igraph - Network Analysis and Visualization
Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Last updated
complex-networksgraph-algorithmsgraph-theorymathematicsnetwork-analysisnetwork-graphlibxml2glpkopenblascpp
21.37 score 612 stars 2.1k dependents 38k scripts 608k downloads
rlang - Functions for Base Types and Core R and 'Tidyverse' Features
A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.
Last updated
20.94 score 567 stars 17k dependents 14k scripts 2.7M downloads
vctrs - Vector Helpers
Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analysing function interfaces.
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s3-vectors
20.18 score 301 stars 15k dependents 1.3k scripts 2.1M downloads
arrow - Integration to 'Apache' 'Arrow'
'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. This package provides an interface to the 'Arrow C++' library.
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arrowparquetcurlopensslcpp
19.90 score 17k stars 180 dependents 23k scripts 266k downloadscli - Helpers for Developing Command Line Interfaces
A suite of tools to build attractive command line interfaces ('CLIs'), from semantic elements: headings, lists, alerts, paragraphs, etc. Supports custom themes via a 'CSS'-like language. It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.
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cli
19.24 score 706 stars 16k dependents 2.0k scripts 2.2M downloadsS7 - An Object Oriented System Meant to Become a Successor to S3 and S4
A new object oriented programming system designed to be a successor to S3 and S4. It includes formal class, generic, and method specification, and a limited form of multiple dispatch. It has been designed and implemented collaboratively by the R Consortium Object-Oriented Programming Working Group, which includes representatives from R-Core, 'Bioconductor', 'Posit'/'tidyverse', and the wider R community.
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18.32 score 480 stars 8.7k dependents 241 scripts 1.5M downloads
loo - Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models
Efficient approximate leave-one-out cross-validation (LOO) for Bayesian models fit using Markov chain Monte Carlo, as described in Vehtari, Gelman, and Gabry (2017) <doi:10.1007/s11222-016-9696-4>. The approximation uses Pareto smoothed importance sampling (PSIS), a new procedure for regularizing importance weights. As a byproduct of the calculations, we also obtain approximate standard errors for estimated predictive errors and for the comparison of predictive errors between models. The package also provides methods for using stacking and other model weighting techniques to average Bayesian predictive distributions.
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bayesbayesianbayesian-data-analysisbayesian-inferencebayesian-methodsbayesian-statisticscross-validationinformation-criterionmodel-comparisonstan
18.29 score 154 stars 311 dependents 3.6k scripts 331k downloads
bayesplot - Plotting for Bayesian Models
Plotting functions for posterior analysis, MCMC diagnostics, prior and posterior predictive checks, and other visualizations to support the applied Bayesian workflow advocated in Gabry, Simpson, Vehtari, Betancourt, and Gelman (2019) <doi:10.1111/rssa.12378>. The package is designed not only to provide convenient functionality for users, but also a common set of functions that can be easily used by developers working on a variety of R packages for Bayesian modeling, particularly (but not exclusively) packages interfacing with 'Stan'.
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bayesianbayesian-workflowggplot2mcmcstanstatistical-graphicsvisualization
18.22 score 440 stars 106 dependents 10k scripts 151k downloads
posterior - Tools for Working with Posterior Distributions
Provides useful tools for both users and developers of packages for fitting Bayesian models or working with output from Bayesian models. The primary goals of the package are to: (a) Efficiently convert between many different useful formats of draws (samples) from posterior or prior distributions. (b) Provide consistent methods for operations commonly performed on draws, for example, subsetting, binding, or mutating draws. (c) Provide various summaries of draws in convenient formats. (d) Provide lightweight implementations of state of the art posterior inference diagnostics. References: Vehtari et al. (2021) <doi:10.1214/20-BA1221>.
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bayesbayesianmcmc
17.13 score 170 stars 371 dependents 5.4k scripts 342k downloadslater - Utilities for Scheduling Functions to Execute Later with Event Loops
Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied. The functions are scheduled in an event loop.
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event-loopcpp
16.76 score 149 stars 2.9k dependents 386 scripts 670k downloads
rstanarm - Bayesian Applied Regression Modeling via Stan
Estimates previously compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the customary R syntax with a formula and data.frame plus some additional arguments for priors.
