R Weekly 2023-W00
This week’s release was curated by , with help from the R Weekly team members and contributors.
Highlight
Insights
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Fisher’s Exact Test in R: How to Interpret & do Post Hoc Analysis
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LIVE FROM CHICAGO: REAL WORLD DATA SCIENCE AT POSIT::CONF(2023)
R in the Real World
R in Organizations
R in Academia
- Guide to understanding the intuition behind the Dirichlet distribution: Learn about the Dirichlet distribution and explore how it’s just a fancier version of the Beta distribution
Resources
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The notebook seen in Jeremy Howard’s keynote at posit::conf(2023)
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Parameterized Quarto reports improve understanding of soil health
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It’s All About Perspective, Making A Case for Generative Art
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Empowering Educators and Researchers with Interactive Quarto Documents Using webR
New Packages
CRAN
- {newscatcheR} 0.0.1: Programmatically Collect Normalized News from (Almost) Any Website
- {genius} 2.2.2: Easily Access Song Lyrics from Genius.com
- {almanac} 0.1.0: Tools for Working with Recurrence Rules
- {tidylo} 0.1.0: Weighted Tidy Log Odds Ratio
- {nombre} 0.1.0: Number Names
- {nhlapi} 0.1.2: A Minimum-Dependency ‘R’ Interface to the ‘NHL’ API
- {applicable} 0.0.1: A Compilation of Applicability Domain Methods
- {upsetjs} 1.0.2: ‘HTMLWidget’ Wrapper of ‘UpSet.s’ for Exploring Large Set Intersections
- {sketcher} 0.1.3: Pencil Sketch Effect
- {BOJ} 0.2.2: Interface to Bank of Japan Statistics
- {ROpenCVLite} 0.4.430: Install ‘OpenCV’
Bioconductor
GitHub or Bitbucket
Updated Packages
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{mirai} 0.10.0: Minimalist Async Evaluation Framework for R.
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{mirai.promises} 0.3.0: Make ‘Mirai’ ‘Promises’ in Shiny and Plumber Pipelines.
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- {pavo} 2.9.0: Perceptual Analysis, Visualization and Organization of Spectral Colour Data - diffify
- {markovchain} 0.9.5: Easy Handling Discrete Time Markov Chains - diffify
- {checkdown} 0.0.10: Check-Fields and Check-Boxes for ‘rmarkdown’ - diffify
- {lgpr} 1.2.4: Longitudinal Gaussian Process Regression - diffify
- {pedSimulate} 1.4.1: Pedigree, Genetic Merit, Phenotype, and Genotype Simulation - diffify
- {and} 0.1.5: Construct Natural-Language Lists with Internationalization - diffify
- {raqs} 1.0.1: Interface to the US EPA Air Quality System (AQS) API - diffify
- {rtsplot} 0.1.5: Time Series Plot - diffify
- {panelView} 1.1.17: Visualizing Panel Data - diffify
- {ctmm} 1.2.0: Continuous-Time Movement Modeling - diffify
- {csurvey} 1.9: Constrained Regression for Survey Data - diffify
- {clustermq} 0.9.0: Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM, PBS/Torque) - diffify
- {blastula} 0.3.4: Easily Send HTML Email Messages - diffify
- {bayesm} 3.1-6: Bayesian Inference for Marketing/Micro-Econometrics - diffify
- {uci} 0.3.0: Urban Centrality Index - diffify
- {recmap} 1.0.17: Compute the Rectangular Statistical Cartogram - diffify
- {ohun} 1.0.0: Optimizing Acoustic Signal Detection - diffify
- {nodbi} 0.9.8: ‘NoSQL’ Database Connector - diffify
- {import} 1.3.1: An Import Mechanism for R - diffify
- {fastcpd} 0.7.2: Fast Change Point Detection via Sequential Gradient Descent - diffify
- {CopulaCenR} 1.2.3: Copula-Based Regression Models for Multivariate Censored Data - diffify
- {BTSR} 0.1.5: Bounded Time Series Regression - diffify
