writexl - Export Data Frames to Excel 'xlsx' Format
Zero-dependency data frame to xlsx exporter based on 'libxlsxwriter' <https://libxlsxwriter.github.io>. Fast and no Java or Excel required.
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excellibxlsxwriterxlsxzlib
17.86 score 214 stars 270 dependents 18k scripts 263k downloadsmagick - Advanced Graphics and Image-Processing in R
Bindings to 'ImageMagick': the most comprehensive open-source image processing library available. Supports many common formats (png, jpeg, tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio images are automatically previewed when printed to the console, resulting in an interactive editing environment. Also includes a graphics device for creating drawing onto images using pixel coordinates.
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image-manipulationimage-processingimagemagickcpp
17.67 score 484 stars 334 dependents 18k scripts 159k downloads
skimr - Compact and Flexible Summaries of Data
A simple to use summary function that can be used with pipes and displays nicely in the console. The default summary statistics may be modified by the user as can the default formatting. Support for data frames and vectors is included, and users can implement their own skim methods for specific object types as described in a vignette. Default summaries include support for inline spark graphs. Instructions for managing these on specific operating systems are given in the "Using skimr" vignette and the README.
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peer-reviewedropenscisummary-statisticsunconfunconf17
16.86 score 1.1k stars 16 dependents 23k scripts 38k downloads
rnaturalearth - World Map Data from Natural Earth
Facilitates mapping by making natural earth map data from <https://www.naturalearthdata.com/> more easily available to R users.
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peer-reviewed
16.48 score 267 stars 60 dependents 15k scripts 30k downloads
gert - Simple Git Client for R
Simple git client for R based on 'libgit2' <https://libgit2.org> with support for SSH and HTTPS remotes. All functions in 'gert' use basic R data types (such as vectors and data-frames) for their arguments and return values. User credentials are shared with command line 'git' through the git-credential store and ssh keys stored on disk or ssh-agent.
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libgit2
15.56 score 162 stars 381 dependents 506 scripts 180k downloadsrentrez - 'Entrez' in R
Provides an R interface to the NCBI's 'EUtils' API, allowing users to search databases like 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and 'PubMed' <https://pubmed.ncbi.nlm.nih.gov/>, process the results of those searches and pull data into their R sessions.
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15.26 score 221 stars 129 dependents 1.3k scripts 60k 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
15.20 score 1.1k stars 28 dependents 7.3k scripts 13k downloads
osmdata - Import 'OpenStreetMap' Data as Simple Features or Spatial Objects
Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web server (<https://overpass-api.de/>) and processed with very fast 'C++' routines for return to 'R'.
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open0street0mapopenstreetmapoverpass0apiosmcpposm-dataoverpass-apipeer-reviewedcpp
15.02 score 343 stars 19 dependents 4.0k scripts 8.0k downloadspdftools - Text Extraction, Rendering and Converting of PDF Documents
Utilities based on 'libpoppler' <https://poppler.freedesktop.org> for extracting text, fonts, attachments and metadata from a PDF file. Also supports high quality rendering of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for further processing in R.
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pdf-filespdf-formatpdftoolspopplerpoppler-librarytext-extractioncpp
14.29 score 554 stars 67 dependents 4.9k scripts 64k downloads
rgbif - Interface to the Global Biodiversity Information Facility API
A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/developer/summary>). GBIF is a database of species occurrence records from sources all over the globe. rgbif includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, getting counts of occurrence records, and using the GBIF tile map service to make rasters summarizing huge amounts of data.
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gbifspecimensapiweb-servicesoccurrencesspeciestaxonomybiodiversitydatalifewatchoscibiospocc
13.99 score 184 stars 27 dependents 2.9k scripts 11k downloads
visdat - Preliminary Visualisation of Data
Create preliminary exploratory data visualisations of an entire dataset to identify problems or unexpected features using 'ggplot2'.
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exploratory-data-analysismissingnesspeer-reviewedropenscivisualisation
13.72 score 463 stars 14 dependents 2.9k scripts 21k downloads
crul - HTTP Client
A simple HTTP client, with tools for making HTTP requests, and mocking HTTP requests. The package is built on R6, and takes inspiration from Ruby's 'faraday' gem (<https://rubygems.org/gems/faraday>). The package name is a play on curl, the widely used command line tool for HTTP, and this package is built on top of the R package 'curl', an interface to 'libcurl' (<https://curl.se/libcurl/>).
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httphttpsapiweb-servicescurldownloadlibcurlasyncmockingcaching
12.85 score 108 stars 151 dependents 90 scripts 21k downloadstaxize - Taxonomic Information from Around the Web
Interacts with a suite of web application programming interfaces (API) for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. Some of the services supported include 'NCBI E-utilities' (<https://www.ncbi.nlm.nih.gov/books/NBK25501/>), 'Encyclopedia of Life' (<https://eol.org/docs/what-is-eol/data-services>), 'Global Biodiversity Information Facility' (<https://techdocs.gbif.org/en/openapi/>), and many more. Links to the API documentation for other supported services are available in the documentation for their respective functions in this package.
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taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperbiodiversitydarwincoredatataxize
12.69 score 303 stars 13 dependents 1.5k scripts 5.4k downloadsreadODS - Read and Write ODS Files
Read ODS (OpenDocument Spreadsheet) into R as data frame. Also support writing data frame into ODS file.
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cpp
12.68 score 60 stars 30 dependents 1.1k scripts 11k downloadsgit2r - Provides Access to Git Repositories
Interface to the 'libgit2' library, which is a pure C implementation of the 'Git' core methods. Provides access to 'Git' repositories to extract data and running some basic 'Git' commands.
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gitgit-clientlibgit2libgit2-library
12.62 score 223 stars 39 dependents 1.1k scripts 30k downloads
treeio - Base Classes and Functions for Phylogenetic Tree Input and Output
'treeio' is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.
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softwareannotationclusteringdataimportdatarepresentationalignmentmultiplesequencealignmentphylogeneticsexporterparserphylogenetic-trees
12.55 score 103 stars 153 dependents 2.9k scriptshunspell - High-Performance Stemmer, Tokenizer, and Spell Checker
Low level spell checker and morphological analyzer based on the famous 'hunspell' library <https://hunspell.github.io>. The package can analyze or check individual words as well as parse text, latex, html or xml documents. For a more user-friendly interface use the 'spelling' package which builds on this package to automate checking of files, documentation and vignettes in all common formats.
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hunspellspell-checkspellcheckerstemmertokenizercpp
12.37 score 116 stars 38 dependents 462 scripts 63k downloadscommonmark - High Performance CommonMark and Github Markdown Rendering in R
The CommonMark specification <https://github.github.com/gfm/> defines a rationalized version of markdown syntax. This package uses the 'cmark' reference implementation for converting markdown text into various formats including html, latex and groff man. In addition it exposes the markdown parse tree in xml format. Also includes opt-in support for GFM extensions including tables, autolinks, and strikethrough text.
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cmarkcmark-gfmgfmmarkdown
12.27 score 102 stars 2.7k dependents 4 scripts 630k 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
12.20 score 186 stars 13 dependents 228 scripts 1.2k downloadssodium - A Modern and Easy-to-Use Crypto Library
Bindings to 'libsodium' <https://doc.libsodium.org/>: a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. Sodium uses curve25519, a state-of-the-art Diffie-Hellman function by Daniel Bernstein, which has become very popular after it was discovered that the NSA had backdoored Dual EC DRBG.
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libsodium
12.11 score 74 stars 61 dependents 425 scripts 28k downloads
rotl - Interface to the 'Open Tree of Life' API
An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.
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metadataropensciphylogeneticsindependant-contrastsbiodiversitypeer-reviewedphylogenytaxonomy
11.96 score 46 stars 18 dependents 474 scripts 5.2k downloads
goodpractice - Advice on R Package Building
Give advice about good practices when building R packages. Advice includes functions and syntax to avoid, package structure, code complexity, code formatting, etc.
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11.75 score 481 stars 4 dependents 108 scripts 1.5k downloads
rix - Reproducible Data Science Environments with 'Nix'
Simplifies the creation of reproducible data science environments using the 'Nix' package manager, as described in Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()` function generates a complete description of the environment as a `default.nix` file, which can then be built using 'Nix'. This results in project specific software environments with pinned versions of R, packages, linked system dependencies, and other tools or programming languages such as Python or Julia. Additional helpers make it easy to run R code in 'Nix' software environments for testing and production.
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nixpeer-reviewedreproducibilityreproducible-research
11.67 score 384 stars 269 scripts 399 downloadstokenizers - Fast, Consistent Tokenization of Natural Language Text
Convert natural language text into tokens. Includes tokenizers for shingled n-grams, skip n-grams, words, word stems, sentences, paragraphs, characters, shingled characters, lines, Penn Treebank, regular expressions, as well as functions for counting characters, words, and sentences, and a function for splitting longer texts into separate documents, each with the same number of words. The tokenizers have a consistent interface, and the package is built on the 'stringi' and 'Rcpp' packages for fast yet correct tokenization in 'UTF-8'.
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nlppeer-reviewedtext-miningtokenizercpp
11.61 score 188 stars 79 dependents 22 scripts 35k downloads
EML - Read and Write Ecological Metadata Language Files
Work with Ecological Metadata Language ('EML') files. 'EML' is a widely used metadata standard in the ecological and environmental sciences, described in Jones et al. (2006), <doi:10.1146/annurev.ecolsys.37.091305.110031>.
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emleml-metadatametadata-standard
11.48 score 101 stars 10 dependents 338 scripts 1.6k downloadsassertr - Assertive Programming for R Analysis Pipelines
Provides functionality to assert conditions that have to be met so that errors in data used in analysis pipelines can fail quickly. Similar to 'stopifnot()' but more powerful, friendly, and easier for use in pipelines.
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analysis-pipelineassertion-libraryassertion-methodsassertionspeer-reviewedpredicate-functions
11.35 score 484 stars 9 dependents 852 scripts 2.1k downloadsbiomartr - Genomic Data Retrieval
Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. with only one command.
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biomartgenomic-data-retrievalannotation-retrievaldatabase-retrievalncbiensemblbiological-data-retrievalensembl-serversgenomegenome-annotationgenome-retrievalgenomicsmeta-analysismetagenomicsncbi-genbankpeer-reviewedproteomesequenced-genomes
11.13 score 226 stars 3 dependents 178 scripts 1.3k downloads
credentials - Tools for Managing SSH and Git Credentials
Setup and retrieve HTTPS and SSH credentials for use with 'git' and other services. For HTTPS remotes the package interfaces the 'git-credential' utility which 'git' uses to store HTTP usernames and passwords. For SSH remotes we provide convenient functions to find or generate appropriate SSH keys. The package both helps the user to setup a local git installation, and also provides a back-end for git/ssh client libraries to authenticate with existing user credentials.
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gitpasswordssh
11.11 score 75 stars 398 dependents 2 scripts 144k downloads
osfr - Interface to the 'Open Science Framework' ('OSF')
An interface for interacting with 'OSF' (<https://osf.io>). 'osfr' enables you to access open research materials and data, or create and manage your own private or public projects.
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open-scienceosfreproducible-research
11.09 score 154 stars 11 dependents 748 scripts 853 downloads
openalexR - Getting Bibliographic Records from 'OpenAlex' Database Using 'DSL' API
A set of tools to extract bibliographic content from 'OpenAlex' database using API <https://help.openalex.org/>.
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bibliographic-databibliographic-databasebibliometricsbibliometrixscience-mapping
11.07 score 150 stars 7 dependents 443 scripts 16k downloads
stplanr - Sustainable Transport Planning
Tools for transport planning with an emphasis on spatial transport data and non-motorized modes. The package was originally developed to support the 'Propensity to Cycle Tool', a publicly available strategic cycle network planning tool (Lovelace et al. 2017) <doi:10.5198/jtlu.2016.862>, but has since been extended to support public transport routing and accessibility analysis (Moreno-Monroy et al. 2017) <doi:10.1016/j.jtrangeo.2017.08.012> and routing with locally hosted routing engines such as 'OSRM' (Lowans et al. 2023) <doi:10.1016/j.enconman.2023.117337>. The main functions are for creating and manipulating geographic "desire lines" from origin-destination (OD) data (building on the 'od' package); calculating routes on the transport network locally and via interfaces to routing services such as <https://cyclestreets.net/> (Desjardins et al. 2021) <doi:10.1007/s11116-021-10197-1>; and calculating route segment attributes such as bearing. The package implements the 'travel flow aggregration' method described in Morgan and Lovelace (2020) <doi:10.1177/2399808320942779> and the 'OD jittering' method described in Lovelace et al. (2022) <doi:10.32866/001c.33873>. Further information on the package's aim and scope can be found in the vignettes and in a paper in the R Journal (Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053>, and in a paper outlining the landscape of open source software for geographic methods in transport planning (Lovelace, 2021) <doi:10.1007/s10109-020-00342-2>.
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cyclecyclingdesire-linesorigin-destinationpeer-reviewedpubic-transportroute-networkroutesroutingspatialtransporttransport-planningtransportationwalking
11.06 score 443 stars 1 dependents 634 scripts 1.4k downloads
gutenbergr - Download and Process Public Domain Works from Project Gutenberg
Download and process public domain works in the Project Gutenberg collection <https://www.gutenberg.org/>. Includes metadata for all Project Gutenberg works, so that they can be searched and retrieved.
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digital-humanitiesnatural-language-processingnlppeer-reviewedproject-gutenbergpublic-domaintext-mining
11.03 score 117 stars 1 dependents 1.3k scripts 1.8k downloads
osmextract - Download and Import Open Street Map Data Extracts
Match, download, convert and import Open Street Map data extracts obtained from several providers.
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geogeofabrik-zoneopen-dataosmosm-pbf
11.01 score 196 stars 1 dependents 467 scripts 1.4k 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
11.00 score 153 stars 12 dependents 2.6k scripts 4.3k downloadsjsonvalidate - Validate 'JSON' Schema
Uses the node library 'is-my-json-valid' or 'ajv' to validate 'JSON' against a 'JSON' schema. Drafts 04, 06 and 07 of 'JSON' schema are supported.
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jsonjson-validationjsonvalidate
10.99 score 52 stars 69 dependents 76 scripts 16k downloadsssh - Secure Shell (SSH) Client for R
Connect to a remote server over SSH to transfer files via SCP, setup a secure tunnel, or run a command or script on the host while streaming stdout and stderr directly to the client.
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libsshsshssh-client
10.97 score 130 stars 12 dependents 153 scripts 3.6k downloadstesseract - Open Source OCR Engine
Bindings to 'Tesseract': a powerful optical character recognition (OCR) engine that supports over 100 languages. The engine is highly configurable in order to tune the detection algorithms and obtain the best possible results.
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ocrtesseracttesseract-ocrcpp
10.89 score 252 stars 1 dependents 567 scripts 12k downloads
qualtRics - Download 'Qualtrics' Survey Data
Provides functions to access survey results directly into R using the 'Qualtrics' API. 'Qualtrics' <https://www.qualtrics.com/about/> is an online survey and data collection software platform. See <https://api.qualtrics.com/> for more information about the 'Qualtrics' API. This package is community-maintained and is not officially supported by 'Qualtrics'.
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apiqualtricsqualtrics-apisurveysurvey-data
10.84 score 231 stars 1 dependents 359 scripts 3.4k downloadsbibtex - Bibtex Parser
Utility to parse a bibtex file.
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bibtexparser
10.83 score 41 stars 20 dependents 809 scripts 14k downloadsgeojsonio - Convert Data from and to 'GeoJSON' or 'TopoJSON'
Convert data to 'GeoJSON' or 'TopoJSON' from various R classes, including vectors, lists, data frames, shape files, and spatial classes. 'geojsonio' does not aim to replace packages like 'sp', 'rgdal', 'rgeos', but rather aims to be a high level client to simplify conversions of data from and to 'GeoJSON' and 'TopoJSON'.
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geojsontopojsongeospatialconversiondatainput-outputio
10.77 score 154 stars 13 dependents 2.8k scripts 4.7k 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
10.73 score 65 stars 15 dependents 271 scripts 4.5k downloadsrnaturalearthdata - World Vector Map Data from Natural Earth Used in 'rnaturalearth'
Vector map data from <https://www.naturalearthdata.com/>. Access functions are provided in the accompanying package 'rnaturalearth'.
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10.71 score 12 stars 10 dependents 5.9k scripts 18k downloadsrerddap - General Purpose Client for 'ERDDAP™' Servers
General purpose R client for 'ERDDAP™' servers. Includes functions to search for 'datasets', get summary information on 'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format. 'ERDDAP™' information: <https://upwell.pfeg.noaa.gov/erddap/information.html>.
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earthscienceclimateprecipitationtemperaturestormbuoynoaaapi-clienterddapnoaa-data
10.71 score 43 stars 7 dependents 486 scripts 1.2k downloadsRSelenium - R Bindings for 'Selenium WebDriver'
Provides a set of R bindings for the 'Selenium 2.0 WebDriver' (see <https://www.selenium.dev/documentation/> for more information) using the 'JsonWireProtocol' (see <https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol> for more information). 'Selenium 2.0 WebDriver' allows driving a web browser natively as a user would either locally or on a remote machine using the Selenium server it marks a leap forward in terms of web browser automation. Selenium automates web browsers (commonly referred to as browsers). Using RSelenium you can automate browsers locally or remotely.