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bayesianbayesian-data-analysisbayesian-inferencebayesian-methodsbayesian-statisticsmultilevel-modelsrstanrstanarmstanstatistical-modelingcpp
16.48 score 401 stars 13 dependents 6.7k scripts 31k downloads
mirai - Minimalist Async Evaluation Framework for R
Evaluates R expressions asynchronously and in parallel, locally or distributed across networks. An official parallel cluster type for R. Built on 'nanonext' and 'NNG', its non-polling, event-driven architecture scales from a laptop to thousands of processes across high-performance computing clusters and cloud platforms. Features FIFO scheduling with task cancellation and bounded queues, promises for reactive programming, 'OpenTelemetry' distributed tracing, and custom serialization for cross-language data types.
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asyncasynchronous-tasksconcurrencydistributed-computinghigh-performance-computingparallel-computing
16.05 score 323 stars 162 dependents 510 scripts 77k downloads
targets - Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
Pipeline tools coordinate the pieces of computationally demanding analysis projects. The 'targets' package is a 'Make'-like pipeline tool for statistics and data science in R. The package skips costly runtime for tasks that are already up to date, orchestrates the necessary computation with implicit parallel computing, and abstracts files as R objects. If all the current output matches the current upstream code and data, then the whole pipeline is up to date, and the results are more trustworthy than otherwise. The methodology in this package borrows from GNU 'Make' (2015, ISBN:978-9881443519) and 'drake' (2018, <doi:10.21105/joss.00550>).
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data-sciencehigh-performance-computingmakepeer-reviewedpipeliner-targetopiareproducibilityreproducible-researchtargetsworkflow
15.38 score 1.1k stars 24 dependents 7.6k scripts 17k downloads
duckdb - DBI Package for the DuckDB Database Management System
The DuckDB project is an embedded analytical data management system with support for the Structured Query Language (SQL). This package includes all of DuckDB and an R Database Interface (DBI) connector.
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databaseduckdbolapcpp
15.23 score 215 stars 115 dependents 3.3k scripts 123k downloadsprophet - Automatic Forecasting Procedure
Implements a procedure for forecasting time series data based on an additive model where non-linear trends are fit with yearly, weekly, and daily seasonality, plus holiday effects. It works best with time series that have strong seasonal effects and several seasons of historical data. Prophet is robust to missing data and shifts in the trend, and typically handles outliers well.
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forecastingpythoncpp
14.69 score 20k stars 14 dependents 1.3k scripts 11k downloads
tidyterra - 'tidyverse' Methods and 'ggplot2' Helpers for 'terra' Objects
Extension of the 'tidyverse' for 'SpatRaster' and 'SpatVector' objects of the 'terra' package. It includes also new 'geom_' functions that provide a convenient way of visualizing 'terra' objects with 'ggplot2'.
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terraggplot-extensionr-spatialrspatialquarto
14.28 score 216 stars 36 dependents 3.9k scripts 21k downloadslitedown - A Lightweight Version of R Markdown
Render R Markdown to Markdown (without using 'knitr'), and Markdown to lightweight HTML or 'LaTeX' documents with the 'commonmark' package (instead of 'Pandoc'). Some missing Markdown features in 'commonmark' are also supported, such as raw HTML or 'LaTeX' blocks, 'LaTeX' math, superscripts, subscripts, footnotes, element attributes, and appendices, but not all 'Pandoc' Markdown features are (or will be) supported. With additional JavaScript and CSS, you can also create HTML slides and articles. This package can be viewed as a trimmed-down version of R Markdown and 'knitr'. It does not aim at rich Markdown features or a large variety of output formats (the primary formats are HTML and 'LaTeX'). Book and website projects of multiple input documents are also supported.
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litedownmarkdownr-markdownreport-generatorreproducible-research
13.93 score 258 stars 577 dependents 42 scripts 374k downloads
shinystan - Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models
A graphical user interface for interactive Markov chain Monte Carlo (MCMC) diagnostics and plots and tables helpful for analyzing a posterior sample. The interface is powered by the 'Shiny' web application framework from 'RStudio' and works with the output of MCMC programs written in any programming language (and has extended functionality for 'Stan' models fit using the 'rstan' and 'rstanarm' packages).