- {StanMoMo} 1.2.0: Bayesian Mortality Modelling with ‘Stan’ - diffify
- {plu} 0.3.0: Dynamically Pluralize Phrases - diffify
- {multifear} 0.1.3: Multiverse Analyses for Conditioning Data - diffify
- {forestploter} 1.1.1: Create Flexible Forest Plot - diffify
- {cpd} 0.3.2: Complex Pearson Distributions - diffify
- {Temporal} 0.3.0.1: Parametric Time to Event Analysis - diffify
- {UKFE} 0.3.0: UK Flood Estimation - diffify
- {dann} 1.0.0: Discriminant Adaptive Nearest Neighbor Classification - diffify
- {kernelshap} 0.3.8: Kernel SHAP - diffify
- {GeoModels} 1.1.3: Procedures for Gaussian and Non Gaussian Geostatistical (Large) Data Analysis - diffify
- {skmeans} 0.2-16: Spherical k-Means Clustering - diffify
- {clue} 0.3-65: Cluster Ensembles - diffify
- {funkyheatmap} 0.5.0: Generating Funky Heatmaps for Data Frames - diffify
- {radiant.multivariate} 1.6.1: Multivariate Menu for Radiant: Business Analytics using R and Shiny - diffify
- {halk} 0.0.4: Methods to Create Hierarchical Age Length Keys for Age Assignment - diffify
- {walkboutr} 0.2.0: Generate Walk Bouts from GPS and Accelerometry Data - diffify
- {phylosem} 1.0.2: Phylogenetic Structural Equation Model - diffify
- {OmicSense} 0.2.0: Biosensor Development using Omics Data - diffify
- {ggseqplot} 0.8.3: Render Sequence Plots using ‘ggplot2’ - diffify
- {geostatsp} 2.0.1: Geostatistical Modelling with Likelihood and Bayes - diffify
- {RchivalTag} 0.1.7: Analyzing and Interactive Visualization of Archival Tagging Data - diffify
- {consort} 1.2.1: Create Consort Diagram - diffify
- {RcppColors} 0.5.0: Color Mappings and ‘C++’ Header Files for Color Conversion - diffify
- {colorednoise} 1.1.1: Simulate Temporally Autocorrelated Populations - diffify
- {varTestnlme} 1.3.5: Variance Components Testing for Linear and Nonlinear Mixed Effects Models - diffify
- {ExactMed} 0.3.0: Exact Mediation Analysis for Binary Outcomes - diffify
- {condir} 0.1.4: Computation of P Values and Bayes Factors for Conditioning Data - diffify
- {tigris} 2.0.4: Load Census TIGER/Line Shapefiles - diffify
- {mcompanion} 0.5.8: Objects and Methods for Multi-Companion Matrices - diffify
- {timetk} 2.8.4: A Tool Kit for Working with Time Series - diffify
- {RMixtCompUtilities} 4.1.6: Utility Functions for ‘MixtComp’ Outputs - diffify
- {accumulate} 0.9.3: Split-Apply-Combine with Dynamic Groups - diffify
- {pedquant} 0.2.3: Public Economic Data and Quantitative Analysis - diffify
- {gnonadd} 1.0.2: Various Non-Additive Models for Genetic Associations - diffify
- {easy.utils} 0.0.2: Frequently Used Functions for Easy R Programming - diffify
- {arrow} 13.0.0.1: Integration to ‘Apache’ ‘Arrow’ - diffify
- {REPPlabShiny} 0.4.2: ‘REPPlab’ via a Shiny Application - diffify
- {oosse} 1.0.10: Out-of-Sample R² with Standard Error Estimation - diffify
- {lakemorpho} 1.3.2: Lake Morphometry Metrics - diffify
- {gRbase} 2.0.0: A Package for Graphical Modelling in R - diffify
- {R3port} 0.2.5: Report Functions to Create HTML and PDF Files - diffify
- {vdiffr} 1.0.7: Visual Regression Testing and Graphical Diffing - diffify
- {pkgload} 1.3.3: Simulate Package Installation and Attach - diffify
- {piecepackr} 1.13.8: Board Game Graphics - diffify
- {mvMAPIT} 2.0.2: Multivariate Genome Wide Marginal Epistasis Test - diffify
- {MazamaTimeSeries} 0.2.15: Core Functionality for Environmental Time Series - diffify
- {malariaAtlas} 1.2.0: An R Interface to Open-Access Malaria Data, Hosted by the ‘Malaria Atlas Project’ - diffify
- {hdf5r.Extra} 0.0.2: Extensions for ‘HDF5’ R Interfaces - diffify
- {fqar} 0.4.2: Floristic Quality Assessment Tools for R - diffify
- {dtwSat} 1.0.0: Time-Weighted Dynamic Time Warping for Satellite Image Time Series Analysis - diffify