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rseleniumseleniumwebdriver
10.70 score 351 stars 10 dependents 3 scripts 2.4k downloadsfrictionless - Read and Write Frictionless Data Packages
Read and write Frictionless Data Packages. A 'Data Package' (<https://datapackage.org/>) is a simple container format and standard to describe and package a collection of (tabular) data. It is typically used to publish FAIR (<https://www.gofair.foundation/fair-principles>) and open datasets.
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frictionlessdataoscibio
10.70 score 37 stars 8 dependents 125 scripts 1.4k downloads
cffr - Generate Citation File Format ('CFF') Metadata
Citation File Format ('CFF') version 1.2.0 <doi:10.5281/zenodo.5171937> is a human- and machine-readable file format for software citation metadata. Core utilities generate, read, write and validate Citation File Format metadata for 'R' packages.
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attributioncitationcreditcitation-filescffmetadatacitation-file-formatropensciquarto
10.54 score 26 stars 3 dependents 215 scripts 5.7k downloads
spocc - Interface to Species Occurrence Data Sources
A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'iNaturalist', 'eBird', Integrated Digitized 'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes functionality for retrieving species occurrence data, and combining those data.
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specimensapiweb-servicesoccurrencesspeciestaxonomygbifinatvertnetebirdidigbioobisalaantwebbisondataecoengineinaturalistoccurrencespecies-occurrencespocc
10.44 score 127 stars 6 dependents 599 scripts 4.8k downloadstsbox - Class-Agnostic Time Series
Time series toolkit with identical behavior for all time series classes: 'ts','xts', 'data.frame', 'data.table', 'tibble', 'zoo', 'timeSeries', 'tsibble', 'tis' or 'irts'. Also converts reliably between these classes.
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graphicstime-series
10.38 score 149 stars 5 dependents 423 scripts 3.4k downloadsspelling - Tools for Spell Checking in R
Spell checking common document formats including latex, markdown, manual pages, and description files. Includes utilities to automate checking of documentation and vignettes as a unit test during 'R CMD check'. Both British and American English are supported out of the box and other languages can be added. In addition, packages may define a 'wordlist' to allow custom terminology without having to abuse punctuation.
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spell-checkspell-checkerspellcheckspellcheckerspelling
10.35 score 108 stars 13 dependents 173 scripts 62k downloadsspatsoc - Group Animal Relocation Data by Spatial and Temporal Relationship and Measure Intragroup Social Dynamics
Detects spatial and temporal groups in GPS relocations (Robitaille et al. (2019) <doi:10.1111/2041-210X.13215>). It can be used to convert GPS relocations to gambit-of-the-group format to build proximity-based social networks, and perform data-stream randomization methods suitable for GPS data. Also provides measures of intragroup social dynamics including distance and direction to leaders, centroids and nearest neighbours.
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animalcentroiddirectiondistancegpsleader-followernetworksocialspatial
10.33 score 25 stars 3 dependents 188 scripts 489 downloads
rfishbase - R Interface to 'FishBase'
A programmatic interface to 'FishBase', re-written based on an accompanying 'RESTful' API. Access tables describing over 30,000 species of fish, their biology, ecology, morphology, and more. This package also supports experimental access to 'SeaLifeBase' data, which contains nearly 200,000 species records for all types of aquatic life not covered by 'FishBase.'
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fishfishbasetaxonomy
10.28 score 127 stars 3 dependents 592 scripts 1.6k downloadspkgcheck - Package Checks for 'rOpenSci'
Check whether a package is ready for submission to the 'rOpenSci' peer review system ('rOpenSci' authors (2026) <doi:10.5281/zenodo.2553043> "'rOpenSci' Packages: Development, Maintenance, and Peer Review"). Incorporates the 'goodpractice' package and many additional checks, including aspects related to maintenance of online public code repositories.
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compliance-automationsoftware-analysissoftware-checking
10.20 score 29 stars 3 dependents 62 scripts 929 downloads
dbparser - Drugs Databases Parser
This tool is for parsing public drug databases such as 'DrugBank' XML database <https://go.drugbank.com/>. The parsed data are then returned in a proper 'R' object called 'dvobject'.
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10.10 score 67 stars 262 scripts 622 downloadsav - Working with Audio and Video in R
Bindings to 'FFmpeg' <http://www.ffmpeg.org/> AV library for working with audio and video in R. Generates high quality video from images or R graphics with custom audio. Also offers high performance tools for reading raw audio, creating 'spectrograms', and converting between countless audio / video formats. This package interfaces directly to the C API and does not require any command line utilities.
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ffmpeg
10.06 score 94 stars 17 dependents 756 scripts 11k downloadsrdhs - API Client and Dataset Management for the Demographic and Health Survey (DHS) Data
Provides a client for (1) querying the DHS API for survey indicators and metadata (<https://api.dhsprogram.com/#/index.html>), (2) identifying surveys and datasets for analysis, (3) downloading survey datasets from the DHS website, (4) loading datasets and associate metadata into R, and (5) extracting variables and combining datasets for pooled analysis.
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datasetdhsdhs-apiextractpeer-reviewedsurvey-data
10.01 score 38 stars 4 dependents 373 scripts 2.1k downloads
vcr - Record 'HTTP' Calls to Disk
Record test suite 'HTTP' requests and replays them during future runs. A port of the Ruby gem of the same name (<https://github.com/vcr/vcr/>). Works by recording real 'HTTP' requests/responses on disk in 'cassettes', and then replaying matching responses on subsequent requests.
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httphttpsapiweb-servicescurlmockmockinghttp-mockingtestingtesting-toolstddunit-testingvcr
10.00 score 96 stars 112 scripts 3.8k downloads
rebird - R Client for the eBird Database of Bird Observations
A programmatic client for the eBird database (<https://ebird.org/home>), including functions for searching for bird observations by geographic location (latitude, longitude), eBird hotspots, location identifiers, by notable sightings, by region, and by taxonomic name.
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birdsbirdingebirddatabasedatabiologyobservationssightingsornithologyebird-apiebird-webservicesspocc
9.93 score 95 stars 7 dependents 79 scripts 4.1k downloads
tidyhydat - Extract and Tidy Canadian 'Hydrometric' Data
Provides functions to access historical and real-time national 'hydrometric' data from Water Survey of Canada data sources and then applies tidy data principles.
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citzgovernment-datahydrologyhydrometricstidy-datawater-resources
9.91 score 74 stars 3 dependents 163 scripts 732 downloadsworrms - World Register of Marine Species (WoRMS) Client
Client for World Register of Marine Species (<https://www.marinespecies.org/>). Includes functions for each of the API methods, including searching for names by name, date and common names, searching using external identifiers, fetching synonyms, as well as fetching taxonomic children and taxonomic classification.
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biologysciencemarineapiwebapi-clientwormsspeciesapi-wrapperbiological-datafishjerico-relevantmarine-biologymarine-speciestaxizetaxonomy
9.89 score 28 stars 20 dependents 405 scripts 4.5k downloads
rsvg - Render SVG Images into PDF, PNG, (Encapsulated) PostScript, or Bitmap Arrays
Renders vector-based svg images into high-quality custom-size bitmap arrays using 'librsvg2'. The resulting bitmap can be written to e.g. png, jpeg or webp format. In addition, the package can convert images directly to various formats such as pdf or postscript.
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librsvgcairoglib
9.84 score 104 stars 62 dependents 11 scripts 32k downloads
piggyback - Managing Larger Data on a GitHub Repository
Helps store files as GitHub release assets, which is a convenient way for large/binary data files to piggyback onto public and private GitHub repositories. Includes functions for file downloads, uploads, and managing releases via the GitHub API.
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data-storegit-lfspeer-reviewed
9.81 score 205 stars 16 dependents 2 scripts 2.7k downloadscharlatan - Make Fake Data
Make fake data that looks realistic, supporting addresses, person names, dates, times, colors, coordinates, currencies, digital object identifiers ('DOIs'), jobs, phone numbers, 'DNA' sequences, doubles and integers from distributions and within a range.
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datadatasetfake-datafakerpeer-reviewed
9.79 score 307 stars 1 dependents 173 scripts 696 downloads
RNeXML - Semantically Rich I/O for the 'NeXML' Format
Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
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metadatanexmlphylogeneticslinked-data
9.69 score 15 stars 19 dependents 39 scripts 5.4k downloads
auk - eBird Data Extraction and Processing in R
Extract and process bird sightings records from eBird (<http://ebird.org>), an online tool for recording bird observations. Public access to the full eBird database is via the eBird Basic Dataset (EBD; see <http://ebird.org/ebird/data/download> for access), a downloadable text file. This package is an interface to AWK for extracting data from the EBD based on taxonomic, spatial, or temporal filters, to produce a manageable file size that can be imported into R.
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datasetebird
9.69 score 160 stars 1 dependents 313 scripts 1.0k downloads
tabulapdf - Extract Tables from PDF Documents
Bindings for the 'Tabula' <https://tabula.technology/> 'Java' library, which can extract tables from PDF files. This tool can reduce time and effort in data extraction processes in fields like investigative journalism. It allows for automatic and manual table extraction, the latter facilitated through a 'Shiny' interface, enabling manual areas selection\ with a computer mouse for data retrieval.
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javapdfpdf-documentpeer-reviewedropenscitabulatabular-dataopenjdk
9.66 score 567 stars 2 dependents 284 scripts 1.2k downloadsprism - Access Data from the Oregon State Prism Climate Project
Allows users to access the Oregon State Prism climate data (<https://prism.nacse.org/>). Using the web service API data can easily downloaded in bulk and loaded into R for spatial analysis. Some user friendly visualizations are also provided.
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9.63 score 63 stars 380 scripts 871 downloadsckanr - Client for the Comprehensive Knowledge Archive Network ('CKAN')
Client for the Comprehensive Knowledge Archive Network ('CKAN') application programming interface ('API') (<https://ckan.org/>). Includes interface to 'CKAN' 'APIs' for search, list, show for packages, organizations, and resources. In addition, provides an interface to the 'datastore' extension.
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databaseopen-datackanapidatadatasetapi-wrapperckan-api
9.55 score 104 stars 4 dependents 473 scripts 816 downloads
aorsf - Accelerated Oblique Random Forests
Fit, interpret, and compute predictions with oblique random forests. Includes support for partial dependence, variable importance, passing customized functions for variable importance and identification of linear combinations of features. Methods for the oblique random survival forest are described in Jaeger et al., (2023) <DOI:10.1080/10618600.2023.2231048>.
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data-scienceobliquerandom-forestsurvivalopenblascppopenmp
9.53 score 59 stars 3 dependents 103 scripts 2.6k downloadslingtypology - Linguistic Typology and Mapping
Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.
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abvdafboatlasautotypebivaltypglottolog-databasegrambanklinguistic-mapslinguisticsphoiblesailstypologywals
9.49 score 54 stars 1.4k scripts 765 downloadsbib2df - Parse a BibTeX File to a Data Frame
Parse a BibTeX file to a data.frame to make it accessible for further analysis and visualization.
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bibtexpeer-reviewed
9.49 score 101 stars 6 dependents 279 scripts 1.2k downloadsrobotstxt - A 'robots.txt' Parser and 'Webbot'/'Spider'/'Crawler' Permissions Checker
Provides functions to download and parse 'robots.txt' files. Ultimately the package makes it easy to check if bots (spiders, crawler, scrapers, ...) are allowed to access specific resources on a domain.
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crawlerpeer-reviewedrobotstxtscraperspiderwebscraping
9.43 score 69 stars 4 dependents 465 scripts 1.7k downloadsgoogleLanguageR - Call Google's 'Natural Language', 'Cloud Translation', 'Cloud Speech', and 'Cloud Text-to-Speech' APIs
Access Google Cloud machine learning APIs for text and speech tasks. Use the Cloud Translation API for text detection and translation, the Natural Language API to analyze sentiment, entities, and syntax, the Cloud Speech API to transcribe audio to text, and the Cloud Text-to-Speech API to synthesize text into audio files.
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cloud-speech-apicloud-translation-apigoogle-api-clientgoogle-cloudgoogle-cloud-speechgoogle-nlpgoogleauthrnatural-language-processingpeer-reviewedsentiment-analysisspeech-apitranslation-api
9.33 score 201 stars 1 dependents 177 scripts 692 downloadsgeojson - Classes for 'GeoJSON'
Classes for 'GeoJSON' to make working with 'GeoJSON' easier. Includes S3 classes for 'GeoJSON' classes with brief summary output, and a few methods such as extracting and adding bounding boxes, properties, and coordinate reference systems; working with newline delimited 'GeoJSON'; and serializing to/from 'Geobuf' binary 'GeoJSON' format.
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geojsongeospatialconversiondatainput-outputbboxpolygongeobufcrsndgeojsonspatial
9.32 score 32 stars 14 dependents 3.9k downloadswdman - 'Webdriver'/'Selenium' Binary Manager
There are a number of binary files associated with the 'Webdriver'/'Selenium' project. This package provides functions to download these binaries and to manage processes involving them.
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rseleniumseleniumwebdriverwebdriver-manager
9.31 score 30 stars 11 dependents 296 scripts 2.0k downloadsqpdf - Split, Combine and Compress PDF Files
Content-preserving transformations transformations of PDF files such as split, combine, and compress. This package interfaces directly to the 'qpdf' C++ library <https://qpdf.sourceforge.io/> and does not require any command line utilities. Note that 'qpdf' does not read actual content from PDF files: to extract text and data you need the 'pdftools' package.
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libjpeg-turbozlibcpp
9.31 score 64 stars 100 dependents 2 scripts 53k 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
9.29 score 118 stars 212 scripts 101 downloadsUSAboundaries - Historical and Contemporary Boundaries of the United States of America
The boundaries for geographical units in the United States of America contained in this package include state, county, congressional district, and zip code tabulation area. Contemporary boundaries are provided by the U.S. Census Bureau (public domain). Historical boundaries for the years from 1629 to 2000 are provided form the Newberry Library's Atlas of Historical County Boundaries (licensed CC BY-NC-SA). Additional data is provided in the USAboundariesData package; this package provides an interface to access that data.
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digital-historyhistoryspatial-data
9.24 score 68 stars 1.2k scripts 650 downloadsparzer - Parse Messy Geographic Coordinates
Parse messy geographic coordinates from various character formats to decimal degree numeric values. Parse coordinates into their parts (degree, minutes, seconds); calculate hemisphere from coordinates; pull out individually degrees, minutes, or seconds; add and subtract degrees, minutes, and seconds. C++ code herein originally inspired from code written by Jeffrey D. Bogan, but then completely re-written.
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geospatialdatalatitudelongitudeparsercoordinatesgeoquartocpp
9.23 score 64 stars 3 dependents 246 scripts 639 downloadsjqr - Client for 'jq', a 'JSON' Processor
Client for 'jq', a 'JSON' processor (<https://jqlang.github.io/jq/>), written in C. 'jq' allows the following with 'JSON' data: index into, parse, do calculations, cut up and filter, change key names and values, perform conditionals and comparisons, and more.
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jqjson
9.19 score 145 stars 35 dependents 60 scripts 5.7k downloadstextreuse - Detect Text Reuse and Document Similarity
Tools for measuring similarity among documents and detecting passages which have been reused. Implements shingled n-gram, skip n-gram, and other tokenizers; similarity/dissimilarity functions; pairwise comparisons; minhash and locality sensitive hashing algorithms; and a version of the Smith-Waterman local alignment algorithm suitable for natural language.
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peer-reviewedcpp
9.15 score 200 stars 254 scripts 562 downloads
nasapower - NASA POWER API Client
An API client for NASA POWER global meteorology, surface solar energy and climatology data API. POWER (Prediction Of Worldwide Energy Resources) data are freely available for download with varying spatial resolutions dependent on the original data and with several temporal resolutions depending on the POWER parameter and community. This work is funded through the NASA Earth Science Directorate Applied Science Program. For more on the data themselves, the methodologies used in creating, a web-based data viewer and web access, please see <https://power.larc.nasa.gov/>.
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nasameteorological-dataweatherglobalweather-datameteorologynasa-poweragroclimatologyearth-sciencedata-accessclimate-dataagroclimatology-dataweather-variables
9.08 score 108 stars 6 dependents 243 scripts 2.1k downloads
comtradr - Interface with the United Nations Comtrade API
Interface with and extract data from the United Nations 'Comtrade' API <https://comtradeplus.un.org/>. 'Comtrade' provides country level shipping data for a variety of commodities, these functions allow for easy API query and data returned as a tidy data frame.
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apicomtradepeer-reviewedsupply-chain
9.02 score 85 stars 132 scripts 1.0k downloadsiheatmapr - Interactive, Complex Heatmaps
Make complex, interactive heatmaps. 'iheatmapr' includes a modular system for iteratively building up complex heatmaps, as well as the iheatmap() function for making relatively standard heatmaps.
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heatmapplotlyinteractive-visualizationsdata-visualizationhtmlwidgetspeer-reviewed
8.95 score 270 stars 1 dependents 74 scripts 553 downloadspkgstats - Metrics of R Packages
Static code analyses for R packages using the external code-tagging libraries 'ctags' and 'gtags'. Static analyses enable packages to be analysed very quickly, generally a couple of seconds at most. The package also provides access to a database generating by applying the main function to the full 'CRAN' archive, enabling the statistical properties of any package to be compared with all other 'CRAN' packages.