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bayesianbayesian-data-analysisbayesian-inferencebayesian-methodsbayesian-statisticsmcmcshiny-appsstanstatistical-graphics
13.71 score 199 stars 15 dependents 1.7k scripts 140k downloads
nanonext - Lightweight Toolkit for Messaging, Concurrency and the Web
R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. A toolkit for messaging, concurrency and the web. High-performance socket messaging over in-process, IPC, TCP, WebSocket and secure TLS transports implements 'Scalability Protocols', a standard for common communications patterns including publish/subscribe, request/reply and survey. A threaded concurrency framework with intuitive 'aio' objects that resolve automatically upon completion of asynchronous operations, and synchronisation primitives that allow R to wait on events signalled by concurrent threads. A unified HTTP server hosting REST endpoints, WebSocket connections and streaming on a single port, with a built-in HTTP client.
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concurrencyhttp-clienthttp-serveripc-messagemessaging-libraryrpcsocket-communicationsynchronization-primitivestcp-protocoltlswebsocketmbedtls
13.69 score 82 stars 170 dependents 63 scripts 82k downloadshuxtable - Easily Create and Style Tables for LaTeX, HTML and Other Formats
Creates styled tables for data presentation. Export to HTML, LaTeX, RTF, 'Word', 'Excel', 'PowerPoint', 'typst', SVG and PNG. Simple, modern interface to manipulate borders, size, position, captions, colours, text styles and number formatting. Table cells can span multiple rows and/or columns. Includes a 'huxreg' function to create regression tables, and 'quick_*' one-liners to print tables to a new document.
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htmlhuxtablelatexmicrosoft-wordpowerpointreproducible-researchtables
13.56 score 331 stars 17 dependents 2.1k scripts 15k downloadsqqman - Q-Q and Manhattan Plots for GWAS Data
Create Q-Q and manhattan plots for GWAS data from PLINK results.
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genomicsgwas
12.77 score 172 stars 20 dependents 2.9k scripts 7.9k downloadswk - Lightweight Well-Known Geometry Parsing
Provides a minimal R and C++ API for parsing well-known binary and well-known text representation of geometries to and from R-native formats. Well-known binary is compact and fast to parse; well-known text is human-readable and is useful for writing tests. These formats are useful in R only if the information they contain can be accessed in R, for which high-performance functions are provided here.
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cpp
12.44 score 51 stars 1.5k dependents 126 scripts 241k downloadsadbcdrivermanager - 'Arrow' Database Connectivity ('ADBC') Driver Manager
Provides a developer-facing interface to 'Arrow' Database Connectivity ('ADBC') for the purposes of driver development, driver testing, and building high-level database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is an API standard for database access libraries that uses 'Arrow' for result sets and query parameters.
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arrowdatabasecpp
12.38 score 588 stars 6 dependents 129 scripts 7.5k downloadsnanoarrow - Interface to the 'nanoarrow' 'C' Library
Provides an 'R' interface to the 'nanoarrow' 'C' library and the 'Apache Arrow' application binary interface. Functions to import and export 'ArrowArray', 'ArrowSchema', and 'ArrowArrayStream' 'C' structures to and from 'R' objects are provided alongside helpers to facilitate zero-copy data transfer among 'R' bindings to libraries implementing the 'Arrow' 'C' data interface.
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arrowlibzstdcpp
12.19 score 233 stars 51 dependents 52 scripts 26k downloads
crew - A Distributed Worker Launcher Framework
In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'NNG'-powered 'mirai' R package by Gao (2023) <doi:10.5281/zenodo.7912722> is a sleek and sophisticated scheduler that efficiently processes these intense workloads. The 'crew' package extends 'mirai' with a unifying interface for third-party worker launchers. Inspiration also comes from packages. 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischel, and Surmann (2017) <doi:10.21105/joss.00135>.
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high-performance-computing
11.61 score 151 stars 3 dependents 532 scripts 3.8k downloads
tarchetypes - Archetypes for Targets
Function-oriented Make-like declarative pipelines for Statistics and data science are supported in the 'targets' R package. As an extension to 'targets', the 'tarchetypes' package provides convenient user-side functions to make 'targets' easier to use. By establishing reusable archetypes for common kinds of targets and pipelines, these functions help express complicated reproducible pipelines concisely and compactly. The methods in this package were influenced by the 'targets' R package. by Will Landau (2018) <doi:10.21105/joss.00550>.
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data-sciencehigh-performance-computingpeer-reviewedpipeliner-targetopiareproducibilitytargetsworkflow
11.59 score 151 stars 12 dependents 3.6k scripts 5.6k downloads
rredlist - 'IUCN' Red List Client
'IUCN' Red List (<https://api.iucnredlist.org/>) client. The 'IUCN' Red List is a global list of threatened and endangered species. Functions cover all of the Red List 'API' routes. An 'API' key is required.