- {palm} 1.1.5: Fitting Point Process Models via the Palm Likelihood - diffify
- {smacpod} 2.6: Statistical Methods for the Analysis of Case-Control Point Data - diffify
- {BayesFactor} 0.9.12-4.5: Computation of Bayes Factors for Common Designs - diffify
- {survstan} 0.0.4: Fitting Survival Regression Models via ‘Stan’ - diffify
- {prqlr} 0.5.3: R Bindings for the ‘prql-compiler’ Rust Library - diffify
- {isotracer} 1.1.5: Isotopic Tracer Analysis Using MCMC - diffify
- {diseasemapping} 2.0.3: Modelling Spatial Variation in Disease Risk for Areal Data - diffify
- {PheVis} 1.0.3: Automatic Phenotyping of Electronic Health Record at Visit Resolution - diffify
- {paws.common} 0.6.1: Paws Low-Level Amazon Web Services API - diffify
- {fqadata} 1.1.0: Contains Regional Floristic Quality Assessment Databases - diffify
- {clarify} 0.2.0: Simulation-Based Inference for Regression Models - diffify
- {limSolve} 1.5.7: Solving Linear Inverse Models - diffify
- {neighbours} 0.1-3: Neighbourhood Functions for Local-Search Algorithms - diffify
- {ExclusionTable} 1.1.0: Creating Tables of Excluded Observations - diffify
- {tabr} 0.4.9: Music Notation Syntax, Manipulation, Analysis and Transcription in R - diffify
- {mapmisc} 2.0.1: Utilities for Producing Maps - diffify
- {rootSolve} 1.8.2.4: Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations - diffify
- {chromer} 0.6: Interface to Chromosome Counts Database API - diffify
- {bvpSolve} 1.4.4.1: Solvers for Boundary Value Problems of Differential Equations - diffify
- {wdpar} 1.3.7: Interface to the World Database on Protected Areas - diffify
- {rbioacc} 1.2-0: Inference and Prediction of ToxicoKinetic (TK) Models - diffify
- {AzureRMR} 2.4.4: Interface to ‘Azure Resource Manager’ - diffify
- {ICS} 1.4-1: Tools for Exploring Multivariate Data via ICS/ICA - diffify
- {snowFT} 1.6-1: Fault Tolerant Simple Network of Workstations - diffify
- {NMsim} 0.0.4: Seamless ‘Nonmem’ Simulation Platform - diffify
- {ISRaD} 2.5.5: Tools and Data for the International Soil Radiocarbon Database - diffify
- {geobr} 1.8.1: Download Official Spatial Data Sets of Brazil - diffify
- {fastcpd} 0.7.2: Fast Change Point Detection via Sequential Gradient Descent - diffify
- {romic} 1.1.3: R for High-Dimensional Omic Data - diffify
- {geocausal} 0.2.0: Causal Inference with Spatio-Temporal Data - diffify
- {accessibility} 1.2.0: Transport Accessibility Measures - diffify
- {rbmi} 1.2.5: Reference Based Multiple Imputation - diffify
- {nonmemica} 1.0.8: Create and Evaluate NONMEM Models in a Project Context - diffify
- {NMsim} 0.0.4: Seamless ‘Nonmem’ Simulation Platform - diffify
- {EloSteepness} 0.5.0: Bayesian Dominance Hierarchy Steepness via Elo Rating and David’s Scores - diffify
- {ggstatsplot} 0.12.1: ‘ggplot2’ Based Plots with Statistical Details - diffify
- {echarty} 1.6.0: Minimal R/Shiny Interface to JavaScript Library ‘ECharts’ - diffify
- {ottrpal} 1.2: Companion Tools for Open-Source Tools for Training Resources (OTTR) - diffify
- {connectwidgets} 0.2.1: Organize and Curate Your Content Within ‘Posit Connect’ - diffify
- {jqr} 1.3.0: Client for ‘jq’, a ‘JSON’ Processor - diffify
- {europepmc} 0.4.3: R Interface to the Europe PubMed Central RESTful Web Service - diffify
- {envalysis} 0.6.0: Miscellaneous Functions for Environmental Analyses - diffify
- {datetimeutils} 0.6-2: Utilities for Dates and Times - diffify
- {sisireg} 1.1.1: Sign-Simplicity-Regression-Solver - diffify
- {reslife} 0.1.2: Calculate Mean Residual Life (MRL) and Related Values for Different Distributions - diffify
- {harmony} 1.0.1: Fast, Sensitive, and Accurate Integration of Single Cell Data - diffify
- {BFS} 0.5.5: Get Data from the Swiss Federal Statistical Office - diffify