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code-analysiscode-statisticssoftware-analysisquartocpp
8.84 score 22 stars 4 dependents 6 scripts 510 downloads
ijtiff - Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files
General purpose TIFF file I/O for R users. Currently the only such package with read and write support for TIFF files with floating point (real-numbered) pixels, and the only package that can correctly import TIFF files that were saved from 'ImageJ' and write TIFF files than can be correctly read by 'ImageJ' <https://imagej.net/ij/>. Also supports text image I/O.
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image-manipulationimagejpeer-reviewedtiff-filestiff-imagestiff
8.74 score 16 stars 8 dependents 53 scripts 1.1k downloadsbabette - Control 'BEAST2'
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is commonly accompanied by 'BEAUti 2', 'Tracer' and 'DensiTree'. 'babette' provides for an alternative workflow of using all these tools separately. This allows doing complex Bayesian phylogenetics easily and reproducibly from 'R'.
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bayesian-inferencebeast2phylogeneticsopenjdk
8.74 score 46 stars 1 dependents 79 scripts 443 downloadsrnoaa - 'NOAA' Weather Data from R
Client for many 'NOAA' data sources including the 'NCDC' climate 'API' at <https://www.ncdc.noaa.gov/cdo-web/webservices/v2>, with functions for each of the 'API' 'endpoints': data, data categories, data sets, data types, locations, location categories, and stations. In addition, we have an interface for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS', tornado data via the 'NOAA' storm prediction center, and more.
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earthscienceclimateprecipitationtemperaturestormbuoyncdcnoaatornadoesea iceisdnoaa-data
8.70 score 342 stars 1 dependents 623 scripts 309 downloads
katex - Rendering Math to HTML, 'MathML', or R-Documentation Format
Convert latex math expressions to HTML and 'MathML' for use in markdown documents or package manual pages. The rendering is done in R using the V8 engine (i.e. server-side), which eliminates the need for embedding the 'MathJax' library into your web pages. In addition a 'math-to-rd' wrapper is provided to automatically render beautiful math in R documentation files.
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8.69 score 36 stars 12 dependents 51 scripts 15k downloads
weatherOz - An API Client for Australian Weather and Climate Data Resources
Provides automated downloading, parsing and formatting of weather data for Australia through API endpoints provided by the Department of Primary Industries and Regional Development (DPIRD) of Western Australia and by the Science and Technology Division of the Queensland Government's Department of Environment and Science (DES). As well as the Bureau of Meteorology (BOM) of the Australian government precis and coastal forecasts, and downloading and importing radar and satellite imagery files. DPIRD weather data are accessed through public APIs provided by DPIRD, <https://www.dpird.wa.gov.au/online-tools/apis/>, providing access to weather station data from the DPIRD weather station network. Australia-wide weather data are based on data from the Australian Bureau of Meteorology (BOM) data and accessed through SILO (Scientific Information for Land Owners) Jeffrey et al. (2001) <doi:10.1016/S1364-8152(01)00008-1>. DPIRD data are made available under a Creative Commons Attribution 3.0 Licence (CC BY 3.0 AU) license <https://creativecommons.org/licenses/by/3.0/au/deed.en>. SILO data are released under a Creative Commons Attribution 4.0 International licence (CC BY 4.0) <https://creativecommons.org/licenses/by/4.0/>. BOM data are (c) Australian Government Bureau of Meteorology and released under a Creative Commons (CC) Attribution 3.0 licence or Public Access Licence (PAL) as appropriate, see <https://www.bom.gov.au/copyright> for further details.
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dpirdbommeteorological-dataweather-forecastaustraliaweatherweather-datameteorologywestern-australiaaustralia-bureau-of-meteorologywestern-australia-agricultureaustralia-agricultureaustralia-climateaustralia-weatherapi-clientclimatedatarainfallweather-api
8.68 score 40 stars 1 dependents 67 scripts 620 downloads
distionary - Create and Evaluate Probability Distributions
Create and evaluate probability distribution objects from a variety of families or define custom distributions. Automatically compute distributional properties, even when they have not been specified. This package supports statistical modeling and simulations, and forms the core of the probaverse suite of R packages.
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distributions
8.66 score 9 stars 3 dependents 51 scripts 522 downloadsphylogram - Dendrograms for Evolutionary Analysis
Contains functions for developing phylogenetic trees as deeply-nested lists ("dendrogram" objects). Enables bi-directional conversion between dendrogram and "phylo" objects (see Paradis et al (2004) <doi:10.1093/bioinformatics/btg412>), and features several tools for command-line tree manipulation and import/export via Newick parenthetic text.
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peer-reviewed
8.63 score 12 stars 9 dependents 263 scripts 766 downloadsrcrossref - Client for Various 'CrossRef' 'APIs'
Client for various 'CrossRef' 'APIs', including 'metadata' search with their old and newer search 'APIs', get 'citations' in various formats (including 'bibtex', 'citeproc-json', 'rdf-xml', etc.), convert 'DOIs' to 'PMIDs', and 'vice versa', get citations for 'DOIs', and get links to full text of articles when available.
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text-mingliteraturepdfxmlpublicationscitationsfull-texttdmcrossrefapiapi-wrappercrossref-apidoimetadata
8.57 score 180 stars 7 dependents 7 scripts 2.0k downloads
opentripplanner - Setup and connect to 'OpenTripPlanner'
Setup and connect to 'OpenTripPlanner' (OTP) <http://www.opentripplanner.org/>. OTP is an open source platform for multi-modal and multi-agency journey planning written in 'Java'. The package allows you to manage a local version or connect to remote OTP server to find walking, cycling, driving, or transit routes. This package has been peer-reviewed by rOpenSci (v. 0.2.0.0).
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dataisochronesjavaopentripplannerotppublic-transportroutingtransporttransportation-planning
8.56 score 90 stars 168 scripts 475 downloadssits - Satellite Image Time Series Analysis for Earth Observation Data Cubes
An end-to-end toolkit for land use and land cover classification using big Earth observation data. Builds satellite image data cubes from cloud collections. Supports visualization methods for images and time series and smoothing filters for dealing with noisy time series. Enables merging of multi-source imagery (SAR, optical, DEM). Includes functions for quality assessment of training samples using self-organized maps and to reduce training samples imbalance. Provides machine learning algorithms including support vector machines, random forests, extreme gradient boosting, multi-layer perceptrons, temporal convolution neural networks, and temporal attention encoders. Performs efficient classification of big Earth observation data cubes and includes functions for post-classification smoothing based on Bayesian inference. Enables best practices for estimating area and assessing accuracy of land change. Includes object-based spatio-temporal segmentation for space-time OBIA. Minimum recommended requirements: 16 GB RAM and 4 CPU dual-core.
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big-earth-datacbersearth-observationeo-datacubesgeospatialimage-time-seriesland-cover-classificationlandsatplanetary-computerr-spatialremote-sensingrspatialsatellite-image-time-seriessatellite-imagerysentinel-2stac-apistac-catalogopenblascppopenmp
8.56 score 549 stars 820 scripts 659 downloads
nlrx - Setup, Run and Analyze 'NetLogo' Model Simulations from 'R' via 'XML'
Setup, run and analyze 'NetLogo' (<https://www.netlogo.org>) model simulations in 'R'. 'nlrx' experiments use a similar structure as 'NetLogos' Behavior Space experiments. However, 'nlrx' offers more flexibility and additional tools for running and analyzing complex simulation designs and sensitivity analyses. The user defines all information that is needed in an intuitive framework, using class objects. Experiments are submitted from 'R' to 'NetLogo' via 'XML' files that are dynamically written, based on specifications defined by the user. By nesting model calls in future environments, large simulation design with many runs can be executed in parallel. This also enables simulating 'NetLogo' experiments on remote high performance computing machines. In order to use this package, 'Java' and 'NetLogo' (>= 5.3.1) need to be available on the executing system.
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agent-based-modelingindividual-based-modellingnetlogopeer-reviewed
8.53 score 80 stars 201 scripts 392 downloadsopencage - Geocode with the OpenCage API
Geocode with the OpenCage API, either from place name to longitude and latitude (forward geocoding) or from longitude and latitude to the name and address of a location (reverse geocoding), see <https://opencagedata.com>.
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geocodegeocoderopencageopencage-apiopencage-geocoderpeer-reviewedplacenamesrspatial
8.49 score 89 stars 96 scripts 306 downloads
oai - General Purpose 'Oai-PMH' Services Client
A general purpose client to work with any 'OAI-PMH' (Open Archives Initiative Protocol for 'Metadata' Harvesting) service. The 'OAI-PMH' protocol is described at <http://www.openarchives.org/OAI/openarchivesprotocol.html>. Functions are provided to work with the 'OAI-PMH' verbs: 'GetRecord', 'Identify', 'ListIdentifiers', 'ListMetadataFormats', 'ListRecords', and 'ListSets'.
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data-accessoai-pmhpeer-reviewedscholarly-api
8.46 score 15 stars 33 dependents 7.7k downloads
galamm - Generalized Additive Latent and Mixed Models
Estimates generalized additive latent and mixed models using maximum marginal likelihood, as defined in Sorensen et al. (2023) <doi:10.1007/s11336-023-09910-z>, which is an extension of Rabe-Hesketh and Skrondal (2004)'s unifying framework for multilevel latent variable modeling <doi:10.1007/BF02295939>. Efficient computation is done using sparse matrix methods, Laplace approximation, and automatic differentiation. The framework includes generalized multilevel models with heteroscedastic residuals, mixed response types, factor loadings, smoothing splines, crossed random effects, and combinations thereof. Syntax for model formulation is close to 'lme4' (Bates et al. (2015) <doi:10.18637/jss.v067.i01>) and 'PLmixed' (Rockwood and Jeon (2019) <doi:10.1080/00273171.2018.1516541>).
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generalized-additive-modelshierarchical-modelsitem-response-theorylatent-variable-modelsstructural-equation-modelscpp
8.43 score 37 stars 54 scripts 451 downloadsplater - Read, Tidy, and Display Data from Microtiter Plates
Tools for interacting with data from experiments done in microtiter plates. Easily read in plate-shaped data and convert it to tidy format, combine plate-shaped data with tidy data, and view tidy data in plate shape.
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8.38 score 26 stars 2 dependents 203 scripts 524 downloadsbeautier - 'BEAUti' from R
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAUti 2' (which is part of 'BEAST2') is a GUI tool that allows users to specify the many possible setups and generates the XML file 'BEAST2' needs to run. This package provides a way to create 'BEAST2' input files without active user input, but using R function calls instead.
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bayesianbeastbeast2beautiphylogenetic-inferencephylogenetics
8.36 score 15 stars 5 dependents 224 scripts 641 downloadsgeonames - Interface to the "Geonames" Spatial Query Web Service
The web service at <https://www.geonames.org/> provides a number of spatial data queries, including administrative area hierarchies, city locations and some country postal code queries. A (free) username is required and rate limits exist.
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8.35 score 41 stars 17 dependents 118 scripts 1.3k downloads
UCSCXenaTools - Download and Explore Datasets from UCSC Xena Data Hubs
Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
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api-clientbioinformaticsccledownloadericgctcgatoiltreehouseucscucsc-xena
8.35 score 117 stars 1 dependents 195 scripts 1.6k downloads
nodbi - Document 'NoSQL' Database DBI Connector
R database connector for creating, reading (querying and listing fields), updating and deleting of individual or many JSON documents, providing a common API across supported databases ('SQLite', 'PostgreSQL', 'DuckDB', 'MariaDB' or 'MySQL' as well as 'NoSQL' databases 'MongoDB', 'CouchDB' and 'Elasticsearch').
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databasemongodbelasticsearchcouchdbsqlitepostgresqlmariadbmysqlduckdbnosqljsondocuments
8.32 score 75 stars 1 dependents 39 scripts 607 downloadscyphr - High Level Encryption Wrappers
Encryption wrappers, using low-level support from 'sodium' and 'openssl'. 'cyphr' tries to smooth over some pain points when using encryption within applications and data analysis by wrapping around differences in function names and arguments in different encryption providing packages. It also provides high-level wrappers for input/output functions for seamlessly adding encryption to existing analyses.
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encryptionopensslpeer-reviewedsodium
8.32 score 98 stars 2 dependents 51 scripts 612 downloadslandscapetools - Landscape Utility Toolbox
Provides utility functions for some of the less-glamorous tasks involved in landscape analysis. It includes functions to coerce raster data to the common 'tibble' format and vice versa, it helps with flexible reclassification tasks of raster data and it provides a function to merge multiple raster. Furthermore, 'landscapetools' helps landscape scientists to visualize their data by providing optional themes and utility functions to plot single landscapes, 'rasterstacks', '-bricks' and lists of raster.
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landscapelandscape-ecologyrastervisualizationworkflow
8.26 score 50 stars 132 scripts 354 downloadseuropepmc - R Interface to the Europe PubMed Central RESTful Web Service
An R Client for the Europe PubMed Central RESTful Web Service (see <https://europepmc.org/RestfulWebService> for more information). It gives access to both metadata on life science literature and open access full texts. Europe PMC indexes all PubMed content and other literature sources including Agricola, a bibliographic database of citations to the agricultural literature, or Biological Patents. In addition to bibliographic metadata, the client allows users to fetch citations and reference lists. Links between life-science literature and other EBI databases, including ENA, PDB or ChEMBL are also accessible. No registration or API key is required. See the vignettes for usage examples.
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bibliometricseurope-pmcpubmedpubmedcentralscientific-literaturescientific-publications
8.25 score 32 stars 3 dependents 111 scripts 1.4k downloadscodemetar - Generate 'CodeMeta' Metadata for R Packages
The 'Codemeta' Project defines a 'JSON-LD' format for describing software metadata, as detailed at <https://codemeta.github.io>. This package provides utilities to generate, parse, and modify 'codemeta.json' files automatically for R packages, as well as tools and examples for working with 'codemeta.json' 'JSON-LD' more generally.
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metadatacodemetaropenscicitationcreditlinked-datajson-ldpeer-reviewed
8.24 score 67 stars 2 dependents 46 scripts 656 downloadsrinat - Access 'iNaturalist' Data Through APIs
A programmatic interface to the API provided by the 'iNaturalist' website <https://www.inaturalist.org/> to download species occurrence data submitted by citizen scientists.
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inaturalistspocc
8.23 score 70 stars 243 scripts 896 downloads
rb3 - Download and Parse Public Data Released by B3 Exchange
Download and parse public files released by B3 and convert them into useful formats and data structures common to data analysis practitioners.
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brazilexchange-datafinancefinancial-datafinancial-servicesmarket-data
8.22 score 107 stars 104 scripts 475 downloads
yfR - Downloads and Organizes Financial Data from Yahoo Finance
Facilitates download of financial data from Yahoo Finance <https://finance.yahoo.com/>, a vast repository of stock price data across multiple financial exchanges. The package offers a local caching system and support for parallel computation.
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8.20 score 51 stars 2 dependents 144 scripts 1.2k downloads
babelquarto - Renders a Multilingual Quarto Book
Automate rendering and cross-linking of Quarto books following a prescribed structure.
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quarto
8.19 score 62 stars 1 dependents 35 scripts
NLMR - Simulating Neutral Landscape Models
Provides neutral landscape models (<doi:10.1007/BF02275262>, <https://sci-hub.in/10.1007/bf02275262>). Neutral landscape models range from "hard" neutral models (completely random distributed), to "soft" neutral models (definable spatial characteristics) and generate landscape patterns that are independent of ecological processes. Thus, these patterns can be used as null models in landscape ecology. 'NLMR' combines a large number of algorithms from other published software for simulating neutral landscapes. The simulation results are obtained in a spatial data format (SpatRaster objects from the 'terra' package) and can, therefore, be used in any sort of raster data operation that is performed with standard observation data.
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landscape-ecologyneutral-landscape-modelpeer-reviewedspatialcpp
8.18 score 69 stars 247 scripts 39 downloadsghql - General Purpose 'GraphQL' Client
A 'GraphQL' client, with an R6 interface for initializing a connection to a 'GraphQL' instance, and methods for constructing queries, including fragments and parameterized queries. Queries are checked with the 'libgraphqlparser' C++ parser via the 'graphql' package.
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httpapiweb-servicescurldatagraphqlgraphql-apigraphql-client
8.17 score 151 stars 3 dependents 218 scripts 740 downloadsrvertnet - Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Retrieve, map and summarize data from the 'VertNet.org' archives (<https://vertnet.org/>). Functions allow searching by many parameters, including 'taxonomic' names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large 'datasets' via email.
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speciesoccurrencesbiodiversitymapsvertnetmammalsmammaliaspecimensapi-wrapperspecimenspocc
8.16 score 7 stars 7 dependents 33 scripts 4.3k downloads
lightr - Read Spectrometric Data and Metadata
Parse various reflectance/transmittance/absorbance spectra file formats to extract spectral data and metadata, as described in Gruson, White & Maia (2019) <doi:10.21105/joss.01857>. Among other formats, it can import files from 'Avantes' <https://www.avantes.com/>, 'CRAIC' <https://www.microspectra.com/>, and 'OceanOptics'/'OceanInsight' <https://www.oceanoptics.com/> brands.