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iucnbiodiversityapiweb-servicestraitshabitatspeciesconservationapi-wrapperiucn-red-listtaxize
11.54 score 63 stars 13 dependents 272 scripts 7.0k downloads
cmdstanr - R Interface to 'CmdStan'
A lightweight interface to 'Stan' <https://mc-stan.org>. The 'CmdStanR' interface is an alternative to 'RStan' that calls the command line interface for compilation and running algorithms instead of interfacing with C++ via 'Rcpp'. This has many benefits including always being compatible with the latest version of Stan, fewer installation errors, fewer unexpected crashes in RStudio, and a more permissive license.
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bayesbayesianmarkov-chain-monte-carlomaximum-likelihoodmcmcstanvariational-inference
11.39 score 159 stars 7 dependents 8.8k scriptshttpgd - A 'HTTP' Server Graphics Device
A graphics device for R that is accessible via network protocols. This package was created to make it easier to embed live R graphics in integrated development environments and other applications. The included 'HTML/JavaScript' client (plot viewer) aims to provide a better overall user experience when dealing with R graphics. The device asynchronously serves graphics via 'HTTP' and 'WebSockets'.
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cpp
10.96 score 505 stars 690 scripts 7.2k downloads
projpred - Projection Predictive Feature Selection
Performs projection predictive feature selection for generalized linear models (Piironen, Paasiniemi, and Vehtari, 2020, <doi:10.1214/20-EJS1711>) with or without multilevel or additive terms (Catalina, Bürkner, and Vehtari, 2022, <https://proceedings.mlr.press/v151/catalina22a.html>), for some ordinal and nominal regression models (Weber, Glass, and Vehtari, 2025, <doi:10.1007/s00180-024-01506-0>), and for many other regression models (using the latent projection by Catalina, Bürkner, and Vehtari, 2021, <doi:10.48550/arXiv.2109.04702>, which can also be applied to most of the former models). The package is compatible with the 'rstanarm' and 'brms' packages, but other reference models can also be used. See the vignettes and the documentation for more information and examples.
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bayesbayesianbayesian-inferencebayesian-workflowrstanarmstanstatisticsvariable-selectionopenblascpp
10.87 score 114 stars 298 scripts 5.2k downloadswebchem - Chemical Information from the Web
Chemical information from around the web. This package interacts with a suite of web services for chemical information. Sources include: Alan Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver, ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet, NIST Chemistry WebBook, OPSIN, PubChem, SRS, Wikidata.
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cas-numberchemical-informationchemspideridentifierropensciwebscraping
10.66 score 184 stars 9 dependents 199 scripts 1.1k downloads
deeptime - Plotting Tools for Anyone Working in Deep Time
Extends the functionality of other plotting packages (notably 'ggplot2') to help facilitate the plotting of data over long time intervals, including, but not limited to, geological, evolutionary, and ecological data. The primary goal of 'deeptime' is to enable users to add highly customizable timescales to their visualizations. Other functions are also included to assist with other areas of deep time visualization.
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geologyggplot2paleontologyvisualization
10.45 score 106 stars 3 dependents 350 scripts 827 downloadspolars - R Bindings for the 'polars' Rust Library
Lightning-fast 'DataFrame' library written in 'Rust'. Convert R data to 'Polars' data and vice versa. Perform fast, lazy, larger-than-memory and optimized data queries. 'Polars' is interoperable with the package 'arrow', as both are based on the 'Apache Arrow' Columnar Format.
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arrowpolarsrust
10.21 score 561 stars 2 dependents 274 scripts 6 downloadsgeoarrow - Extension Types for Spatial Data for Use with 'Arrow'
Provides extension types and conversions to between R-native object types and 'Arrow' columnar types. This includes integration among the 'arrow', 'nanoarrow', 'sf', and 'wk' packages such that spatial metadata is preserved wherever possible. Extension type implementations ensure first-class geometry data type support in the 'arrow' and 'nanoarrow' packages.
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cpp
9.53 score 185 stars 10 dependents 181 scripts 4.9k downloadsweathercan - Download Weather Data from Environment and Climate Change Canada
Provides means for downloading historical weather data from the Environment and Climate Change Canada website (<https://climate.weather.gc.ca/historical_data/search_historic_data_e.html>). Data can be downloaded from multiple stations and over large date ranges and automatically processed into a single dataset. Tools are also provided to identify stations either by name or proximity to a location.