- {regspec} 2.7: Non-Parametric Bayesian Spectrum Estimation for Multirate Data - diffify
- {crew.cluster} 0.1.2: Crew Launcher Plugins for Traditional High-Performance Computing Clusters - diffify
- {caretEnsemble} 2.0.3: Ensembles of Caret Models - diffify
- {MTest} 1.0.1: A Procedure for Multicollinearity Testing using Bootstrap - diffify
- {newscatcheR} 0.1.2: Programmatically Collect Normalized News from (Almost) Any Website - diffify
- {IOHanalyzer} 0.1.8.2: Data Analysis Part of ‘IOHprofiler’ - diffify
- {mlr3misc} 0.13.0: Helper Functions for ‘mlr3’ - diffify
- {zen4R} 0.9: Interface to ‘Zenodo’ REST API - diffify
- {timsac} 1.3.8-3: Time Series Analysis and Control Package - diffify
- {SqlRender} 1.16.0: Rendering Parameterized SQL and Translation to Dialects - diffify
- {RoBTT} 1.2.1: Robust Bayesian T-Test - diffify
- {FrF2} 2.3-3: Fractional Factorial Designs with 2-Level Factors - diffify
- {exactextractr} 0.10.0: Fast Extraction from Raster Datasets using Polygons - diffify
- {reReg} 1.4.6: Recurrent Event Regression - diffify
- {recommenderlab} 1.0.6: Lab for Developing and Testing Recommender Algorithms - diffify
- {MixSemiRob} 1.1.0: Mixture Models: Parametric, Semiparametric, and Robust - diffify
- {ie2misc} 0.9.1: Irucka Embry’s Miscellaneous USGS Functions - diffify
- {himach} 0.3.2: High Mach Finds Routes for Supersonic Aircraft - diffify
- {fastverse} 0.3.2: A Suite of High-Performance Packages for Statistics and Data Manipulation - diffify
- {CoxAIPW} 0.0.3: Doubly Robust Inference for Cox Marginal Structural Model with Informative Censoring - diffify
- {CalibrationCurves} 2.0.0: Calibration Performance - diffify
- {BGmisc} 1.0: An R Package for Extended Behavior Genetics Analysis - diffify
- {aggTrees} 2.0.2: Aggregation Trees - diffify
- {VedicDateTime} 0.1.9: Vedic Calendar System - diffify
- {PDtoolkit} 1.2.0: Collection of Tools for PD Rating Model Development and Validation - diffify
- {yulab.utils} 0.1.0: Supporting Functions for Packages Maintained by ‘YuLab-SMU’ - diffify
- {rsm} 2.10.4: Response-Surface Analysis - diffify
- {NEONiso} 0.6.4: Tools to Calibrate and Work with NEON Atmospheric Isotope Data - diffify
- {rugarch} 1.5-1: Univariate GARCH Models - diffify
- {rmass2} 0.0.0.2: Repeated Measures with Attrition: Sample Sizes and Power Levels for 2 Groups - diffify
- {jab.adverse.reactions} 1.0.3: Possible Adverse Events/Reactions from the Vaccinations/Experimental Gene Therapies - diffify
- {greenclust} 1.1.1: Combine Categories Using Greenacre’s Method - diffify
- {epoxy} 1.0.0: String Interpolation for Documents, Reports and Apps - diffify
- {Nmix} 2.0.5: Bayesian Inference on Univariate Normal Mixtures - diffify
- {IRTest} 1.11.0: Parameter Estimation of Item Response Theory with Estimation of Latent Distribution - diffify
- {apcluster} 1.4.11: Affinity Propagation Clustering - diffify
- {skilljaR} 0.1.2: Connect to Your ‘Skilljar’ Data - diffify
- {SpatEntropy} 2.2-1: Spatial Entropy Measures - diffify
- {diseasemapping} 2.0.3: Modelling Spatial Variation in Disease Risk for Areal Data - diffify
- {RcppInt64} 0.0.3: ‘Rcpp’-Based Helper Functions to Pass ‘Int64’ and ‘nanotime’ Values Between ‘R’ and ‘C++’ - diffify
- {alone} 0.3: Datasets from the Survival TV Series Alone - diffify
- {abess} 0.4.8: Fast Best Subset Selection - diffify
- {selection.index} 1.2.0: Analysis of Selection Index in Plant Breeding - diffify
- {rio} 1.0.1: A Swiss-Army Knife for Data I/O - diffify
- {mvQuad} 1.0-8: Methods for Multivariate Quadrature - diffify
- {ggblanket} 5.1.0: Simplify ‘ggplot2’ Visualisation - diffify
- {graphlayouts} 1.0.1: Additional Layout Algorithms for Network Visualizations - diffify