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file-importreproducibilityreproducible-researchreproducible-sciencespectral-dataspectroscopy
8.14 score 15 stars 3 dependents 19 scripts 778 downloadsgendercoder - Recodes Sex/Gender Descriptions into a Standard Set
Provides dictionary-based tools for recoding free-text gender responses into consistent categories while preserving gender diversity where possible. The package standardises spelling, capitalization, whitespace, and common variants through curated named character-vector dictionaries, supports either detailed or collapsed output categories, and can retain original unmatched responses for manual review. It also includes helpers for creating custom dictionaries from approximate string matches and a local interactive application for recoding uploaded data files.
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gender-diversityozunconf18unconf
8.03 score 48 stars 56 scripts 247 downloads
datefixR - Standardize Dates in Different Formats or with Missing Data
There are many different formats dates are commonly represented with: the order of day, month, or year can differ, different separators ("-", "/", or whitespace) can be used, months can be numerical, names, or abbreviations and year given as two digits or four. 'datefixR' takes dates in all these different formats and converts them to R's built-in date class. If 'datefixR' cannot standardize a date, such as because it is too malformed, then the user is told which date cannot be standardized and the corresponding ID for the row. 'datefixR' also allows the imputation of missing days and months with user-controlled behavior.
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dateswranglingrustcargo
8.02 score 33 stars 53 scripts 650 downloadswebmockr - Stubbing and Setting Expectations on 'HTTP' Requests
Stubbing and setting expectations on 'HTTP' requests. Includes tools for stubbing 'HTTP' requests, including expected request conditions and response conditions. Match on 'HTTP' method, query parameters, request body, headers and more. Can be used for unit tests or outside of a testing context.
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httphttpsapiweb-servicescurlmockmockingfakewebhttp-mockingtestingtesting-toolstddhttp-mock
8.02 score 50 stars 151 scripts 2.8k downloadsosmplotr - Bespoke Images of 'OpenStreetMap' Data
Bespoke images of 'OpenStreetMap' ('OSM') data and data visualisation using 'OSM' objects.
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data-visualisationhighlighting-clustersopenstreetmaposmoverpassoverpass-apipeer-reviewed
7.98 score 143 stars 111 scripts 77 downloadsxslt - Extensible Style-Sheet Language Transformations
An extension for the 'xml2' package to transform XML documents by applying an 'xslt' style-sheet.
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xmlxsltlibxsltlibxml2cpp
7.97 score 29 stars 18 dependents 71 scripts 8.4k downloadsrglobi - Interface to Global Biotic Interactions
A programmatic interface to the web service methods provided by Global Biotic Interactions ('GloBI') (<https://www.globalbioticinteractions.org/>). 'GloBI' provides access to spatial-temporal species interaction records from sources all over the world. 'rglobi' provides methods to search species interactions by location, interaction type, and taxonomic name.
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7.97 score 18 stars 2 dependents 48 scripts 197 downloadsbinman - A Binary Download Manager
Tools and functions for managing the download of binary files. Binary repositories are defined in 'YAML' format. Defining new pre-download, download and post-download templates allow additional repositories to be added.
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7.97 score 16 stars 12 dependents 53 scripts 2.0k downloads
autotest - Automatic Package Testing
Automatic testing of R packages by tracing function calls made in examples and tests, then systematically varying the inputs to check that functions respond sensibly. The package is a development aid for authors submitting to the 'rOpenSci' statistical software review project ('rOpenSci' authors, 2021; <doi:10.5281/zenodo.5556756>).
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automated-testingfuzzingtesting
7.94 score 54 stars 27 scripts 682 downloads
dataset - Create Data Frames for Exchange and Reuse
The 'dataset' package extends tidy data frames with machine-readable metadata, semantic definitions, and provenance information. It supports incremental semantic stabilization, interoperable dataset exchange, and FAIR-oriented publication workflows by preserving contextual metadata directly within R objects. The package facilitates the creation, exchange, reuse, and RDF serialization of datasets in line with ISO and W3C standards.
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datasetmetadata-management
7.94 score 24 stars 2 dependents 937 downloads
drake - A Pipeline Toolkit for Reproducible Computation at Scale
A general-purpose computational engine for data analysis, drake rebuilds intermediate data objects when their dependencies change, and it skips work when the results are already up to date. Not every execution starts from scratch, there is native support for parallel and distributed computing, and completed projects have tangible evidence that they are reproducible. Extensive documentation, from beginner-friendly tutorials to practical examples and more, is available at the reference website <https://docs.ropensci.org/drake/> and the online manual <https://books.ropensci.org/drake/>.
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data-sciencedrakehigh-performance-computingmakefilepeer-reviewedpipelinereproducibilityreproducible-researchropensciworkflow
7.94 score 1.3k stars 1.2k downloadstidync - Tidy Approach to 'NetCDF' Data Exploration and Extraction
Tidy tools for 'NetCDF' data sources. Explore the contents of a 'NetCDF' source (file or URL) presented as variables organized by grid with a database-like interface. The hyper_filter() interactive function translates the filter value or index expressions to array-slicing form. No data is read until explicitly requested, as a data frame or list of arrays via hyper_tibble() or hyper_array().
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7.91 score 95 stars 4 dependents 5 scripts 1.0k downloadsnatserv - 'NatureServe' Interface
Interface to 'NatureServe' (<https://www.natureserve.org/>). Includes methods to get data, image metadata, search taxonomic names, and make maps.
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taxonomyspeciesapiweb-servicesnatureservemetadatamapstaxize
7.87 score 11 stars 15 dependents 21 scripts 3.6k downloadshoardr - Manage Cached Files
Suite of tools for managing cached files, targeting use in other R packages. Uses 'rappdirs' for cross-platform paths. Provides utilities to manage cache directories, including targeting files by path or by key; cached directories can be compressed and uncompressed easily to save disk space.
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cachingdatafilesxmlpdf
7.87 score 23 stars 26 dependents 2.1k downloads
opencv - Bindings to 'OpenCV' Computer Vision Library
Exposes some of the available 'OpenCV' <https://opencv.org/> algorithms, such as a QR code scanner, and edge, body or face detection. These can either be applied to analyze static images, or to filter live video footage from a camera device.
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opencvopencv-libraryunconfunconf18cpp
7.86 score 143 stars 162 scripts 1.6k downloads
rnassqs - Access Data from the NASS 'Quick Stats' API
Interface to access data via the United States Department of Agriculture's National Agricultural Statistical Service (NASS) 'Quick Stats' web API <https://quickstats.nass.usda.gov/api/>. Convenience functions facilitate building queries based on available parameters and valid parameter values. This product uses the NASS API but is not endorsed or certified by NASS.
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7.85 score 48 stars 1 dependents 123 scripts 522 downloadsEDIutils - An API Client for the Environmental Data Initiative Repository
A client for the Environmental Data Initiative repository REST API. The 'EDI' data repository <https://portal.edirepository.org/nis/home.jsp> is for publication and reuse of ecological data with emphasis on metadata accuracy and completeness. It is built upon the 'PASTA+' software stack <https://pastaplus-core.readthedocs.io/en/latest/index.html#> and was developed in collaboration with the US 'LTER' Network <https://lternet.edu/>. 'EDIutils' includes functions to search and access existing data, evaluate and upload new data, and assist other data management tasks common to repository users.
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ecologyeml-metadataopen-accessopen-dataresearch-data-managementresearch-data-repository
7.85 score 10 stars 1 dependents 234 scripts 459 downloads
MODIStsp - Find, Download and Process MODIS Land Products Data
Allows automating the creation of time series of rasters derived from MODIS satellite land products data. It performs several typical preprocessing steps such as download, mosaicking, reprojecting and resizing data acquired on a specified time period. All processing parameters can be set using a user-friendly GUI. Users can select which layers of the original MODIS HDF files they want to process, which additional quality indicators should be extracted from aggregated MODIS quality assurance layers and, in the case of surface reflectance products, which spectral indexes should be computed from the original reflectance bands. For each output layer, outputs are saved as single-band raster files corresponding to each available acquisition date. Virtual files allowing access to the entire time series as a single file are also created. Command-line execution exploiting a previously saved processing options file is also possible, allowing users to automatically update time series related to a MODIS product whenever a new image is available. For additional documentation refer to the following article: Busetto and Ranghetti (2016) <doi:10.1016/j.cageo.2016.08.020>.
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gdalmodismodis-datamodis-land-productspeer-reviewedpreprocessingremote-sensingsatellite-imagerytime-series
7.83 score 162 stars 103 scripts 93 downloadsezknitr - Avoid the Typical Working Directory Pain When Using 'knitr'
An extension of 'knitr' that adds flexibility in several ways. One common source of frustration with 'knitr' is that it assumes the directory where the source file lives should be the working directory, which is often not true. 'ezknitr' addresses this problem by giving you complete control over where all the inputs and outputs are, and adds several other convenient features to make rendering markdown/HTML documents easier.
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knitrpeer-reviewedreproducibilityrmarkdownrmd
7.83 score 113 stars 396 scripts 315 downloadsdataspice - Create Lightweight Schema.org Descriptions of Data
The goal of 'dataspice' is to make it easier for researchers to create basic, lightweight, and concise metadata files for their datasets. These basic files can then be used to make useful information available during analysis, create a helpful dataset "README" webpage, and produce more complex metadata formats to aid dataset discovery. Metadata fields are based on the 'Schema.org' and 'Ecological Metadata Language' standards.
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datadatasetmetadataschema-orgunconfunconf18
7.81 score 164 stars 52 scripts 345 downloadswikitaxa - Taxonomic Information from 'Wikipedia'
'Taxonomic' information from 'Wikipedia', 'Wikicommons', 'Wikispecies', and 'Wikidata'. Functions included for getting taxonomic information from each of the sources just listed, as well performing taxonomic search.
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taxonomyspeciesapiweb-serviceswikipediavernacularwikispecieswikicommonstaxizewikipedia-api
7.76 score 22 stars 14 dependents 5 scripts 4.2k downloads
dynamite - Bayesian Modeling and Causal Inference for Multivariate Longitudinal Data
Easy-to-use and efficient interface for Bayesian inference of complex panel (time series) data using dynamic multivariate panel models by Helske and Tikka (2024) <doi:10.1016/j.alcr.2024.100617>. The package supports joint modeling of multiple measurements per individual, time-varying and time-invariant effects, and a wide range of discrete and continuous distributions. Estimation of these dynamic multivariate panel models is carried out via 'Stan'. For an in-depth tutorial of the package, see (Tikka and Helske, 2025) <doi:10.18637/jss.v115.i05>.
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bayesian-inferencepanel-datastanstatistical-modelsquarto
7.75 score 38 stars 31 scripts 630 downloadstinkr - Cast '(R)Markdown' Files to 'XML' and Back Again
Parsing '(R)Markdown' files with numerous regular expressions can be fraught with peril, but it does not have to be this way. Converting '(R)Markdown' files to 'XML' using the 'commonmark' package allows in-memory editing via of 'markdown' elements via 'XPath' through the extensible 'R6' class called 'yarn'. These modified 'XML' representations can be written to '(R)Markdown' documents via an 'xslt' stylesheet which implements an extended version of 'GitHub'-flavoured 'markdown' so that you can tinker to your hearts content.
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commonmarkxmlxpath
7.75 score 62 stars 3 dependents 5 scripts 584 downloadstic - Tasks Integrating Continuously: CI-Agnostic Workflow Definitions
Provides a way to describe common build and deployment workflows for R-based projects: packages, websites (e.g. blogdown, pkgdown), or data processing (e.g. research compendia). The recipe is described independent of the continuous integration tool used for processing the workflow (e.g. 'GitHub Actions' or 'Circle CI'). This package has been peer-reviewed by rOpenSci (v0.3.0.9004).
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appveyorcontinuous-integrationdeploymentgithubactionstravis-ci
7.60 score 155 stars 34 scripts
occCite - Querying and Managing Large Biodiversity Occurrence Datasets
Facilitates the gathering of biodiversity occurrence data from disparate sources. Metadata is managed throughout the process to facilitate reporting and enhanced ability to repeat analyses.
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biodiversity-databiodiversity-informaticsbiodiversity-standardscitationsmuseum-collection-specimensmuseum-collectionsmuseum-metadata
7.54 score 24 stars 48 scripts 479 downloadstracerer - Tracer from R
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'Tracer' (<https://github.com/beast-dev/tracer/>) is a GUI tool to parse and analyze the files generated by 'BEAST2'. This package provides a way to parse and analyze 'BEAST2' input files without active user input, but using R function calls instead.
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cpp
7.54 score 8 stars 3 dependents 80 scripts 384 downloadsroadoi - Find Free Versions of Scholarly Publications via Unpaywall
This web client interfaces Unpaywall <https://unpaywall.org/products/api>, formerly oaDOI, a service finding free full-texts of academic papers by linking DOIs with open access journals and repositories. It provides unified access to various data sources for open access full-text links including Crossref and the Directory of Open Access Journals (DOAJ). API usage is free and no registration is required.
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altmetricscode4liboadoiopen-accesspeer-reviewedunpaywallwebclient
7.46 score 67 stars 107 scripts 403 downloadsfingertipsR - Fingertips Data for Public Health
Fingertips (<http://fingertips.phe.org.uk/>) contains data for many indicators of public health in England. The underlying data is now more easily accessible by making use of the API.
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api-wrapperfingertipshealthopen-datapeer-reviewedpublic-healthpublic-health-england
7.44 score 104 stars 187 scripts 232 downloads
sofa - Connector to 'CouchDB'
Provides an interface to the 'NoSQL' database 'CouchDB' (<https://couchdb.apache.org/>). Methods are provided for managing databases within 'CouchDB', including creating/deleting/updating/transferring, and managing documents within databases. One can connect with a local 'CouchDB' instance, or a remote 'CouchDB' database such as 'IBM Cloudant'. Documents can be inserted directly from vectors, lists, data.frames, and 'JSON'. Targeted at 'CouchDB' v2 or greater.
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couchdbdatabasenosqldocumentscloudantcouchdb-client
7.42 score 33 stars 22 scripts 487 downloads
ruODK - An 'R' Client for the 'ODK Central' API
Access and tidy up data from the 'ODK Central' API. 'ODK Central' is a clearinghouse for digitally captured data using 'ODK' <https://docs.getodk.org/central-intro/>. It manages user accounts and permissions, stores form definitions, and allows data collection clients like 'ODK Collect' to connect to it for form download and submission upload. The 'ODK Central' API is documented at <https://docs.getodk.org/central-api/>.
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databaseopen-dataodkapidatadatasetodataodata-clientodk-centralopendatakit
7.41 score 46 stars 75 scripts
medrxivr - Access and Search MedRxiv and BioRxiv Preprint Data
An increasingly important source of health-related bibliographic content are preprints - preliminary versions of research articles that have yet to undergo peer review. The two preprint repositories most relevant to health-related sciences are medRxiv <https://www.medrxiv.org/> and bioRxiv, both of which are operated by the Cold Spring Harbor Laboratory. 'medrxivr' provides programmatic access to the 'Cold Spring Harbour Laboratory (CSHL)' API <https://api.biorxiv.org/>, allowing users to easily download medRxiv and bioRxiv preprint metadata (e.g. title, abstract, publication date, author list, etc) into R. 'medrxivr' also provides functions to search the downloaded preprint records using regular expressions and Boolean logic, as well as helper functions that allow users to export their search results to a .BIB file for easy import to a reference manager and to download the full-text PDFs of preprints matching their search criteria.
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bibliographic-databasebiorxivevidence-synthesismedrxiv-datapeer-reviewedpreprint-recordssystematic-reviews
7.40 score 65 stars 64 scripts 439 downloadsrdataretriever - R Interface to the Data Retriever
Provides an R interface to the Data Retriever <https://retriever.readthedocs.io/en/latest/> via the Data Retriever's command line interface. The Data Retriever automates the tasks of finding, downloading, and cleaning public datasets, and then stores them in a local database.
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datadata-sciencedatabasedatasetsscience
7.39 score 47 stars 35 scripts 270 downloads
ciecl - International Classification of Diseases 'ICD-10'/'ICD-11' for Chile
Tools for working with the International Classification of Diseases ('ICD-10' Chile official 'MINSAL'/'DEIS' v2018). Includes optimized 'SQL' search with 'SQLite', fuzzy matching of medical terms ('Jaro-Winkler'), Charlson and Elixhauser comorbidity calculation, 'WHO' 'ICD-11' 'API' integration, and hierarchical code validation. Data from Centro FIC Chile 'DEIS' <https://deis.minsal.cl/centrofic/>.
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7.37 score 5 stars 56 scripts 523 downloadsbeastier - Call 'BEAST2'
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is a command-line tool. This package provides a way to call 'BEAST2' from an 'R' function call.
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bayesianbeastbeast2phylogenetic-inferencephylogeneticsopenjdk
7.37 score 11 stars 4 dependents 59 scripts 559 downloadsohun - Optimizing Acoustic Signal Detection
Facilitates the automatic detection of acoustic signals, providing functions to diagnose and optimize the performance of detection routines. Detections from other software can also be explored and optimized. This package has been peer-reviewed by rOpenSci. Araya-Salas et al. (2022) <doi:10.1101/2022.12.13.520253>.
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audio-processingbioacousticssound-event-detectionspectrogramstreamline-analysis
7.31 score 19 stars 1 dependents 60 scripts 418 downloads
suwo - Access Nature Media Repositories
Streamline searching, downloading and formatting of nature media files (e.g. audios, photos) from online repositories. The package offers functions for obtaining media metadata from online repositories, downloading associated media files and updating data sets with new records.