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environment-canadapeer-reviewedweather-dataweather-downloader
9.18 score 117 stars 222 scripts
santoku - A Versatile Cutting Tool
A tool for cutting data into intervals. Allows singleton intervals. Always includes the whole range of data by default. Flexible labelling. Convenience functions for cutting by quantiles etc. Handles dates, times, units and other vectors.
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cpp
8.75 score 147 stars 2 dependents 124 scripts 1.0k downloads
tidypolars - More Efficient Tidyverse Code, Using Polars in the Background
Polars is a cross-language tool for manipulating very large data. However, one drawback is that the R implementation has a syntax that will look odd to many R users who are not used to Python syntax. The objective of tidypolars is to improve the ease-of-use of Polars in R by providing tidyverse syntax to polars.
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8.73 score 234 stars 59 scriptssecretbase - Cryptographic Hash Functions and Data Encoding
Fast and memory-efficient streaming hash functions, binary/text encoding and serialization. Hashes strings and raw vectors directly. Stream hashes files which can be larger than memory, as well as in-memory objects through R's serialization mechanism. Implements the SHA-256, SHA-3 and 'Keccak' cryptographic hash functions, SHAKE256 extendable-output function (XOF), 'SipHash' pseudo-random function, base64 and base58 encoding, 'CBOR' and 'JSON' serialization.
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base58checkbase64cborcryptographic-hash-functionsextendable-output-functionskeccaksha256sha3shake256siphash
8.45 score 19 stars 32 dependents 13 scripts 20k downloadssedonadb - Bindings for Apache SedonaDB
Provides bindings for Apache SedonaDB, a lightweight query engine optimized for spatial workflows.
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cdatabasegeospatialhacktoberfestpythonrustspatial-analysisspatial-queryspatial-sqlcargogeos
8.24 score 462 stars 1 dependents 20 scriptsadbcbigquery - 'Arrow' Database Connectivity ('ADBC') 'BigQuery' Driver
Provides a developer-facing interface to the 'Arrow' Database Connectivity ('ADBC') 'BigQuery' driver for the purposes of building high-level database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is an API standard for database access libraries that uses 'Arrow' for result sets and query parameters.
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arrowdatabasegolang
8.14 score 588 stars 1 scriptsadbcflightsql - 'Arrow' Database Connectivity ('ADBC') 'FlightSQL' Driver
Provides a developer-facing interface to the 'Arrow' Database Connectivity ('ADBC') 'FlightSQL' driver for the purposes of building high-level database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is an API standard for database access libraries that uses 'Arrow' for result sets and query parameters.
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arrowdatabasegolang
8.14 score 588 stars 2 scriptsadbcsnowflake - Arrow Database Connectivity ('ADBC') 'Snowflake' Driver
Provides a developer-facing interface to the 'Arrow' Database Connectivity ('ADBC') 'Snowflake' driver for the purposes of building high-level database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is an API standard for database access libraries that uses 'Arrow' for result sets and query parameters.
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arrowdatabasegolang
8.14 score 588 stars 5 scripts
unigd - Universal Graphics Device
A unified R graphics backend. Render R graphics fast and easy to many common file formats. Provides a thread safe 'C' interface for asynchronous rendering of R graphics.
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cairotifflibpngzlibcpp
7.96 score 28 stars 1 dependents 9 scripts 6.0k downloads
geotargets - 'targets' Extensions for Geographic Spatial Formats
Provides extensions for various geographic spatial file formats, such as shape files and rasters. Currently provides support for the 'terra' geographic spatial formats. See the vignettes for worked examples, demonstrations, and explanations of how to use the various package extensions.
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geospatialpipeliner-targetopiarasterreproducibilityreproducible-researchtargetsvectorworkflow
7.94 score 93 stars 117 scripts 591 downloads
ichimoku - Visualization and Tools for Ichimoku Kinko Hyo Strategies
An implementation of 'Ichimoku Kinko Hyo', also commonly known as cloud charts. Static and interactive visualizations with tools for creating, backtesting and development of quantitative ichimoku strategies. As described in Sasaki (1996, ISBN:4925152009), the technique is a refinement on candlestick charting, originating from Japan and now in widespread use in technical analysis worldwide. Translating as one-glance equilibrium chart, it allows the price action and market structure of financial securities to be determined at-a-glance. Incorporates an interface with the 'OANDA fxTrade' API <https://developer.oanda.com/> for retrieving historical and live streaming price data for major currencies, metals, commodities, government bonds and stock indices.
