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-graphfortranlibxml2glpkopenblascpp
21.32 score 604 stars 2.0k dependents 40k scripts 563k 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.
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20.19 score 545 stars 16k dependents 13k scripts 1.8M 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
19.86 score 16k stars 139 dependents 15k scripts 545k 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
19.04 score 690 stars 15k dependents 1.8k scripts 1.7M 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
18.54 score 298 stars 14k dependents 1.1k scripts 1.6M 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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bayesianggplot2mcmcpandocstanstatistical-graphicsvisualization
18.25 score 440 stars 98 dependents 9.4k scripts 234k 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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17.70 score 476 stars 8.2k dependents 206 scripts 1.2M 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
17.18 score 155 stars 298 dependents 3.6k scripts 379k 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
16.88 score 168 stars 355 dependents 4.3k scripts 394k 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
16.47 score 400 stars 14 dependents 6.8k scripts 27k 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
16.39 score 147 stars 2.8k dependents 346 scripts 718k 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
16.08 score 20k stars 15 dependents 1.3k scripts 18k 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
15.36 score 1.0k stars 23 dependents 5.5k scripts 19k downloads
mirai - Minimalist Async Evaluation Framework for R
Designed for simplicity, a 'mirai' evaluates an R expression asynchronously, locally or distributed over the network. Built on 'nanonext' and 'NNG' for modern networking and concurrency, scales efficiently to millions of tasks over thousands of persistent parallel processes. Provides optimal scheduling over fast 'IPC', TCP, and TLS connections, integrating with SSH or cluster managers. Implements event-driven promises for reactive programming, and supports custom serialization for cross-language data types.
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asyncasynchronous-tasksconcurrencydistributed-computinghigh-performance-computingparallel-computing
15.26 score 296 stars 72 dependents 364 scripts 49k downloadsshinystan - 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
14.42 score 200 stars 16 dependents 1.6k scripts 213k 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
14.18 score 200 stars 76 dependents 2.2k scripts 40k 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
14.03 score 237 stars 534 dependents 31 scripts 463k 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-spatialrspatial
13.65 score 210 stars 33 dependents 2.6k scripts 16k 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
12.81 score 171 stars 20 dependents 2.7k scripts 9.3k 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
12.21 score 155 stars 9 dependents 8.0k scripts
nanonext - NNG (Nanomsg Next Gen) Lightweight Messaging Library
R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is a socket library for reliable, high-performance 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 service discovery. As its own threaded concurrency framework, provides a toolkit for asynchronous programming and distributed computing. Intuitive 'aio' objects resolve automatically when asynchronous operations complete, and synchronisation primitives allow R to wait upon events signalled by concurrent threads.
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concurrencyhttpsipc-messagemessaging-librarynngrpcsocket-communicationsynchronization-primitivestcp-protocolwebsocketmbedtls
12.16 score 75 stars 78 dependents 48 scripts 43k 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
12.13 score 526 stars 6 dependents 106 scripts 6.3k 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
12.05 score 61 stars 23 dependents 261 scripts 7.6k 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
11.91 score 216 stars 36 dependents 46 scripts 27k 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
11.82 score 147 stars 3 dependents 404 scripts 5.9k 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
11.61 score 146 stars 10 dependents 2.5k 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-inferencerstanarmstanstatisticsvariable-selectionopenblascpp
11.33 score 113 stars 289 scripts 9.9k 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
11.22 score 174 stars 9 dependents 172 scripts 3.3k 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
10.11 score 541 stars 2 dependents 223 scripts 4 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
10.01 score 104 stars 3 dependents 340 scripts 1.0k downloadshttpgd - 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
8.87 score 481 stars 428 scripts 128 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
8.87 score 114 stars 219 scripts 3 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
8.63 score 92 stars 115 scripts 628 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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8.52 score 218 stars 45 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
8.05 score 526 stars 1 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
8.05 score 526 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
8.05 score 526 stars 2 scriptssecretbase - Cryptographic Hash, Extendable-Output and Base64 Functions
Fast and memory-efficient streaming hash functions and base64 encoding / decoding. 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. Implementations include the SHA-256, SHA-3 and 'Keccak' cryptographic hash functions, SHAKE256 extendable-output function (XOF), and 'SipHash' pseudo-random function.
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base64cryptographic-hash-functionsextendable-output-functionskeccaksha256sha3shake256siphash
7.66 score 12 stars 25 dependents 13 scripts 16k downloads
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
7.27 score 58 stars 18 scripts 621 downloads
riem - 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
6.88 score 45 stars 189 scripts 473 downloads
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
6.77 score 24 stars 1 dependents 9 scripts 1.4k downloads
taxizedb - 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
6.67 score 33 stars 119 scripts 422 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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rustcargo
6.67 score 101 stars 12 scripts 19k 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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6.66 score 77 stars 7 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
6.36 score 9 stars 6 scripts 275 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 710 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 scripts
trelliscope - Create Interactive Multi-Panel Displays
Trelliscope enables interactive exploration of data frames of visualizations.
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visualization
5.87 score 32 stars 115 scripts 12 downloadsbridgestan - 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
5.84 score 107 stars 10 scriptsposteriordb - R Functionality for PosteriorDB
R functionality of easy handling of the posteriordb posteriors.
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5.75 score 9 stars 124 scriptsSBC - Simulation Based Calibration for rstan/cmdstanr 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
5.28 score 62 stars 124 scripts
stantargets - Targets for Stan Workflows
Bayesian data analysis usually incurs long runtimes and cumbersome custom code. A pipeline toolkit tailored to Bayesian statisticians, the 'stantargets' R package leverages 'targets' and 'cmdstanr' to ease these burdens. 'stantargets' makes it super easy to set up scalable Stan 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. 'stantargets' can access all of 'cmdstanr''s major algorithms (MCMC, variational Bayes, and optimization) and it supports both single-fit workflows and multi-rep simulation studies. For the statistical methodology, please refer to 'Stan' documentation (Stan Development Team 2020) <https://mc-stan.org/>.
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bayesianhigh-performance-computingmaker-targetopiareproducibilitystanstatisticstargets
5.23 score 50 stars 225 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
4.95 score 18 stars 6 scripts 700 downloads
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 132 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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4.22 score 3 stars 37 scripts 686 downloadssaperlipopette - Create Example Git Messes
Holds functions creating Git messes, that users would then solve, to follow <https://ohshitgit.com/>.
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git
4.09 score 31 stars 2 scriptstidytab - Create Tables of Frequencies
Functions to create tables of frequencies.
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exploratory-data-analysistidy-table
4.08 score 21 stars 57 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
4.00 score 20 stars 5 scripts 157 downloads
mutagen - Extensions to dplyr's mutate
Extensions to dplyr's mutate.
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dplyrmutate
3.93 score 17 stars 2 scripts
demographr - R package for mapping UK demographics
A package to distribute UK demographic data.
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3.56 score 2 stars 60 scripts
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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3.48 score 2 stars 2 scripts 218 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 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 scripts
loneliness - A Loneliness Prescription Index for the UK
A loneliness prescription index for the UK.
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2.68 score 2 stars 16 scripts
tidytensor - 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.
Last updated
cpp
1.70 score 1 stars 6 scripts