an introduction.

forwards v0.1.0: Anonymized data from surveys conducted by Forwards, the R Foundation task force on women and other under-represented groups. Currently, a single data set of responses to a survey of attendees at useR! 2016. The vignette provides an overview.

GeoMongo v1.0.1: Utilizes methods from the PyMongo library to initialize, insert and query ‘GeoJson’ data. There is a vignette.

Rnightlights v0.1.2: Provides an interface to extract raster and zonal statistics from satellite nightlight rasters, downloaded from the United States National Oceanic and Atmospheric Administration free data repositories.

Knoema v0.1.7: Provides an API interface to Knoema, one of the largest collections of public data and statistics on the Internet, featuring about 2.5 billion time series from thousands of sources. The README file will get you started.

rwalkr v0.3.1: Provides an API to the Melbourne pedestrian data in tidy data form. See README for an example.

vegetable v0.1.0: Provides functions to import and manipulate data from vegetation-plot databases, especially data stored in Turboveg. The package also implements import/export routines for exchanging data with Juice.

Machine Learning

partitionComparison v0.2.2: Provides several measures (dissimilarity, distance/metric, correlation, entropy) for comparing two partitions of the same set of objects. See the paper by Marina Meilă for details.

spm v1.0.0: Introduces hybrid methods of geostatistical and machine learning methods for spatial predictive modelling. The vignette provides an introduction.

Miscellaneous

LearnGeom v1.0: Provides functions for learning and teaching basic plane Geometry at the undergraduate level, with the aim of being helpful to young students with few programming skills. The vignette offers several examples.

Science

PGRdup v0.2.3.2: Provides functions to aid the identification of probable/possible duplicates in Plant Genetic Resources collections using ‘passport databases’ comprising information records from each constituent sample. The vignette provides an overview.

rtimicropem v1.3: Supports the input and reproducible analysis of RTI MicroPEM output files such as those produced by the Chai Project. There is an Introduction and a vignette on MicroPEM Cleaning.

snpReady v0.9.3: Provides functions to clean, summarize and prepare genomic data sets to Genome Selection and Genome Association analysis and to estimate population genetic parameters. See the vignette for details.

Statistics

blink v0.1.0: Implements the model in Steorts, which performs Bayesian entity resolution for categorical and text data, for any distance function defined by the user. Reproducible experiments are illustrated in the vignette.

cholera v0.2.1: Amends errors, augments data and aids analysis of John Snow’s map of the 1854 London cholera outbreak. The original data come from Rusty Dodson and Waldo Tobler’s 1992 digitization of Snow’s map. Those data are no longer available. However, they are preserved in the HistData package. There are vignettes on Missing Data, Pump Neighborhoods, Roads, Time Series, and “Unstacking bars”.

drtmle v1.0.0: Provides targeted minimum loss-based estimators for counter-factual means and causal effects that are doubly robust with respect both to consistency and asymptotic normality van der Laan. The extensive vignette does the math.

esvis v0.1.0: Provides a variety of methods to estimate and visualize distributional differences in terms of effect sizes, with emphasis on evaluating differences between two or more distributions across the entire scale, rather than at a single point (e.g., differences in means). Look here for an example.

fuser v1.0.0: Provides functions for high-dimensional penalized regression across heterogeneous subgroups. The underlying model is described in detail in Dondelinger and Mukherjee. The vignette shows how to use the package for prediction over subgroups.

gamlss.spatial v1.3.4: Provides functions to fit Gaussian Markov Random Fields within the Generalized Additive Models for Location Scale and Shape algorithms. The vignette introduces the package and provides several examples.

INLAutils v0.0.4: Provides a number of utility functions for solving models using the Integrated Nested Laplace Approximation INLA, a new approach to statistical inference with latent Gaussian Markov random fields (GMRF). Look here for examples and plots.

missRanger v1.0.0: Provides an implementation of the MissForest algorithm for imputing mixed-type data sets by chaining tree ensembles that was introduced by Stekhoven and Buehlmann. Look here for an example.

naniar v0.1.0: Provides data structures and functions that facilitate the plotting of missing values and examination of imputations. There is a Getting Started Guide and a Gallery of Missing Data Visualizations.

powdist v0.1.3: Provides density, distribution, and quantile functions, as well as a function for random draws from power and reversal power distributions.

RATest v0.1.0: Provides a collection of randomization tests, data sets, and examples currently focusing on permutation tests for baseline covariates in the sharp regression discontinuity design. See Canay and Kamat and the vignette.

skpr v0.35.1: Is an open-source design of experiments suite, for generating and evaluating optimal designs in R. The README file shows how to get started.

Utilities

blastula v0.1: Allows users to compose and send HTML email messages that render across a range of email clients and device sizes. Messages are composed using Markdown and a text interpolation system that allows for the injection of evaluated R code within the message body. The README file describes how to use the package.

blogdown v0.1: Enables users to write blog posts (like this one) and web pages in R Markdown. This package supports the static site generator Hugo best, but it also supports Jekyll and Hexo.

cetcolor v0.1.0: Offers a collection of perceptually uniform colour maps described by Peter Kovesi in the paper Good Colour Maps: How to Design Them. The vignette shows several examples.

googledrive v0.1.1: See the googledrive website for an example and instructions for getting started with the package.

pointblank v0.1: Provides functions to validate data in local data frames, local tibble objects, in csv and tsv files, and in PostgreSQL and MySQL database tables. Look at the README file for an example.

reqres v0.2.0: Provides functions to facilitate parsing of HTTP requests, creation of appropriate responses, and handling of the housekeeping involved in working with HTTP exchanges. See README to get started.

rmapzen v0.3.3: Provides an interface to the Mapzen API for geographic search and geocoding, isochrone calculation, and vector data to draw map tiles. Look here for examples.

spelling v1.0: Provides spell checking for common document formats including latex, markdown, manual pages, and description files.

splashr v0.4.0: Provides tools to work with the Splash JavaScript Rendering and Scraping Service. There is an Introduction and vignettes on Helper Functions and Working with the splashrDSL.

writexl v0.2: Implements a portable, light-weight data-frame-to-xlsx exporter based on libxlsxwriter. No ‘Java’ or ‘Excel’ required.

Visualizations

billboarder v0.0.3: Provides an htmlwidgets interface to billboard.js, a re-usable, easy interface to the JavaScript chart library, based on D3 v4+. Chart types include line charts, scatter plots, bar charts, pie/donut charts, and gauge charts. There is an Introduction and a vignette on Options for Styling Charts.

cdparcoord v1.0.0: Provides functions for plotting parallel coordinates with resolutions for large data sets and missing values. The vignette offers several examples.

gggenes v0.2.0: Provides a ggplot2 geom and helper functions for drawing gene arrow maps.

quickplot v0.1.1: Offers a high-level plotting system, built using ‘grid’ graphics, which is optimized for speed and modularity. The vignette provides examples.

treemapify v2.3.2: Provides ggplot2 geoms for drawing treemaps. There is a vignette with examples.