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ichimokuichimoku-cloudoandaquantitative-finance
6.88 score 36 stars 35 scripts 336 downloads
rwasm - Build R Packages for WebAssembly
Utility functions to help build R packages compiled for WebAssembly (Wasm), manage Wasm binary R package libraries and repositories, and prepare webR compatible filesystem images for static web hosting of data files and R packages.
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6.52 score 83 stars 9 scripts
prqlr - R Bindings for the 'prqlc' Rust Library
Provides a function to convert 'PRQL' strings to 'SQL' strings. Combined with other R functions that take 'SQL' as an argument, 'PRQL' can be used on R.
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prqlrustsql
6.50 score 58 stars 18 scripts 613 downloadsriem - Accesses Weather Data from the Iowa Environment Mesonet
Allows to get weather data from Automated Surface Observing System (ASOS) stations (airports) in the whole world thanks to the Iowa Environment Mesonet website.
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airportsasosiowa-environment-mesonetmetarpeer-reviewedtemperatureweatherweather-api
6.46 score 47 stars 206 scripts 449 downloadsdoctest - Generate Tests from Examples Using 'roxygen' and 'testthat'
Creates 'testthat' tests from 'roxygen' examples using simple tags.
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6.45 score 31 stars 3 scripts 347 downloadsstring2path - Rendering Font into 'data.frame'
Extract glyph information from font data, and translate the outline curves to flattened paths or tessellated polygons. The converted data is returned as a 'data.frame' in easy-to-plot format.
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rustcargofontconfig
6.36 score 103 stars 13 scripts 8.6k downloadstaxizedb - Offline Access to Taxonomic Databases
Download taxonomic databases, convert them into 'SQLite' format, and query them locally for fast, reliable, and reproducible access to taxonomic data.
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itistaxizetaxonomic-databasestaxonomy
6.36 score 33 stars 116 scripts 324 downloadsSBC - Simulation Based Calibration for Bayesian models
SBC helps perform Simulation Based Calibration on Bayesian models. SBC lets you check for bugs in your model code and/or algorithm that fits the model. SBC focuses on models built with 'Stan' <https://mc-stan.org>, but can support other modelling languages as well.
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diagnosticssimulation-based-inference
6.30 score 62 stars 130 scripts
ggsurveillance - Tools for Outbreak Investigation/Infectious Disease Surveillance
Create epicurves, epigantt charts, and diverging bar charts using 'ggplot2'. Prepare data for visualisation or other reporting for infectious disease surveillance and outbreak investigation (time series data). Includes tidy functions to solve date based transformations for common reporting tasks, like (A) seasonal date alignment for respiratory disease surveillance, (B) date-based case binning based on specified time intervals like isoweek, epiweek, month and more, (C) automated detection and marking of the new year based on the date/datetime axis of the 'ggplot2', (D) labelling of the last value of a time-series. An introduction on how to use epicurves can be found on the US CDC website (2012, <https://www.cdc.gov/training/quicklearns/epimode/index.html>).
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epidemiologyinfectious-disease-surveillanceinfectious-diseasesoutbreaks
6.29 score 10 stars 6 scripts 253 downloads
jagstargets - Targets for JAGS Pipelines
Bayesian data analysis usually incurs long runtimes and cumbersome custom code. A pipeline toolkit tailored to Bayesian statisticians, the 'jagstargets' R package is leverages 'targets' and 'R2jags' to ease this burden. 'jagstargets' makes it super easy to set up scalable JAGS pipelines that automatically parallelize the computation and skip expensive steps when the results are already up to date. Minimal custom code is required, and there is no need to manually configure branching, so usage is much easier than 'targets' alone. For the underlying methodology, please refer to the documentation of 'targets' <doi:10.21105/joss.02959> and 'JAGS' (Plummer 2003) <https://www.r-project.org/conferences/DSC-2003/Proceedings/Plummer.pdf>.
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bayesianhigh-performance-computingjagsmaker-targetopiareproducibilityrjagsstatisticstargetscpp
6.25 score 11 stars 40 scripts 660 downloadsposteriordb - R Functionality for PosteriorDB
R functionality of easy handling of the posteriordb posteriors.
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6.12 score 9 stars 117 scripts
trelliscope - Create Interactive Multi-Panel Displays
Trelliscope enables interactive exploration of data frames of visualizations.