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7.29 score 9 stars 32 scripts 379 downloadssrr - 'rOpenSci' Software Review 'Roclets'
Companion package to 'rOpenSci' statistical software review project ('rOpenSci' authors, 2021; <doi:10.5281/zenodo.5556756>), to facilitate documenting software compliance with statistical standards using 'Roxygen2' 'roclets'.
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compliance-automationstatistical-softwarecpp
7.25 score 5 stars 4 dependents 2 scripts 1.5k downloads
redland - RDF Library Bindings in R
Provides methods to parse, query and serialize information stored in the Resource Description Framework (RDF). RDF is described at <https://www.w3.org/TR/rdf-primer/>. This package supports RDF by implementing an R interface to the Redland RDF C library, described at <https://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph consisting of Statements composed of Subject, Predicate, and Object Nodes.
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redland
7.25 score 16 stars 13 dependents 2.0k downloads
traits - Species Trait Data from Around the Web
Species trait data from many sources, including sequence data from NCBI (<https://www.ncbi.nlm.nih.gov/>), plant traits from BETYdb, and data from EOL Traitbank and BirdLife International.
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traitsapiweb-servicesspeciestaxonomybiodiversityecologyenvironmental-dataspecies-traitsapi-client
7.23 score 42 stars 50 scripts 536 downloads
osmapiR - 'OpenStreetMap' API
Interface to 'OpenStreetMap API' for fetching and saving data from/to the 'OpenStreetMap' database (<https://wiki.openstreetmap.org/wiki/API_v0.6>).
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open street mapopenstreetmaposmopenstreetmap-apiosmapiapi
7.21 score 27 stars 16 scripts 446 downloads
DataSpaceR - Interface to 'the CAVD DataSpace'
Provides a convenient API interface to access immunological data within 'the CAVD DataSpace'(<https://dataspace.cavd.org>), a data sharing and discovery tool that facilitates exploration of HIV immunological data from pre-clinical and clinical HIV vaccine studies.
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cavd-dataspace
7.16 score 5 stars 48 scripts 440 downloadsrsnps - Get 'SNP' ('Single-Nucleotide' 'Polymorphism') Data on the Web
A programmatic interface to various 'SNP' 'datasets' on the web: 'OpenSNP' (<https://opensnp.org>), and 'NBCIs' 'dbSNP' database (<https://www.ncbi.nlm.nih.gov/projects/SNP/>). Functions are included for searching for 'NCBI'. For 'OpenSNP', functions are included for getting 'SNPs', and data for 'genotypes', 'phenotypes', annotations, and bulk downloads of data by user.
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genesnpsequenceapiwebapi-clientspeciesdbsnpopensnpncbigenotypedatasnpsweb-api
7.06 score 55 stars 1 dependents 58 scripts 109 downloadscld2 - Google's Compact Language Detector 2
Bindings to Google's C++ library Compact Language Detector 2 (see <https://github.com/cld2owners/cld2#readme> for more information). Probabilistically detects over 80 languages in plain text or HTML. For mixed-language input it returns the top three detected languages and their approximate proportion of the total classified text bytes (e.g. 80% English and 20% French out of 1000 bytes). There is also a 'cld3' package on CRAN which uses a neural network model instead.
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cldcld2language-detectionlanguage-detectorcpp
7.04 score 39 stars 1 dependents 190 scripts 1.2k 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
7.00 score 99 stars 1 scripts 324 downloadsantiword - Extract Text from Microsoft Word Documents
Wraps the 'AntiWord' utility to extract text from Microsoft Word documents. The utility only supports the old 'doc' format, not the new xml based 'docx' format. Use the 'xml2' package to read the latter.
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antiwordextract-text
6.99 score 59 stars 11 dependents 8 scripts 5.0k downloads
PostcodesioR - API Wrapper Around 'Postcodes.io'
Free UK geocoding using data from Office for National Statistics. It is using several functions to get information about post codes, outward codes, reverse geocoding, nearest post codes/outward codes, validation, or randomly generate a post code. API wrapper around <https://postcodes.io>.
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api-wrappergeocodergeographic-datapeer-reviewedpostcodeuk
6.98 score 42 stars 75 scripts 340 downloadsAthlytics - A Reproducible Framework for Endurance Data Analysis
Tools for reproducible, offline analysis of endurance-training data exported from 'Strava'. Provides data import, quality-control, cohort-reference, and visualization helpers for sports-science indicators including acute:chronic workload ratio, aerobic efficiency, cardiovascular decoupling, exposure, and personal-best profiles.
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activity-trackingacute-chronic-workload-ratioaerobic-decouplingcohort-analysisefficiency-factorendurance-trainingewmaexercise-physiologyggplot2gpx-tcx-fitrolling-averagesports-analyticstidyversetraining-loadtrimp
6.98 score 63 stars 375 downloadsbowerbird - Keep a Collection of Sparkly Data Resources
Tools to get and maintain a data repository from third-party data providers.
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ropensciantarcticsouthern oceandataenvironmentalsatelliteclimatepeer-reviewed
6.94 score 52 stars 1 dependents 16 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
6.92 score 52 stars 269 scriptsritis - Integrated Taxonomic Information System Client
An interface to the Integrated Taxonomic Information System ('ITIS') (<https://www.itis.gov>). Includes functions to work with the 'ITIS' REST API methods (<https://www.itis.gov/ws_description.html>), as well as the 'Solr' web service (<https://www.itis.gov/solr_documentation.html>).
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taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperitistaxize
6.92 score 16 stars 14 dependents 20 scripts 4.1k downloads
reviser - Analyzing Revisions in Real-Time Time Series Vintages
Analyzes revisions in real-time time series vintages. The package converts between wide revision triangles and tidy long vintages, extracts selected releases, computes revision series, visualizes vintage paths, and summarizes revision properties such as bias, dispersion, autocorrelation, and news-noise diagnostics. It also identifies efficient releases and estimates state-space models for revision nowcasting. Methods are based on Howrey (1978) <doi:10.2307/1924972>, Jacobs and Van Norden (2011) <doi:10.1016/j.jeconom.2010.04.010>, and Kishor and Koenig (2012) <doi:10.1198/jbes.2010.08169>.
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forecastingmacroeconomicsnowcastingrevisionstime-series
6.91 score 11 stars 14 scripts 448 downloads
taxadb - A High-Performance Taxonomic Database Interface
Provides fast access to many commonly used taxonomic authorities in a uniform Darwin Core format. Tables are read directly from versioned Parquet snapshots, streamed from cloud storage or from a local copy, and queried with familiar 'dplyr' verbs.
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6.90 score 44 stars 2 dependents 627 downloads
aRxiv - Interface to the arXiv API
An interface to the API for 'arXiv', a repository of electronic preprints for computer science, mathematics, physics, quantitative biology, quantitative finance, and statistics.
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arxivarxiv-analyticsarxiv-apiarxiv-org
6.89 score 64 stars 610 downloadsjsonld - JSON for Linking Data
JSON-LD <https://www.w3.org/TR/json-ld/> is a light-weight syntax for expressing linked data. It is primarily intended for web-based programming environments, interoperable web services and for storing linked data in JSON-based databases. This package provides bindings to the JavaScript library for converting, expanding and compacting JSON-LD documents.
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json-ld
6.88 score 35 stars 13 dependents 47 scripts 2.4k downloads
coevolve - Fit Bayesian Generalized Dynamic Phylogenetic Models using 'Stan' or 'JAX'
Fit Bayesian generalized dynamic phylogenetic models using 'Stan' or 'JAX'. The package allows an arbitrary number of variables with different response distributions to coevolve on a phylogenetic tree via an Ornstein-Uhlenbeck evolutionary process, allowing users to assess directionality between coevolving variables. The optional JAX backend enables high-performance sampling with NumPyro and potential GPU acceleration via 'reticulate'.
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bayesian-statisticscoevolveevolutionstanstatistical-models
6.88 score 15 stars 21 scriptsessurvey - Download Data from the European Social Survey on the Fly
Download data from the European Social Survey directly from their website <http://www.europeansocialsurvey.org/>. There are two families of functions that allow you to download and interactively check all countries and rounds available.
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ess
6.88 score 51 stars 74 scripts 457 downloadspkgmatch - Find R Packages Matching Either Descriptions or Other R Packages
Find R packages from CRAN, 'rOpenSci', or Bioconductor corpora. Packages can be matched to general text descriptions, to names of installed packages, or to local paths to entire source repositories. The package is used to list the most similar packages for each new submission to the 'rOpenSci' software peer-review program ('rOpenSci' authors, 2026; <doi:10.5281/zenodo.18885936>).
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bm25natural-language-processingcpp
6.86 score 9 stars 278 downloads
eia - API Wrapper for U.S. Energy Information Administration ('EIA') Open Data
Provides API access to data from the U.S. Energy Information Administration ('EIA') <https://www.eia.gov/>. Use of the EIA's API and this package requires a free API key obtainable at <https://www.eia.gov/opendata/register.php>. This package includes functions for searching the EIA data directory and returning time series and geoset time series datasets. Datasets returned by these functions are provided by default in a tidy format, or alternatively, in more raw formats. It also offers helper functions for working with EIA date strings and time formats and for inspecting different summaries of series metadata. The package also provides control over API key storage and caching of API request results.
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eiaeia-apienergy-dataenergy-information-administrationopen-data
6.83 score 52 stars 43 scripts 467 downloadstradestatistics - Open Trade Statistics API Wrapper and Utility Program
Access 'Open Trade Statistics' API from R to download international trade data.
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api-wrapperdata-tableinternational-tradejsonliteopen-trade-statistics
6.82 score 82 stars 40 scripts 342 downloadsallcontributors - Acknowledge all Contributors to a Project
Acknowledge all contributors to a project via a single function call. The function appends to a 'README' or other specified file(s) a table with names of all individuals who contributed via code or repository issues. The package also includes several additional functions to extract and quantify contributions to any repository.
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6.80 score 30 stars 1 scripts 418 downloadsbaRcodeR - Label Creation for Tracking and Collecting Data from Biological Samples
Tools to generate unique identifier codes and printable barcoded labels for the management of biological samples. The creation of unique ID codes and printable PDF files can be initiated by standard commands, user prompts, or through a GUI addin for R Studio. Biologically informative codes can be included for hierarchically structured sampling designs.
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6.80 score 37 stars 34 scripts 410 downloadsphylocomr - Interface to 'Phylocom'
Interface to 'Phylocom' (<https://phylodiversity.net/phylocom/>), a library for analysis of 'phylogenetic' community structure and character evolution. Includes low level methods for interacting with the three executables, as well as higher level interfaces for methods like 'aot', 'ecovolve', 'bladj', 'phylomatic', and more.
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phylogenyphylocomphylodiversitycommunity structurecharacter evolutionspeciescommunity-ecologyecologyevolution
6.78 score 15 stars 3 dependents 18 scripts 337 downloads
forcis - Handle the FORCIS Foraminifera Database
Provides an interface to the 'FORCIS' database (Chaabane et al. (2024) <doi:10.5281/zenodo.7390791>) on global foraminifera distribution. This package allows to download and to handle 'FORCIS' data. It is part of the FRB-CESAB working group FORCIS. <https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/forcis/>.
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6.76 score 6 stars 10 scripts 434 downloads
arkdb - Archive and Unarchive Databases Using Flat Files
Flat text files provide a robust, compressible, and portable way to store tables from databases. This package provides convenient functions for exporting tables from relational database connections into compressed text files and streaming those text files back into a database without requiring the whole table to fit in working memory.
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archivingdatabasedbipeer-reviewed
6.68 score 80 stars 617 downloadsrcites - R Interface to the Species+ Database
A programmatic interface to the Species+ <https://speciesplus.net/> database via the Species+/CITES Checklist API <https://api.speciesplus.net/>.
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api-clientcitesdatabaseendangered-speciestrade
6.68 score 14 stars 38 scripts 294 downloads
npi - Access the U.S. National Provider Identifier Registry API
Access the United States National Provider Identifier Registry API <https://npiregistry.cms.hhs.gov/api/>. Obtain and transform administrative data linked to a specific individual or organizational healthcare provider, or perform advanced searches based on provider name, location, type of service, credentials, and other attributes exposed by the API.
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api-wrapperhealth-datahealthcarenpi-number
6.61 score 38 stars 27 scripts 419 downloadsdeposits - A universal client for depositing and accessing research data anywhere
A universal client for depositing and accessing research data anywhere. Currently supported services are zenodo and figshare.
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6.58 score 40 stars 1 dependents 9 scriptstreebase - Discovery, Access and Manipulation of 'TreeBASE' Phylogenies
Interface to the API for 'TreeBASE' <http://treebase.org> from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic trees (of species, population, or genes) and the data used to create them.
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6.57 score 10 stars 1 dependents 41 scripts 394 downloads
nert - Curated Access to TERN Environmental Raster Data
Provides curated access to gridded environmental data published by Australia's Terrestrial Ecosystem Research Network (TERN; <https://www.tern.org.au/>), spanning national soil attribute, soil classification, soil biodiversity, soil moisture, actual evapotranspiration, vegetation canopy height and phenology products. The package reads Cloud-Optimised GeoTIFF and virtual raster files directly from the TERN data server via GDAL /vsicurl range requests, streaming only the requested spatial and temporal subset for efficient data transfer. The environmental raster data are returned as terra::SpatRaster objects. A convenient helper function is also provided that provides a batch-download capability given specific locations and dates, returning the extracted data values in an analysis-ready data.table. Access to the TERN datasets using this package requires a TERN API key.
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ternsoil-dataaustraliaearth-sciencedata-accessagricultural-dataagricultureaustralian-datadata-retrievalecologicalecological-data
6.56 score 4 stars 1 dependents 14 scripts
gitignore - Create Useful .gitignore Files for your Project
Simple interface to query gitignore.io to fetch gitignore templates that can be included in the .gitignore file. More than 450 templates are currently available.
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6.52 score 35 stars 27 scripts 417 downloadstaxa - Classes for Storing and Manipulating Taxonomic Data
Provides classes for storing and manipulating taxonomic data. Most of the classes can be treated like base R vectors (e.g. can be used in tables as columns and can be named). Vectorized classes can store taxon names and authorities, taxon IDs from databases, taxon ranks, and other types of information. More complex classes are provided to store taxonomic trees and user-defined data associated with them.
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taxonomybiologyhierarchydata-cleaningtaxon
6.52 score 51 stars 108 scripts 856 downloads
unifir - A Unifying API for Calling the 'Unity' '3D' Video Game Engine
Functions for the creation and manipulation of scenes and objects within the 'Unity' '3D' video game engine (<https://unity.com/>). Specific focuses include the creation and import of terrain data and 'GameObjects' as well as scene management.
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unifirunityunity3dvisualization
6.49 score 31 stars 1 dependents 22 scripts 419 downloads
fireexposuR - Compute and Visualize Wildfire Exposure
Methods for computing and visualizing wildfire ignition exposure and directional vulnerability that are published in a series of scientific publications are automated by the functions in this package. See Beverly et al. (2010) <doi:10.1071/WF09071>, Beverly et al. (2021) <doi:10.1007/s10980-020-01173-8>, and Beverly and Forbes (2023) <doi:10.1007/s11069-023-05885-3> for background and methodology.
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6.49 score 15 stars 17 scripts 301 downloads
pathviewr - Wrangle, Analyze, and Visualize Animal Movement Data
Tools to import, clean, and visualize movement data, particularly from motion capture systems such as Optitrack's 'Motive', the Straw Lab's 'Flydra', or from other sources. We provide functions to remove artifacts, standardize tunnel position and tunnel axes, select a region of interest, isolate specific trajectories, fill gaps in trajectory data, and calculate 3D and per-axis velocity. For experiments of visual guidance, we also provide functions that use subject position to estimate perception of visual stimuli.
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animal-movementflydramotionmovement-dataoptitracktrajectoriestrajectory-analysisvisual-guidancevisual-perception
6.47 score 11 stars 2 dependents 539 downloads
gtexr - Query the GTEx Portal API
A convenient R interface to the Genotype-Tissue Expression (GTEx) Portal API. The GTEx project is a comprehensive public resource for studying tissue-specific gene expression and regulation in human tissues. Through systematic analysis of RNA sequencing data from 54 non-diseased tissue sites across nearly 1000 individuals, GTEx provides crucial insights into the relationship between genetic variation and gene expression. This data is accessible through the GTEx Portal API enabling programmatic access to human gene expression data. For more information on the API, see <https://gtexportal.org/api/v2/redoc>.
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api-wrapperbioinformaticseqtlgtexsqtl
6.47 score 13 stars 1 dependents 19 scripts 407 downloads
predictNMB - Evaluate Clinical Prediction Models by Net Monetary Benefit
Estimates when and where a model-guided treatment strategy may outperform a treat-all or treat-none approach by Monte Carlo simulation and evaluation of the Net Monetary Benefit. Details can be viewed in Parsons et al. (2023) <doi:10.21105/joss.05328>.