- {editbl} 0.9.6: ‘DT’ Extension for CRUD (Create, Read, Update, Delete) Applications in ‘shiny’ - diffify
- {restatapi} 0.22.1: Search and Retrieve Data from Eurostat Database - diffify
- {LDATS} 0.3.0: Latent Dirichlet Allocation Coupled with Time Series Analyses - diffify
- {volesti} 1.1.2-7: Volume Approximation and Sampling of Convex Polytopes - diffify
- {rngSetSeed} 0.3-3: Seeding the Default RNG with a Numeric Vector - diffify
- {renv} 1.0.3: Project Environments - diffify
- {r3PG} 0.1.6: Simulating Forest Growth using the 3-PG Model - diffify
- {puniform} 0.2.7: Meta-Analysis Methods Correcting for Publication Bias - diffify
- {MBHdesign} 2.3.14: Spatial Designs for Ecological and Environmental Surveys - diffify
- {htsr} 2.1.1: Hydro-Meteorology Time-Series - diffify
- {collin} 0.0.4: Visualization the Effects of Collinearity in Distributed Lag Models and Other Linear Models - diffify
- {cauphy} 1.0.1: Trait Evolution on Phylogenies Using the Cauchy Process - diffify
- {gpbStat} 0.4.1: Comprehensive Statistical Analysis of Plant Breeding Experiments - diffify
- {r2redux} 1.0.16: R2 Statistic - diffify
- {GenSA} 1.1.10.1: R Functions for Generalized Simulated Annealing - diffify
- {fude} 0.3.4: Utilities for Fude Polygon - diffify
- {VGAM} 1.1-9: Vector Generalized Linear and Additive Models - diffify
- {sctransform} 0.4.0: Variance Stabilizing Transformations for Single Cell UMI Data - diffify
- {quarto} 1.3: R Interface to ‘Quarto’ Markdown Publishing System - diffify
- {phylosem} 1.0.2: Phylogenetic Structural Equation Model - diffify
- {RcppHNSW} 0.5.0: ‘Rcpp’ Bindings for ‘hnswlib’, a Library for Approximate Nearest Neighbors - diffify
- {jlmerclusterperm} 1.0.6: Cluster-Based Permutation Analysis for Densely Sampled Time Data - diffify
- {updater} 0.1.2: Utilities for Updating R - diffify
- {netplot} 0.2-0: Beautiful Graph Drawing - diffify
- {nlmixr2est} 2.1.7: Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines - diffify
- {eventPred} 0.2.0: Event Prediction - diffify
- {mark} 0.6.1: Miscellaneous, Analytic R Kernels - diffify
- {DEPONS2R} 1.2.2: Read, Plot and Analyse Output from the DEPONS Model - diffify
- {valr} 0.7.0: Genome Interval Arithmetic - diffify
- {randomizeR} 3.0.2: Randomization for Clinical Trials - diffify
- {TraMineR} 2.2-8: Trajectory Miner: a Sequence Analysis Toolkit - diffify
- {Matrix} 1.6-1.1: Sparse and Dense Matrix Classes and Methods - diffify
- {BSDA} 1.2.2: Basic Statistics and Data Analysis - diffify
- {webSDM} 1.1-4: Including Known Interactions in Species Distribution Models - diffify
Videos and Podcasts
Gist & Cookbook
Shiny Apps
R Internationally
Tutorials
R Project Updates
Updates from R Core:
Upcoming Events in 3 Months
Events in 3 Months:
Grants & Funding
Mark your calendars! The final call for the RUGS grant opportunity is approaching fast - The deadline is September 30th, 2023. Everything you need to know is right here: https://t.co/1MS9KNBecZ #rstats #opensource #RLadiesSaoPaulo pic.twitter.com/DjoU0o1oH9
— R Consortium (@RConsortium) September 22, 2023
Datasets
Jobs
💼 Explore Jobs & Gigs Board on RStudio Community 💼
rtistry
Got a request for this one on my website, curious how y'all feel about the border lines and country annotations?#rstats + #rayshader pic.twitter.com/51Es5BYyNs
— Spencer Schien (@MrPecners) September 19, 2023
Quotes of the Week
What is the most difficult part of becoming a data scientist?
— Matt Dancho (Business Science) (@mdancho84) September 22, 2023
I’ve had to battle through each of these.
And here are 3 tips that worked for me. 🧵#datascience #rstats #python pic.twitter.com/zw0Lm7MiW5
Error messages can be so cruel 😭 #rstats pic.twitter.com/7cCi94Abdy
— Mike Kearney📊 (@kearneymw) September 20, 2023