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visualization
5.94 score 32 stars 137 scripts 6 downloads
geographr - R package for mapping UK geographies
A package to distribute and compute on UK geographical data.
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5.92 score 43 stars 482 scriptsbridgestan - BridgeStan, Accessing Stan Model Functions in R
BridgeStan provides efficient in-memory access to the methods of a Stan model, including log densities, gradients, Hessians, and constraining and unconstraining transforms.
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ccppjuliapythonstan
5.92 score 115 stars 10 scriptsRmlx - R Interface to MLX Arrays (GPU-Accelerated with Metal or CUDA)
S3 class 'mlx' backed by Apple's MLX library, allowing array operations on Apple Silicon GPUs/CPUs and CUDA-enabled Linux systems through lazy evaluation, shared memory between chips, and automatic differentiation.
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openblascpp
5.66 score 18 stars 13 scriptssaperlipopette - Create Example Git Messes
Holds functions creating Git messes, that users would then solve, to follow <https://ohshitgit.com/>.
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gitquarto
5.43 score 34 stars 7 scriptsrcheology - Data on Base and Recommended Packages for Current and Previous Versions of R
Provides a dataset of functions in all base and recommended packages of R versions 0.50 onwards.
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history-of-computing
5.37 score 39 stars 1 dependents 9 scripts 683 downloads
ggmagnify - Create a Magnified Inset of Part of a "Ggplot" Object
Creates a magnified inset of a ggplot, with projection lines and borders around the target area and inset, plus optional shadow. Rectangular, elliptical or arbitrary regions can be magnified. Works with facets and maps. Geoms can optionally be recomputed within the inset area.
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ggplotgraphics
5.31 score 310 stars 133 scripts
ggtypst - Render High-Quality Text and Formulas in 'ggplot2' by Typst
Provides a seamless integration of the 'Typst' typesetting engine into 'ggplot2'. It allows users to render complex mathematical formulas, equations, and rich text directly in plot annotations, axis labels, and titles without requiring a local Typst or LaTeX installation. Under the hood, it leverages Rust FFI to compile Typst code into SVG.
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ggplot2typstrustcargo
4.91 score 27 stars 7 scripts
crew.aws.batch - A Crew Launcher Plugin for AWS Batch
In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'crew.aws.batch' package extends the 'mirai'-powered 'crew' package with a worker launcher plugin for AWS Batch. Inspiration also comes from packages 'mirai' by Gao (2023) <https://github.com/r-lib/mirai>, 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischl, and Surmann (2017). <doi:10.21105/joss.00135>.
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aws-batchcrewhigh-performance-computing
4.73 score 18 stars 9 scripts 651 downloadstidytab - Create Tables of Frequencies
Functions to create tables of frequencies.
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exploratory-data-analysistidy-table
4.58 score 21 stars 60 scripts
healthyr - R package for mapping UK health data
A package to distribute and summarise on UK health data.
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4.30 score 5 stars 133 scripts
asylum - Data on Asylum and Resettlement for the UK
Data on Asylum and Resettlement for the UK, provided by the Home Office <https://www.gov.uk/government/statistical-data-sets/immigration-system-statistics-data-tables>.
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4.23 score 3 stars 38 scripts 822 downloads
mutagen - Extensions to dplyr's mutate
Extensions to dplyr's mutate.
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dplyrmutate
4.08 score 17 stars 2 scriptskgp - 1000 Genomes Project Metadata
Metadata about populations and data about samples from the 1000 Genomes Project, including the 2,504 samples sequenced for the Phase 3 release and the expanded collection of 3,202 samples with 602 additional trios. The data is described in Auton et al. (2015) <doi:10.1038/nature15393> and Byrska-Bishop et al. (2022) <doi:10.1016/j.cell.2022.08.004>, and raw data is available at <http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/>. See Turner (2022) <doi:10.48550/arXiv.2210.00539> for more details.
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1000genomesbioinformaticsgeneticsgenomicsmetadatapopulation-geneticssequencing
4.02 score 21 stars 7 scripts 185 downloadsonetime - Run Code Only Once
Allows code to be run only once on a given computer, using lockfiles. Typical use cases include startup messages shown only when a package is loaded for the very first time.