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6.45 score 10 stars 28 scripts 294 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
6.44 score 47 stars 197 scripts 438 downloadsbaRulho - Quantifying (Animal) Sound Degradation
Intended to facilitate acoustic analysis of (animal) sound propagation experiments, which typically aim to quantify changes in signal structure when transmitted in a given habitat by broadcasting and re-recording animal sounds at increasing distances. The package offers a workflow with functions to prepare the data set for analysis as well as to calculate and visualize several degradation metrics, including blur ratio, signal-to-noise ratio, excess attenuation and envelope correlation among others (Dabelsteen et al 1993 <doi:10.1121/1.406682>).
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acoustic-signalsanimalbehaviorbioacoustics
6.44 score 10 stars 23 scripts 286 downloadshistorydata - Datasets for Historians
These sample data sets are intended for historians learning R. They include population, institutional, religious, military, and prosopographical data suitable for mapping, quantitative analysis, and network analysis.
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6.41 score 92 stars 139 scripts 359 downloadscld3 - Google's Compact Language Detector 3
Google's Compact Language Detector 3 is a neural network model for language identification and the successor of 'cld2' (available from CRAN). The algorithm is still experimental and takes a novel approach to language detection with different properties and outcomes. It can be useful to combine this with the Bayesian classifier results from 'cld2'. See <https://github.com/google/cld3#readme> for more information.
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cldcld3language-detectionlanguage-detectorprotobufcpp
6.41 score 43 stars 1 dependents 107 scripts 1.2k downloads
restez - Create and Query a Local Copy of 'GenBank' in R
Download large sections of 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and generate a local SQL-based database. A user can then query this database using 'restez' functions or through 'rentrez' <https://CRAN.R-project.org/package=rentrez> wrappers.
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dnaentrezgenbanksequence
6.40 score 28 stars 1 dependents 120 scripts 307 downloads
chirps - Access Climate Hazards Center Datasets
Provides access to Climate Hazards Center (CHC) datasets including CHIRPS v2, CHIRPS v3, CHIRTS-daily, and CHIRTS-ERA5. The 'CHIRPS' data is a quasi-global (50°S – 50°N) high-resolution (0.05 arc-degrees) rainfall data set, which incorporates satellite imagery and in-situ station data to create gridded rainfall time series for trend analysis and seasonal drought monitoring. 'CHIRTS' is a quasi-global (60°S – 70°N), high-resolution data set of daily maximum and minimum temperatures. For more details on CHC datasets please visit their official home page <https://www.chc.ucsb.edu/data>.
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chirpsclimatologyprecipitation-data
6.37 score 39 stars 804 downloadsspiro - Manage Data from Cardiopulmonary Exercise Testing
Import, process, summarize and visualize raw data from metabolic carts. See Robergs, Dwyer, and Astorino (2010) <doi:10.2165/11319670-000000000-00000> for more details on data processing.
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6.36 score 15 stars 51 scripts 388 downloadsrzmq - R Bindings for 'ZeroMQ'
Interface to the 'ZeroMQ' lightweight messaging kernel (see <https://zeromq.org/> for more information).
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zeromqzmqzeromq3cpp
6.33 score 87 stars 71 scripts 585 downloads
daiquiri - Data Quality Reporting for Temporal Datasets
Generate reports that enable quick visual review of temporal shifts in record-level data. Time series plots showing aggregated values are automatically created for each data field (column) depending on its contents (e.g. min/max/mean values for numeric data, no. of distinct values for categorical data), as well as overviews for missing values, non-conformant values, and duplicated rows. The resulting reports are shareable and can contribute to forming a transparent record of the entire analysis process. It is designed with Electronic Health Records in mind, but can be used for any type of record-level temporal data (i.e. tabular data where each row represents a single "event", one column contains the "event date", and other columns contain any associated values for the event).
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data-qualityinitial-data-analysisreproducible-researchtemporal-datatime-series
6.31 score 40 stars 17 scripts 535 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
6.27 score 11 stars 42 scripts 511 downloads
mapscanner - Print Maps, Draw on Them, Scan Them Back in
Enables preparation of maps to be printed and drawn on. Modified maps can then be scanned back in, and hand-drawn marks converted to spatial objects.
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mapsscanspatialcpp
6.25 score 89 stars 310 downloadsDoOR.functions - Integrating Heterogeneous Odorant Response Data into a Common Response Model: A DoOR to the Complete Olfactome
This is a function package providing functions to perform data manipulations and visualizations for DoOR.data. See the URLs for the original and the DoOR 2.0 publication.
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peer-reviewed
6.23 score 11 stars 64 scripts
rmangal - 'Mangal' Client
An interface to the 'Mangal' database - a collection of ecological networks. This package includes functions to work with the 'Mangal RESTful API' methods (<https://mangal-interactions.github.io/mangal-api/>).
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ecologynetworksfood websinteractionsdata publicationsopen access
6.23 score 16 stars 281 downloadsrnaturalearthhires - High Resolution World Vector Map Data from Natural Earth used in rnaturalearth
Facilitates mapping by making natural earth map data from http:// www.naturalearthdata.com/ more easily available to R users. Focuses on vector data.
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6.21 score 31 stars 1 dependents 880 scriptspaleobioDB - Download and Process Data from the Paleobiology Database
Includes functions to wrap most endpoints of the 'PaleobioDB' API and to visualize and process the obtained fossil data. The API documentation for the Paleobiology Database can be found at <https://paleobiodb.org/data1.2/>.
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6.21 score 46 stars 71 scripts 458 downloads
mctq - Munich ChronoType Questionnaire Tools
A complete toolkit for processing the Munich ChronoType Questionnaire (MCTQ) in its three versions: standard, micro, and shift. The MCTQ is a quantitative and validated tool used to assess chronotypes based on individuals' sleep behavior. It was originally presented by Till Roenneberg, Anna Wirz-Justice, and Martha Merrow in 2003 (2003, <doi:10.1177/0748730402239679>).
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infrastructurepreprocessingvisualizationbiological-rhythmchronobiologychronotypecircadian-phenotypecircadian-rhythmentrainmentmctqpeer-reviewedsleeptemporal-phenotype
6.20 score 14 stars 38 scripts 411 downloads
sasquatch - Use 'SAS', R, and 'quarto' Together
Use R and 'SAS' within reproducible multilingual 'quarto' documents. Run 'SAS' code blocks interactively, send data back and forth between 'SAS' and R, and render 'SAS' output within 'quarto' documents. 'SAS' connections are established through a combination of 'SASPy' and 'reticulate'.
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6.18 score 17 stars 15 scripts 208 downloads
patentsview - An R Client to the 'PatentsView' API
Provides functions to simplify the 'PatentsView' API (<https://search.patentsview.org/docs/docs/Search%20API/SearchAPIReference/#api-query-language>) query language, send GET and POST requests to the API's twenty seven endpoints, and parse the data that comes back.
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patentspatentsearch-apipatentsviewpatentsview-apipeer-revieweduspto
6.18 score 39 stars 78 scripts 305 downloads
GSODR - Global Surface Summary of the Day ('GSOD') Weather Data Client
Provides automated downloading, parsing, cleaning, unit conversion and formatting of Global Surface Summary of the Day ('GSOD') weather data from the from the USA National Centers for Environmental Information ('NCEI'). The data were retired on 2025-08-29 and are no longer updated. Units are converted from from United States Customary System ('USCS') units to International System of Units ('SI'). Stations may be individually checked for number of missing days defined by the user, where stations with too many missing observations are omitted. Only stations with valid reported latitude and longitude values are permitted in the final data. Additional useful elements, saturation vapour pressure ('es'), actual vapour pressure ('ea') and relative humidity ('RH') are calculated from the original data using the improved August-Roche-Magnus approximation (Alduchov & Eskridge 1996) and included in the final data set. The resulting metadata include station identification information, country, state, latitude, longitude, elevation, weather observations and associated flags. For information on the 'GSOD' data from 'NCEI', please see the 'GSOD' 'readme.txt' file available from, <https://www.ncei.noaa.gov/pub/data/gsod/readme.txt>.
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us-nceimeteorological-dataglobal-weatherweatherweather-datameteorologystation-datasurface-weatherdata-accessus-ncdcdaily-datadaily-weatherglobal-datagsodhistorical-datahistorical-weatherncdcnceiweather-informationweather-stations
6.17 score 98 stars 2 scripts 960 downloads
GLMMcosinor - Fit a Cosinor Model Using a Generalized Mixed Modeling Framework
Allows users to fit a cosinor model using the 'glmmTMB' framework. This extends on existing cosinor modeling packages, including 'cosinor' and 'circacompare', by including a wide range of available link functions and the capability to fit mixed models. The cosinor model is described by Cornelissen (2014) <doi:10.1186/1742-4682-11-16>.
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6.16 score 4 stars 40 scripts 747 downloads
pkgreviewr - rOpenSci package review project template
Creates files and collects materials necessary to complete an rOpenSci package review. Review files are prepopulated with review package specific metadata. Review package source code is also cloned for local testing and inspection.
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reviewropensciropensci-reviewsunconfunconf18
6.14 score 36 stars 43 scriptstaxizedb - 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
6.12 score 35 stars 126 scripts 362 downloads
ibger - Access the 'IBGE' Aggregate Data API from 'R'
'Tidyverse'-friendly interface to the Brazilian Institute of Geography and Statistics ('IBGE') aggregate data 'API' <https://servicodados.ibge.gov.br/api/docs/agregados?versao=3>. Query aggregates, variables, localities, periods, and metadata from surveys and censuses conducted by 'IBGE'.
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6.11 score 5 stars 259 downloads
c14bazAAR - Download and Prepare C14 Dates from Different Source Databases
Query different C14 date databases and apply basic data cleaning, merging and calibration steps. Currently available databases: 14cpalaeolithic, 14sea, adrac, agrichange, aida, austarch, bda, calpal, caribbean, eubar, euroevol, irdd, jomon, katsianis, kiteeastafrica, medafricarbon, mesorad, neonet, neonetatl, nerd, p3k14c, pacea, palmisano, rado.nb, rxpand, sard, tegiszhol, xronos.
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archaeologyradiocarbon-dates
6.11 score 33 stars 56 scripts 22 downloads
gittargets - Data Version Control for the Targets Package
In computationally demanding data analysis pipelines, the 'targets' R package (2021, <doi:10.21105/joss.02959>) maintains an up-to-date set of results while skipping tasks that do not need to rerun. This process increases speed and increases trust in the final end product. However, it also overwrites old output with new output, and past results disappear by default. To preserve historical output, the 'gittargets' package captures version-controlled snapshots of the data store, and each snapshot links to the underlying commit of the source code. That way, when the user rolls back the code to a previous branch or commit, 'gittargets' can recover the data contemporaneous with that commit so that all targets remain up to date.
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data-sciencedata-version-controldata-versioningreproducibilityreproducible-researchtargetsworkflow
6.07 score 90 stars 13 scripts 473 downloadsgraphql - A GraphQL Query Parser
Bindings to the 'libgraphqlparser' C++ library. Parses GraphQL <https://graphql.org> syntax and exports the AST in JSON format.
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graphqllibgraphqlcpp
6.07 score 39 stars 5 dependents 7 scripts 850 downloads
nomisr - Access 'Nomis' UK Labour Market Data
Access UK official statistics from the 'Nomis' database. 'Nomis' includes data from the Census, the Labour Force Survey, DWP benefit statistics and other economic and demographic data from the Office for National Statistics, based around statistical geographies. See <https://www.nomisweb.co.uk/api/v01/help> for full API documentation.
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api-clientcensus-datademographygeographic-datanational-statisticsofficial-statisticsofficialstatisticspeer-revieweduk
6.05 score 50 stars 111 scripts 112 downloadsmregions2 - Access Data from Marineregions.org: Gazetteer & Data Products
Explore and retrieve marine geospatial data from the Marine Regions Gazetteer <https://marineregions.org/gazetteer.php?p=webservices> and the Marine Regions Data Products <https://marineregions.org/webservices.php>.
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6.02 score 12 stars 2 dependents 73 scripts 340 downloads
emodnet.wfs - Access 'EMODnet' Web Feature Service Data
Access and interrogate 'EMODnet' (European Marine Observation and Data Network) Web Feature Service data <https://emodnet.ec.europa.eu/en/emodnet-web-service-documentation#data-download-services>. This includes listing existing data sources, and getting data from each of them.
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biologydataproductsemodnetmarine-datawfs
6.02 score 8 stars 29 scripts 474 downloadsbikedata - Download and Aggregate Data from Public Hire Bicycle Systems
Download and aggregate data from all public hire bicycle systems which provide open data, currently including 'Santander' Cycles in London, U.K.; from the U.S.A., 'Ford GoBike' in San Francisco CA, 'citibike' in New York City NY, 'Divvy' in Chicago IL, 'Capital Bikeshare' in Washington DC, 'Hubway' in Boston MA, 'Metro' in Los Angeles LA, 'Indego' in Philadelphia PA, and 'Nice Ride' in Minnesota; 'Bixi' from Montreal, Canada; and 'mibici' from Guadalajara, Mexico.
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bicycle-hire-systemsbike-hire-systemsbike-hirebicycle-hiredatabasebike-datapeer-reviewedcpp
5.98 score 80 stars 15 scripts 110 downloadspangaear - Client for the 'Pangaea' Database
Tools to interact with the 'Pangaea' Database (<https://www.pangaea.de>), including functions for searching for data, fetching 'datasets' by 'dataset' 'ID', and working with the 'Pangaea' 'OAI-PMH' service.
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pangaeaenvironmental scienceearth sciencearchivepaleontologyecologychemistryatmosphereapi-clientdatapaleobiologyscientificwebservice-client
5.94 score 25 stars 443 downloads
terrainr - Landscape Visualizations in R and 'Unity'
Functions for the retrieval, manipulation, and visualization of 'geospatial' data, with an aim towards producing '3D' landscape visualizations in the 'Unity' '3D' rendering engine. Functions are also provided for retrieving elevation data and base map tiles from the 'USGS' National Map <https://apps.nationalmap.gov/services/>.
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datasetsdemsmapmap-tilesmappingnational-mapnhdorthoimagerypeer-reviewedprogressrretrieve-dataterrainrunityunity-rendering-engineusgs
5.89 score 78 stars 542 downloadscircle - R Client Package for Circle CI
Tools for interacting with the 'Circle CI' API (<https://circleci.com/docs/api/v2/>). Besides executing common tasks such as querying build logs and restarting builds, this package also helps setting up permissions to deploy from builds.
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api-clientcircle-cicontinuous-deploymentcontinuous-integration
5.77 score 13 stars 398 downloads
phylotaR - Automated Phylogenetic Sequence Cluster Identification from 'GenBank'
A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.
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blastngenbankpeer-reviewedphylogeneticssequence-alignment
5.75 score 25 stars 91 scripts 9 downloadsBaseSet - Working with Sets the Tidy Way
Implements a class and methods to work with sets, doing intersection, union, complementary sets, power sets, cartesian product and other set operations in a "tidy" way. These set operations are available for both classical sets and fuzzy sets. Import sets from several formats or from other several data structures.
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bioconductorbioconductor-packagesets
5.69 score 11 stars 6 scripts 490 downloads
trud - Query the 'NHS TRUD API'
Provides a convenient R interface to the 'National Health Service NHS Technology Reference Update Distribution (TRUD) API', allowing users to list available releases for their subscribed items, retrieve metadata, and download release files. For more information on the API, see <https://isd.digital.nhs.uk/trud/users/guest/filters/0/api>.
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api-wrapperehricdnhssnomed-ct
5.68 score 8 stars 4 scripts 333 downloads
refsplitr - author name disambiguation, author georeferencing, and mapping of coauthorship networks with 'Web of Science' data
Tools to parse and organize reference records downloaded from the 'Web of Science' citation database into an R-friendly format, disambiguate the names of authors, geocode their locations, and generate/visualize coauthorship networks. This package has been peer-reviewed by rOpenSci (v. 1.0).
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name disambiguationbibliometricscoauthorshipcollaborationgeoreferencingmetasciencereferencesscientometricsscience of scienceweb of science
5.66 score 59 stars 31 scripts
dwctaxon - Edit and Validate Darwin Core Taxon Data
Edit and validate taxonomic data in compliance with Darwin Core standards (Darwin Core 'Taxon' class <https://dwc.tdwg.org/terms/#taxon>).
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database
5.64 score 11 stars 354 downloads
rotemplate - pkgdown template and utilities for rOpenSci docs
This is a private template for use by rOpenSci packages. Please don't use it for your own non-rOpenSci package.
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pkgdown
5.64 score 25 stars 7 scripts
rangr - Mechanistic Simulation of Species Range Dynamics
Integrates population dynamics and dispersal into a mechanistic virtual species simulator. The package can be used to study the effects of environmental change on population growth and range shifts. It allows for simple and straightforward definition of population dynamics (including positive density dependence), extensive possibilities for defining dispersal kernels, and the ability to generate virtual ecologist data. Learn more about the 'rangr' at <https://docs.ropensci.org/rangr/>.
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5.61 score 3 stars 1 dependents 15 scripts 255 downloads
Rpolyhedra - Polyhedra Database
A polyhedra database scraped from various sources as R6 objects and 'rgl' visualizing capabilities.
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geometrypolyhedra-databasergl
5.59 score 13 stars 415 downloads
taxlist - Handling Taxonomic Lists
Handling taxonomic lists through objects of class 'taxlist'. This package provides functions to import species lists from 'Turboveg' (<https://www.synbiosys.alterra.nl/turboveg/>) and the possibility to create backups from resulting R-objects. Also quick displays are implemented as summary-methods.