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4.00 score 2 stars 7 scripts 183 downloads
ExpBites - Analyzing Human Exposure to Mosquito Biting
Tools to analyse human and mosquito behavioral interactions and to compute exposure to mosquito bites estimates. Using behavioral data for human individuals and biting patterns for mosquitoes, you will be able to compute hourly exposure for bed net users and non-users, and summarize (e.g. proportion indoors and outdoors, proportion per time periods, and proportion prevented by bed nets) or visualize these dynamics across a 24-hour cycle.
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3.60 score 4 stars 2 scripts 145 downloads
demographr - R package for mapping UK demographics
A package to distribute UK demographic data.
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3.53 score 2 stars 67 scriptsbedrockbio - Open-Access Computational Biology Datasets
Efficiently access the 'Bedrock Bio' library of open-access computational biology datasets. Lazily query datasets backed by 'DuckDB' and 'Apache Iceberg', with support for predicate pushdown and column projection to the cloud storage backend. This enables quick, iterative access to otherwise massive, unwieldy datasets without downloading them in full. See <https://bedrock.bio> for available datasets and documentation.
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3.48 score 1 stars 12 scripts 203 downloadstargetsketch - Create and Visualize Targets Pipelines
A Shiny app for creating and visualizing targets pipelines (<https://github.com/wlandau/targets>). Simply supply a _targets.R file with the pipeline and supporting functions, and the app shows a dependency graph and manifest.
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data-sciencehigh-performance-computingpipelinereproducibilityshinytargetsworkflow
3.43 score 18 stars 1 scriptsvoucher - 'Trustdown' Interface for R
A R interface to the 'vouch' project (<https://github.com/mitchellh/vouch>), which bills itself as "a community trust management system based on explicit vouches to participate". 'vouch' is a 'Nushell' module, so 'voucher' provides a R application programming interface (API) to modify the 'VOUCHED.td' database without 'Nushell'. 'voucher' does not depend on 'vouch' or 'Nushell'.
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3.18 score 2 scripts 450 downloadsahocorasick - Fast Multi-Pattern String Matching with the 'Aho-Corasick' Algorithm
Provide fast multi-pattern string matching for 'R' using the 'Aho-Corasick' algorithm, powered by the 'Rust' 'aho-corasick' crate. It builds reusable automatons for detecting matches, counting matches, locating character, extracting matched text, and replacing matches in character vectors. For more details on the 'Aho-Corasick' algorithm, please see Aho and Corasick (1975) <doi:10.1145/360825.360855>.
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aho-corasickrustcargo
3.00 score 1 stars 3 scripts
milRex - Query Military Expenditure Data From SIPRI
Queries data from the Military Expenditure Database by SIPRI.
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3.00 score 2 stars 1 scriptsglaredb - R Bindings for 'GlareDB'
R bindings for 'GlareDB', an analytical database based on 'Apache Arrow' and 'Apache DataFusion' that can connect to various data sources and execute queries.
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arrowglaredbrustsql
2.90 score 4 stars 6 scriptsRmlxStats - MLX-Accelerated Statistical Models
Fast statistical routines on Apple Silicon using the Rmlx package.
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2.78 score 1 starstruelies - Bayesian Methods to Estimate the Proportion of Liars in Coin Flip Experiments
Implements Bayesian methods, described in Hugh-Jones (2019) <doi:10.1007/s40881-019-00069-x>, for estimating the proportion of liars in coin flip-style experiments, where subjects report a random outcome and are paid for reporting a "good" outcome.
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experimentlying
2.70 score 2 scripts 162 downloads
loneliness - A Loneliness Prescription Index for the UK
A loneliness prescription index for the UK.
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2.51 score 2 stars 16 scriptstidytensor - TidyTensor
Provides functions for working with tensors (vectors, matrices, or multidimensional arrays) as named hierarchical data structures.
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2.30 score 4 stars 1 scripts
audio.vadwebrtc - Voice Activity Detection using the 'webrtc' Toolkit
Voice Activity Detection using the 'webrtc' toolkit. Identify the locations in audio files where there is an active voice. The is done based on a Gaussian Mixture Model implemented in the 'webrtc' framework.
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cpp
2.00 score 2 stars 7 scriptsbootstrapper - Opinionated R Package Quickstart
Bootstrap new R packages with strongly opinionated defaults. Creates the package scaffold, wires up tests, README and NEWS, configures GitHub Actions and Dependabot, adds Air/Jarl setup, and drop in a default AGENTS.md for building R packages.
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1.70 score 4 scripts