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5.59 score 13 stars 1 dependents 417 downloadsroreviewapi - Plumber API to report package structure and function
Plumber API to report package structure and function.
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5.56 score 3 starschlorpromazineR - Convert Antipsychotic Doses to Chlorpromazine Equivalents
As different antipsychotic medications have different potencies, the doses of different medications cannot be directly compared. Various strategies are used to convert doses into a common reference so that comparison is meaningful. Chlorpromazine (CPZ) has historically been used as a reference medication into which other antipsychotic doses can be converted, as "chlorpromazine-equivalent doses". Using conversion keys generated from widely-cited scientific papers, e.g. Gardner et. al 2010 <doi:10.1176/appi.ajp.2009.09060802> and Leucht et al. 2016 <doi:10.1093/schbul/sbv167>, antipsychotic doses are converted to CPZ (or any specified antipsychotic) equivalents. The use of the package is described in the included vignette. Not for clinical use.
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antipsychoticpharmacologypsychiatryschizophrenia
5.54 score 15 stars 23 scripts 300 downloads
ernest - A Toolkit for Nested Sampling
Bayesian evidence estimation and posterior inference with the nested sampling algorithm, described in Skilling (2006) <doi:10.1214/06-BA127> and Buchner (2023) <doi:10.1214/23-SS144>, along with S3 methods for simulating uncertainty and creating visualisations.
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bayesian-inferencenested-samplingropenscistatisticscpp
5.51 score 4 stars 5 scripts 269 downloadskarel - Learning programming with Karel the robot
This is the R implementation of Karel the robot, a programming language created by Dr. R. E. Pattis at Stanford University in 1981. Karel is an useful tool to teach introductory concepts about general programming, such as algorithmic decomposition, conditional statements, loops, etc., in an interactive and fun way, by writing programs to make Karel the robot achieve certain tasks in the world she lives in. Originally based on Pascal, Karel was implemented in many languages through these decades, including 'Java', 'C++', 'Ruby' and 'Python'. This is the first package implementing Karel in R.
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learningprogrammingr-language
5.50 score 12 stars 44 scripts 70 downloads
nuts - Convert European Regional Data
Motivated by changing administrative boundaries over time, the 'nuts' package can convert European regional data with NUTS codes between versions (2006, 2010, 2013, 2016, 2021 and 2024) and levels (NUTS 1, NUTS 2 and NUTS 3). The package uses spatial interpolation as in Lam (1983) <doi:10.1559/152304083783914958> based on granular (100m x 100m) area, population and land use data provided by the European Commission's Joint Research Center.
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europeeuropean-unioneurostatnomenclaturenutsnuts-codesnuts-regionsregional-data
5.50 score 10 stars 21 scripts 348 downloadstidyqpcr - Quantitative PCR Analysis with the Tidyverse
For reproducible quantitative PCR (qPCR) analysis building on packages from the ’tidyverse’, notably ’dplyr’ and ’ggplot2’. It normalizes (by ddCq), summarizes, and plots pre-calculated Cq data, and plots raw amplification and melt curves from Roche Lightcycler (tm) machines. It does NOT (yet) calculate Cq data from amplification curves.
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miqeqpcrqpcr-analysistidyverse
5.49 score 60 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
5.41 score 37 stars 6 scripts
quadkeyr - Generate Raster Images from QuadKey-Identified Datasets
A set of functions of increasing complexity allows users to (1) convert QuadKey-identified datasets, based on 'Microsoft's Bing Maps Tile System', into Simple Features data frames, (2) transform Simple Features data frames into rasters, and (3) process multiple 'Meta' ('Facebook') QuadKey-identified human mobility files directly into raster files. For more details, see D’Andrea et al. (2024) <doi:10.21105/joss.06500>.
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geospatialquadkeyrastertilemap
5.41 score 17 stars 362 downloadsrOPTRAM - Derive Soil Moisture Using the OPTRAM Algorithm
The OPtical TRapezoid Model (OPTRAM) derives soil moisture based on the linear relation between a vegetation index and Land Surface Temperature (LST). The Short Wave Infra-red (SWIR) band is used as a proxy for LST. See: Sadeghi, M. et al., 2017. <https://doi.org/10.1016/j.rse.2017.05.041> .
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5.40 score 14 stars 12 scriptsrfisheries - Programmatic Interface to the 'openfisheries.org' API
A programmatic interface to 'openfisheries.org'. This package is part of the 'rOpenSci' suite (https://ropensci.org).
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fisheriesopen-dataopenfisheries
5.37 score 28 stars 42 scripts 248 downloads
fastMatMR - High-Performance Matrix Market File Operations
An interface to the 'fast_matrix_market' 'C++' library, this package offers efficient read and write operations for Matrix Market files in R. It supports both sparse and dense matrix formats. Peer-reviewed at 'rOpenSci' (<https://github.com/ropensci/software-review/issues/606>).
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cpp17matrix-marketmatrix-market-formatr-cpp11cpp
5.37 score 5 stars 31 scripts 274 downloadsrepometrics - Metrics for Your Code Repository
Metrics for your code repository. Call one function to generate an interactive dashboard displaying the state of your code.
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dashboardsoftware-metrics
5.33 score 3 stars 1 dependentsdendroNetwork - Create Networks of Dendrochronological Series using Pairwise Similarity
Creating dendrochronological networks based on the similarity between tree-ring series or chronologies. The package includes various functions to compare tree-ring curves building upon the 'dplR' package. The networks can be used to visualise and understand the relations between tree-ring curves. These networks are also very useful to estimate the provenance of wood as described in Visser (2021) <DOI:10.5334/jcaa.79> or wood-use within a structure/context/site as described in Visser and Vorst (2022) <DOI:10.1163/27723194-bja10014>.
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visualizationgraphandnetworkthirdpartyclientnetworkarchaeologydendrochronologydendroprovenancenetwork-analysistree-rings
5.29 score 7 stars 14 scripts 335 downloadsmauricer - Work with 'BEAST2' Packages
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is commonly accompanied by 'BEAUti 2' (<https://www.beast2.org>), which, among others, allows one to install 'BEAST2' package. This package allows to work with 'BEAST2' packages from 'R'.
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openjdk
5.26 score 3 stars 2 dependents 442 downloadsphonfieldwork - Linguistic Phonetic Fieldwork Tools
There are a lot of different typical tasks that have to be solved during phonetic research and experiments. This includes creating a presentation that will contain all stimuli, renaming and concatenating multiple sound files recorded during a session, automatic annotation in 'Praat' TextGrids (this is one of the sound annotation standards provided by 'Praat' software, see Boersma & Weenink 2020 <https://www.fon.hum.uva.nl/praat/>), creating an html table with annotations and spectrograms, and converting multiple formats ('Praat' TextGrid, 'ELAN', 'EXMARaLDA', 'Audacity', subtitles '.srt', and 'FLEx' flextext). All of these tasks can be solved by a mixture of different tools (any programming language has programs for automatic renaming, and Praat contains scripts for concatenating and renaming files, etc.). 'phonfieldwork' provides a functionality that will make it easier to solve those tasks independently of any additional tools. You can also compare the functionality with other packages: 'rPraat' <https://CRAN.R-project.org/package=rPraat>, 'textgRid' <https://CRAN.R-project.org/package=textgRid>.
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audacityeafelanexbexmaraldafieldworkflextextphoneticsphonologypraatsrt-subtitlestextgrid
5.26 score 20 stars 30 scripts 158 downloadshandlr - Convert Among Citation Formats
Converts among many citation formats, including 'BibTeX', 'Citeproc', 'Codemeta', 'RDF XML', 'RIS', 'Schema.org', and 'Citation File Format'. A low level 'R6' class is provided, as well as stand-alone functions for each citation format for both read and write.
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doimetadatacitationbibtexcrossrefcrosscitecodemetarisciteprocrdfxmljsoncitationsdigital-object-identifier
5.24 score 37 stars 31 scripts 441 downloadsbold - Interface to Bold Systems API
A programmatic interface to the Web Service methods provided by Bold Systems (<http://www.boldsystems.org/>) for genetic 'barcode' data. Functions include methods for searching by sequences by taxonomic names, ids, collectors, and institutions; as well as a function for searching for specimens, and downloading trace files.
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biodiversitybarcodednasequencesfastaapi-wrapperbarcodestaxize
5.23 score 21 stars 1 dependents 2 scripts 268 downloads
read.abares - Read Australian Agricultural Data from Government Agencies
Downloads and imports agricultural data from the Australian Bureau of Agricultural and Resource Economics and Sciences (ABARES) <https://www.agriculture.gov.au/abares> and the Australian Bureau of Statistics (ABS) <https://www.abs.gov.au>. Supports multiple data formats including spreadsheets, comma‑separated value (CSV) files, and geospatial data such as shapefiles and GeoTIFFs. Covers topics such as broadacre crops, livestock, soils, commodities and related agricultural information. The package standardises field names and data formats to improve interoperability and simplify analysis. It also streamlines the import of geospatial data and corrects common issues found in these data sources upon loading.
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agricultureagriculture-dataagriculture-datasetagriculture-trade-dataaustraliadata-retrievalland-use-classificationland-use-dataopen-dataopen-datasetstrade-data
5.22 score 5 stars 1 dependents 7 scripts 266 downloads
dataaimsr - AIMS Data Platform API Client
AIMS Data Platform API Client which provides easy access to AIMS Data Platform scientific data and information.
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aimsaustraliadatamarinemonitoringsstweather
5.21 score 6 stars 45 scriptsmcbette - Model Comparison Using 'babette'
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'mcbette' allows to do a Bayesian model comparison over some site and clock models, using 'babette' (<https://github.com/ropensci/babette/>).
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openjdk
5.21 score 7 stars 23 scripts 274 downloadsinternetarchive - An API Client for the Internet Archive
Search the Internet Archive (<https://archive.org>), retrieve metadata, and download files.
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5.19 score 65 stars 12 scripts 32 downloadsqcoder - Lightweight Qualitative Coding
A free, lightweight, open source option for analyzing text-based qualitative data. Enables analysis of interview transcripts, observation notes, memos, and other sources. Supports the work of social scientists, historians, humanists, and other researchers who use qualitative methods. Addresses the unique challenges faced in analyzing qualitative data analysis. Provides opportunities for researchers who otherwise might not develop software to build software development skills.
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unconfunconf18
5.15 score 154 stars 14 scripts
canaper - Categorical Analysis of Neo- And Paleo-Endemism
Provides functions to analyze the spatial distribution of biodiversity, in particular categorical analysis of neo- and paleo-endemism (CANAPE) as described in Mishler et al (2014) <doi:10.1038/ncomms5473>. 'canaper' conducts statistical tests to determine the types of endemism that occur in a study area while accounting for the evolutionary relationships of species.
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biodiversitycanape
5.13 score 9 stars 372 downloads
butterfly - Verification for Continually Updating Time Series Data
Verification of continually updating time series data where we expect new values, but want to ensure previous data remains unchanged. Data previously recorded could change for a number of reasons, such as discovery of an error in model code, a change in methodology or instrument recalibration. Monitoring data sources for these changes is not always possible. Other unnoticed changes could include a jump in time or measurement frequency, due to instrument failure or software updates. Functionality is provided that can be used to check and flag changes to previous data to prevent changes going unnoticed, as well as unexpected jumps in time.
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data-versioningqaqctimeseriesverification
5.12 score 11 stars 12 scripts 297 downloads
ssarp - Species-/Speciation-Area Relationship Projector
Create Species- and Speciation-Area Relationships using occurrence records or presence-absence matrices.
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5.03 score 6 stars 18 scriptstidypmc - Parse Full Text XML Documents from PubMed Central
Parse XML documents from the Open Access subset of Europe PubMed Central <https://europepmc.org> including section paragraphs, tables, captions and references.
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5.00 score 36 stars 28 scripts 70 downloadsgpg - GNU Privacy Guard for R
Bindings to GnuPG for working with OpenGPG (RFC4880) cryptographic methods. Includes utilities for public key encryption, creating and verifying digital signatures, and managing your local keyring. Some functionality depends on the version of GnuPG that is installed on the system. On Windows this package can be used together with 'GPG4Win' which provides a GUI for managing keys and entering passphrases.
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gpgme
4.99 score 21 stars 31 scripts 142 downloadsrdryad - Access for Dryad Web Services
Interface to the Dryad "Solr" API, their "OAI-PMH" service, and fetch datasets. Dryad (<https://datadryad.org/>) is a curated host of data underlying scientific publications.
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datadoidryaddryad-apioai-pmh
4.96 score 26 stars 295 downloadsoutcomerate - AAPOR Survey Outcome Rates
Standardized survey outcome rate functions, including the response rate, contact rate, cooperation rate, and refusal rate. These outcome rates allow survey researchers to measure the quality of survey data using definitions published by the American Association for Public Opinion Research (AAPOR). For details on these standards, see AAPOR (2023) <https://aapor.org/wp-content/uploads/2024/03/Standards-Definitions-10th-edition.pdf>.
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aapordisposition-codespeer-reviewedstandardssurvey
4.95 score 5 stars 36 scripts 256 downloadsrgnparser - Parse Scientific Names
Parse scientific names using 'gnparser' (<https://github.com/gnames/gnparser>), written in Go. 'gnparser' parses scientific names into their component parts; it utilizes a Parsing Expression Grammar specifically for scientific names.
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taxonomy
4.95 score 15 stars 1 dependents 301 downloads
excluder - Checks for Exclusion Criteria in Online Data
Data that are collected through online sources such as Mechanical Turk may require excluding rows because of IP address duplication, geolocation, or completion duration. This package facilitates exclusion of these data for Qualtrics datasets.
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datacleaningexclusionmturkqualtrics
4.95 score 9 stars 462 downloadspvEBayes - Empirical Bayes Methods for Pharmacovigilance
A suite of empirical Bayes methods to use in pharmacovigilance. Contains various model fitting and post-processing functions. For more details see Tan et al. (2025) <doi:10.1002/sim.70195>, <doi:10.48550/arXiv.2512.01057>; Koenker and Mizera (2014) <doi:10.1080/01621459.2013.869224>; Efron (2016) <doi:10.1093/biomet/asv068>.
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pharmacovigilancecpp
4.93 score 3 scripts 419 downloadsrtika - R Interface to 'Apache Tika'
Extract text or metadata from over a thousand file types, using Apache Tika <https://tika.apache.org/>. Get either plain text or structured XHTML content.
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extract-metadataextract-textjavaparsepdf-filespeer-reviewedtesseracttika
4.92 score 55 stars 3 scripts 135 downloads
wateRinfo - Download Time Series Data from Waterinfo.be
wateRinfo facilitates access to waterinfo.be (<https://www.waterinfo.be>), a website managed by the Flanders Environment Agency (VMM) and Flanders Hydraulics Research. The website provides access to real-time water and weather related environmental variables for Flanders (Belgium), such as rainfall, air pressure, discharge, and water level. The package provides functions to search for stations and variables, and download time series.
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apiclimatelifewatchopen-scienceoscibioropensciwaterweather
4.89 score 13 starsgetCRUCLdata - 'CRU' 'CL' v. 2.0 Climatology Client
Provides functions that automate downloading and importing University of East Anglia Climate Research Unit ('CRU') 'CL' v. 2.0 climatology data, facilitates the calculation of minimum temperature and maximum temperature and formats the data into a data.table object or a 'terra' 'SpatRaster' object. 'CRU' 'CL' v. 2.0 data are a gridded climatology of 1961-1990 monthly means released in 2002 and cover all land areas (excluding Antarctica) at 10 arc minutes (0.1666667 degree) resolution. For more information see the description of the data provided by the University of East Anglia Climate Research Unit, <https://crudata.uea.ac.uk/cru/data/hrg/tmc/readme.txt>.
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anglia-cruclimate-datacru-cl2temperaturerainfallelevationdata-accesswindrelative-humiditysolar-radiationdiurnal-temperaturefrostcrupeer-reviewed
4.88 score 17 stars 422 downloadsneotoma - Access to the Neotoma Paleoecological Database Through R
NOTE: This package is deprecated. Please use the neotoma2 package described at https://github.com/NeotomaDB/neotoma2. Access paleoecological datasets from the Neotoma Paleoecological Database using the published API (<http://wnapi.neotomadb.org/>), only containing datasets uploaded prior to June 2020. The functions in this package access various pre-built API functions and attempt to return the results from Neotoma in a usable format for researchers and the public.
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neotomaneotoma-apisneotoma-databasensfpaleoecology
4.85 score 31 stars 91 scripts 120 downloads
agroclimatico - Índices y Estadísticos Climáticos e Hidrológicos
Conjunto de funciones para calcular índices y estadísticos climáticos hidrológicos a partir de datos tidy. Incluye una función para graficar resultados georeferenciados y e información cartográfica.
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agriculturameteorologiacpp
4.76 score 19 stars 10 scriptsbabeldown - Helpers for Automatic Translation of Markdown-based Content
Provide workflows and guidance for automatic translation of Markdown-based R content using DeepL API.
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quarto
4.70 score 31 stars 12 scripts
RAMEN - Regional Association of Methylome variability with the Exposome and geNome
RAMEN is an R package which goal is to identify Variable Methylated Loci (VML) in microarray DNA methylation data. Then, using genome and exposome data, RAMEN identifies which individual genetic (G) or environmental (E) or joint (G+E or GxE) model better explains the VML variability. This package provides estimates of genetic and environmental contribution for each VML, allowing researchers to gain insights into the complex interplay between genetics, environment and DNA methylation.
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dnamethylationgenomewideassociationepigeneticsregressionsnpmicroarraymethylationarraygeneticvariabilitybioinformatics-tooldna-methylationexposomegenomemethylation-analysismethylation-microarraysmultiomics
4.70 score 10 stars 8 scriptsc3dr - Read and Write C3D Motion Capture Files
A wrapper for the 'EZC3D' library to work with C3D motion capture data.
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quartocpp
4.70 score 5 stars 8 scripts 551 downloadsDoOR.data - Integrating Heterogeneous Odorant Response Data into a Common Response Model: A DoOR to the Complete Olfactome
This is a data package providing Drosophila odorant response data for DoOR.functions. See URLs for the original and the DoOR 2.0 publications.
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peer-reviewed
4.65 score 8 stars 1 dependents 188 scripts
smapr - Acquisition and Processing of NASA Soil Moisture Active-Passive (SMAP) Data
Facilitates programmatic access to NASA Soil Moisture Active Passive (SMAP) data with R. It includes functions to search for, acquire, and extract SMAP data.
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acquisitionextract-datanasapeer-reviewedrastersmap-datasoil-mappingsoil-moisturesoil-moisture-sensor
4.64 score 87 stars 59 downloadsrdatacite - Client for the 'DataCite' API
Client for the web service methods provided by 'DataCite' (<https://www.datacite.org/>), including functions to interface with their 'RESTful' search API. The API is backed by 'Elasticsearch', allowing expressive queries, including faceting.
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datascholarlydatasethttpsapiweb-servicesapi-wrapperdataciteidentifiermetadataoai-pmhsolr
4.64 score 24 stars 12 scripts 274 downloads
skynet - Generates Networks from BTS Data
A flexible tool that allows generating bespoke air transport statistics for urban studies based on publicly available data from the Bureau of Transport Statistics (BTS) in the United States <https://www.transtats.bts.gov/databases.asp?Z1qr_VQ=E&Z1qr_Qr5p=N8vn6v10&f7owrp6_VQF=D>.
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air-transportbtsbureau-of-transport-statisticsdb1bpeer-reviewedritaskynett100transtats
4.62 score 12 stars 35 scripts 109 downloads
chromer - Interface to Chromosome Counts Database API
A programmatic interface to the Chromosome Counts Database (<https://ccdb.tau.ac.il/>), Rice et al. (2014) <doi:10.1111/nph.13191>. This package is part of the 'ROpenSci' suite (<https://ropensci.org>).
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4.59 score 13 stars 4 scripts 323 downloads
tacmagic - Positron Emission Tomography Time-Activity Curve Analysis
To facilitate the analysis of positron emission tomography (PET) time activity curve (TAC) data, and to encourage open science and replicability, this package supports data loading and analysis of multiple TAC file formats. Functions are available to analyze loaded TAC data for individual participants or in batches. Major functionality includes weighted TAC merging by region of interest (ROI), calculating models including standardized uptake value ratio (SUVR) and distribution volume ratio (DVR, Logan et al. 1996 <doi:10.1097/00004647-199609000-00008>), basic plotting functions and calculation of cut-off values (Aizenstein et al. 2008 <doi:10.1001/archneur.65.11.1509>). Please see the walkthrough vignette for a detailed overview of 'tacmagic' functions.
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mrineuroimagingneuroscienceneuroscience-methodspetpet-mrpositronpositron-emission-tomographystatistics
4.48 score 6 stars 8 scripts 257 downloads
mapmetadata - Map health metadata onto predefined research domains
Prior to gaining full access to health datasets, explore publicly available metadata and map metadata onto predefined research domains. This package uses structural metadata files downloaded from the Health Data Research Gateway (https://healthdatagateway.org/en). In theory, any metadata file with the same structure as the files downloaded from this gateway can be used with this package, but the package has been developed and tested on metadata files from this gateway only.
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hdrukhdruk-gatewayhealth-datametadatasail-databank
4.45 score 7 stars 4 scriptsqualR - An R package to download São Paulo and Rio de Janeiro air pollution data
A package to download information from CETESB QUALAR <https://cetesb.sp.gov.br/ar/qualar/> and MonitorAr <http://jeap.rio.rj.gov.br/je-metinfosmac/institucional/index.html> systems. It contains function to download different parameters, a set of criteria pollutants and the most frequent meteorological parameters used in air quality data analysis and air quality model evaluation.
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air-pollutantsair-quality-dataair-quality-measurementsbrazilcetesbrio-de-janeirosao-pauloweather-data
4.43 score 27 starshydroscoper - Interface to the Greek National Data Bank for Hydrometeorological Information
R interface to the Greek National Data Bank for Hydrological and Meteorological Information. It covers Hydroscope's data sources and provides functions to transliterate, translate and download them into tidy dataframes.
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climategreecehydrologyhydrometeorologyhydroscopemeteorological-datameteorological-stationspeer-reviewedtidy-datatime-serieswater-resources
4.41 score 13 stars 125 downloadscolocr - Conduct Co-Localization Analysis of Fluorescence Microscopy Images
Automate the co-localization analysis of fluorescence microscopy images. Selecting regions of interest, extract pixel intensities from the image channels and calculate different co-localization statistics. The methods implemented in this package are based on Dunn et al. (2011) <doi:10.1152/ajpcell.00462.2010>.
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colocalizationimage-analysis
4.41 score 26 stars 56 downloadshelminthR - Access London Natural History Museum Host-Helminth Record Database
Access to large host-parasite data is often hampered by the availability of data and difficulty in obtaining it in a programmatic way to encourage analyses. 'helminthR' provides accesss to the London Natural History Museum's host-parasite database, one of the largest host-parasite databases existing currently.
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disease-networkshelminthopen-dataparasites
4.40 score 10 stars 69 downloads
unrtf - Extract Text from Rich Text Format (RTF) Documents
Wraps the 'unrtf' utility <https://www.gnu.org/software/unrtf/> to extract text from RTF files. Supports document conversion to HTML, LaTeX or plain text. Output in HTML is recommended because 'unrtf' has limited support for converting between character encodings.
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extract-textrtfunrtf
4.35 score 15 stars 15 scripts 377 downloadsfluidsynth - Read and Play Digital Music (MIDI)
Bindings to 'libfluidsynth' to parse and synthesize MIDI files. It can read MIDI into a data frame, play it on the local audio device, or convert into an audio file.
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fluidsynthlibsdl3
4.32 score 14 stars 15 scripts 721 downloadspartialling.out - Residuals from Partial Regressions
Creates a data frame with the residuals of partial regressions of the main explanatory variable and the variable of interest. This method follows the Frisch-Waugh-Lovell theorem, as explained in Lovell (2008) <doi:10.3200/JECE.39.1.88-91>.
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econometricsfixed-effects
4.30 score 2 stars 201 downloads
gigs - Assess Fetal, Newborn, and Child Growth with International Standards
Convert between anthropometric measures and z-scores/centiles in multiple growth standards, and classify fetal, newborn, and child growth accordingly. With a simple interface to growth standards from the World Health Organisation and International Fetal and Newborn Growth Consortium for the 21st Century, gigs makes growth assessment easy and reproducible for clinicians, researchers and policy-makers.
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anthropometrygrowth-standardsintergrowthwho
4.26 score 10 stars 18 scriptsbrranching - Fetch 'Phylogenies' from Many Sources
Includes methods for fetching 'phylogenies' from a variety of sources, including the 'Phylomatic' web service (<http://phylodiversity.net/phylomatic/>), and 'Phylocom' (<https://github.com/phylocom/phylocom/>).
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phylogenytreephylomaticmolecularplantsphylogenies
4.23 score 20 stars 34 scripts 64 downloadspromoutils - Utilities for Promoting rOpenSci
Utility functions and workflows for promoting community events and community members on rOpenSci website and social media.
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4.22 score 4 stars 22 scriptsUSAboundariesData - Datasets for the 'USAboundaries' package
Contains datasets, including higher resolution boundary data, for use in the 'USAboundaries' package. These datasets come from the U.S. Census Bureau, the Newberry Library's 'Historical Atlas of U.S. County Boundaries', and Erik Steiner's 'United States Historical City Populations, 1790-2010'.
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4.22 score 10 stars 110 scriptscitecorp - Client for the Open Citations Corpus
Client for the Open Citations Corpus (<http://opencitations.net/>). Includes a set of functions for getting one identifier type from another, as well as getting references and citations for a given identifier.
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doimetadatacitationopencitationsbibtexcitationspmcidpmidsparql
4.22 score 11 stars 7 scripts 398 downloadsramlegacy - Download and Read RAM Legacy Stock Assessment Database
Contains functions to download, cache and read in 'Excel' version of the RAM Legacy Stock Assessment Data Base, an online compilation of stock assessment results for commercially exploited marine populations from around the world. The database is named after Dr. Ransom A. Myers whose original stock-recruitment database, is no longer being updated. More information about the database can be found at <https://ramlegacy.org/>. Ricard, D., Minto, C., Jensen, O.P. and Baum, J.K. (2012) <doi:10.1111/j.1467-2979.2011.00435.x>.
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fisheriesmarine-biologyramlegacyropenscistock-assessment
4.16 score 5 stars 29 scripts 34 downloads
fellingdater - Tree-ring dating and estimating felling dates of historical timbers
fellingdater provides a comprehensive suite of functions for dendrochronological and dendroarchaeological analysis, covering a workflow from tree-ring **data processing** and **crossdating**, up to the estimation and reporting of **felling dates**. Originally designed to assist dendrochronologists in inferring felling dates from dated tree-ring series with partially preserved sapwood, the package has been expanded to include a workflow for tree-ring dating, analysis, and visualization.
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dendrochronologysapwoodtree-rings
4.13 score 9 stars 10 scripts
exoplanets - Access NASA's Exoplanet Archive Data
The goal of exoplanets is to provide access to NASA's Exoplanet Archive TAP Service. For more information regarding the API please read the documentation <https://exoplanetarchive.ipac.caltech.edu/index.html>.
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apiexoplanetsnasa
4.10 score 14 stars 18 scripts 46 downloadsuniverse - Tools for Working with R-universe <https://r-universe.dev>
Utilities to interact with the R-universe platform. Includes functions to manage local package repositories, as well as API wrappers for retrieving data and metadata about packages in r-universe.
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4.04 score 10 stars 22 scriptssuppdata - Downloading Supplementary Data from Published Manuscripts
Downloads data supplementary materials from manuscripts, using papers' DOIs as references. Facilitates open, reproducible research workflows: scientists re-analyzing published datasets can work with them as easily as if they were stored on their own computer, and others can track their analysis workflow painlessly. The main function suppdata() returns a (temporary) location on the user's computer where the file is stored, making it simple to use suppdata() with standard functions like read.csv().
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peer-reviewed
4.02 score 37 stars 14 scripts 90 downloadstif - Text Interchange Format
Provides validation functions for common interchange formats for representing text data in R. Includes formats for corpus objects, document term matrices, and tokens. Other annotations can be stored by overloading the tokens structure.
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corpusnatural-language-processingterm-frequencytext-processingtokenizer
3.96 score 38 stars 24 scriptsantanym - Antarctic Geographic Place Names
Antarctic geographic names from the Composite Gazetteer of Antarctica, and functions for working with those place names.
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antarcticsouthern oceanplace namesgazetteerpeer-reviewed
3.95 score 9 stars
rrricanes - Web Scraper for Atlantic and East Pacific Hurricanes and Tropical Storms
Get archived data of past and current hurricanes and tropical storms for the Atlantic and eastern Pacific oceans. Data is available for storms since 1998. Datasets are updated via the rrricanesdata package. Currently, this package is about 6MB of datasets. See the README or view `vignette("drat")` for more information.
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hurricanepeer-reviewedweather
3.95 score 20 starsbirdsize - Estimate Avian Body Size Distributions
Generate estimated body size distributions for populations or communities of birds, given either species ID or species' mean body size. Designed to work naturally with the North American Breeding Bird Survey, or with any dataset of bird species, abundance, and/or mean size data.
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3.89 score 3 stars 13 scriptsprismjs - Server-Side Syntax Highlighting
Prism <https://prismjs.com/> is a lightweight, extensible syntax highlighter, built with modern web standards in mind. This package provides server-side rendering in R using 'V8' such that no JavaScript library is required in the resulting HTML documents. Over 400 languages are supported.
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3.88 score 5 stars 1 dependents 3 scripts 354 downloadspostdoc - Minimal and Uncluttered Package Documentation
Generates simple and beautiful one-page HTML reference manuals with package documentation. Math rendering and syntax highlighting are done server-side in R such that no JavaScript libraries are needed in the browser, which makes the documentation portable and fast to load.
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3.78 score 12 stars 5 scripts 335 downloads
censo2017 - Base de Datos de Facil Acceso del Censo 2017 de Chile (2017 Chilean Census Easy Access Database)
Provee un acceso conveniente a mas de 17 millones de registros de la base de datos del Censo 2017. Los datos fueron importados desde el DVD oficial del INE usando el Convertidor REDATAM creado por Pablo De Grande. Esta paquete esta documentado intencionalmente en castellano asciificado para que funcione sin problema en diferentes plataformas. (Provides convenient access to more than 17 million records from the Chilean Census 2017 database. The datasets were imported from the official DVD provided by the Chilean National Bureau of Statistics by using the REDATAM converter created by Pablo De Grande and in addition it includes the maps accompanying these datasets.)
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censocensuschiledemografiademographicsduckdbredatam
3.75 score 28 stars 115 downloads
PFW - Filtering and Processing Data from Project FeederWatch
Provides tools to import, clean, filter, and prepare Project FeederWatch data for analysis. Includes functions for taxonomic rollup, easy filtering, zerofilling, merging in site metadata, and more. Project FeederWatch data comes from <https://feederwatch.org/explore/raw-dataset-requests/>.
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3.70 score 1 stars 6 scripts 352 downloadsquartificate - Transform Google Docs into Quarto Books
Automate the Transformation of a Google Document into a Quarto Book source.
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quarto
3.69 score 49 starstreestartr - Generate Starting Trees For Combined Molecular, Morphological and Stratigraphic Data
Combine a list of taxa with a phylogeny to generate a starting tree for use in total evidence dating analyses.
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3.65 score 9 stars 8 scripts 223 downloadsMtreeRing - A Shiny Application for Automatic Measurements of Tree-Ring Widths on Digital Images
Use morphological image processing and edge detection algorithms to automatically measure tree ring widths on digital images. Users can also manually mark tree rings on species with complex anatomical structures. The arcs of inner-rings and angles of successive inclined ring boundaries are used to correct ring-width series. The package provides a Shiny-based application, allowing R beginners to easily analyze tree ring images and export ring-width series in standard file formats.
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dendrochronologyforestforestryshiny-appsshinyapptree-ring-widthtree-rings
3.61 score 37 stars 11 scripts 78 downloadsmonarch - Manage rOpenSci Social Contacts
Tools to find and keep track of contact info and social media handles of rOpenSci community members.
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3.48 score 2 stars 1 dependents 3 scriptsroblog - rOpenSci's blog guidance
It provides templates for roweb2 blogging and help for a GitHub forking workflow.
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3.40 score 5 stars 1 scriptsSymbiotaR2 - Downloading Data from Symbiota2 Portals into R
Download data from Symbiota2 portals using Symbiota's API. Covers the Checklists, Collections, Crowdsource, Exsiccati, Glossary, ImageProcessor, Key, Media, Occurrence, Reference, Taxa, Traits, and UserRoles API families. Each Symbiota2 portal owner can load their own plugins (and modified code), and so this package may not cover every possible API endpoint from a given Symbiota2 instance.
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databaselibraryspecimen-recordssymbiotasymbiota2symbiota2-portal
3.30 score 2 stars 7 scriptsgitcellar - Helps Download Archives of GitHub Repositories
Provide functionality to download archives (backups) for all repositories in a GitHub organization (useful for backups!).
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githubgithub-backupgithub-backups
3.23 score 17 stars 7 scriptspixelclasser - Classifies Image Pixels by Colour
Contains functions to classify the pixels of an image file (jpeg or tiff) by its colour. It implements a simple form of the techniques known as Support Vector Machine adapted to this particular problem.
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3.04 score 2 stars 11 scripts 245 downloads
jenkins - Simple Jenkins Client for R
Manage jobs and builds on your Jenkins CI server <https://jenkins.io/>. Create and edit projects, schedule builds, manage the queue, download build logs, and much more.
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3.00 score 20 stars 5 scripts 12 downloadsicepalace - Snapshot Current Versions of CRAN-like Repositories
What the package does (one paragraph).
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2.30 score 4 stars 5 scriptsrrricanesdata - Data for Atlantic and east Pacific tropical cyclones since 1998
Includes storm discussions, forecast/advisories, public advisories, wind speed probabilities, strike probabilities and more. This package can be used along with rrricanes (>= 0.2.0-6). Data is considered public domain via the National Hurricane Center.
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weather
2.18 score 3 stars 10 scriptscommonmetar - Wraps Commonmeta For rOpenSci Blog's Needs
Uses the commonmeta Go library to generate random DOI strings.
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1.70 score 1 stars 5 scripts