magick - 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

17.63 score 470 stars 276 dependents 11k scripts 133k 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

16.89 score 1.1k stars 15 dependents 18k scripts 39k 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

16.16 score 251 stars 42 dependents 13k scripts 28k downloads

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

15.89 score 213 stars 224 dependents 18k scripts 174k 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

15.42 score 1.0k stars 23 dependents 5.0k scripts 18k 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

14.71 score 326 stars 16 dependents 3.5k scripts 5.5k 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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14.71 score 156 stars 380 dependents 201 scripts 144k downloads

rentrez - '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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14.16 score 207 stars 106 dependents 944 scripts 26k 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

14.08 score 107 stars 169 dependents 203 scripts 35k downloads

commonmark - 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

13.80 score 98 stars 2.3k dependents 93 scripts 474k downloads

pdftools - 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

13.72 score 537 stars 60 dependents 3.8k scripts 51k downloads

git2r - 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

13.66 score 221 stars 45 dependents 852 scripts 52k downloads

taxize - 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

13.60 score 286 stars 21 dependents 1.7k scripts 7.1k downloads

hunspell - 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

13.54 score 113 stars 32 dependents 568 scripts 223k 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

13.35 score 169 stars 20 dependents 2.3k scripts 7.6k downloads

tokenizers - 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

13.32 score 186 stars 73 dependents 1.2k scripts 36k downloads

sodium - 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

13.23 score 71 stars 54 dependents 298 scripts 175k 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

13.13 score 460 stars 12 dependents 2.3k scripts 23k downloads

RSelenium - 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

12.94 score 346 stars 10 dependents 2.0k scripts 4.2k 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

12.93 score 194 stars 11 dependents 246 scripts 119k 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

12.56 score 73 stars 392 dependents 107 scripts 132k downloads

readODS - 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

12.43 score 53 stars 26 dependents 916 scripts 7.9k 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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librsvgglibcairo

12.20 score 97 stars 49 dependents 1.0k scripts 28k 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

12.11 score 103 stars 128 dependents 1.7k scripts

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

12.10 score 44 stars 27 dependents 448 scripts 5.8k downloads

rredlist - 'IUCN' Red List Client

'IUCN' Red List (<https://api.iucnredlist.org/>) client. The 'IUCN' Red List is a global list of threatened and endangered species. Functions cover all of the Red List 'API' routes. An 'API' key is required.

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iucnbiodiversityapiweb-servicestraitshabitatspeciesconservationapi-wrapperiucn-red-listtaxize

12.09 score 59 stars 22 dependents 240 scripts 7.3k downloads

RefManageR - Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management

Provides tools for importing and working with bibliographic references. It greatly enhances the 'bibentry' class by providing a class 'BibEntry' which stores 'BibTeX' and 'BibLaTeX' references, supports 'UTF-8' encoding, and can be easily searched by any field, by date ranges, and by various formats for name lists (author by last names, translator by full names, etc.). Entries can be updated, combined, sorted, printed in a number of styles, and exported. 'BibTeX' and 'BibLaTeX' '.bib' files can be read into 'R' and converted to 'BibEntry' objects. Interfaces to 'NCBI Entrez', 'CrossRef', and 'Zotero' are provided for importing references and references can be created from locally stored 'PDF' files using 'Poppler'. Includes functions for citing and generating a bibliography with hyperlinks for documents prepared with 'RMarkdown' or 'RHTML'.

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peer-reviewed

11.97 score 119 stars 15 dependents 2.4k scripts 5.3k 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

11.64 score 146 stars 10 dependents 2.0k scripts 5.8k downloads

rdhs - 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

11.60 score 38 stars 5 dependents 336 scripts 25k downloads

biomartr - 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

11.39 score 222 stars 3 dependents 171 scripts 1.2k downloads

CoordinateCleaner - Automated Cleaning of Occurrence Records from Biological Collections

Automated flagging of common spatial and temporal errors in biological and paleontological collection data, for the use in conservation, ecology and paleontology. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. The reference for the methodology is: Zizka et al. (2019) <doi:10.1111/2041-210X.13152>.

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11.38 score 85 stars 4 dependents 364 scripts 1.5k 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

11.36 score 98 stars 10 dependents 372 scripts 1.0k 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

11.35 score 430 stars 2 dependents 744 scripts 1.2k downloads

assertr - 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

11.30 score 480 stars 11 dependents 524 scripts 2.5k downloads

ssh - 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

11.28 score 130 stars 10 dependents 147 scripts 3.1k downloads

qpdf - 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

11.19 score 57 stars 90 dependents 296 scripts 28k 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

11.16 score 321 stars 156 scripts 334 downloads

spelling - 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

11.07 score 108 stars 8 dependents 197 scripts 153k downloads

webchem - Chemical Information from the Web

Chemical information from around the web. This package interacts with a suite of web services for chemical information. Sources include: Alan Wood's Compendium of Pesticide Common Names, Chemical Identifier Resolver, ChEBI, Chemical Translation Service, ChemSpider, ETOX, Flavornet, NIST Chemistry WebBook, OPSIN, PubChem, SRS, Wikidata.

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cas-numberchemical-informationchemspideridentifierropensciwebscraping

11.01 score 171 stars 10 dependents 178 scripts 1.3k downloads

tesseract - 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

10.87 score 249 stars 588 scripts 34k 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

10.81 score 1.3k stars 1 dependents 1.7k scripts 1.8k downloads

rcrossref - 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

10.76 score 174 stars 10 dependents 466 scripts 1.5k downloads

geojsonio - 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

10.75 score 153 stars 13 dependents 3.4k scripts 3.7k downloads

rerddap - 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

10.70 score 41 stars 6 dependents 494 scripts 1.2k 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

10.67 score 225 stars 1 dependents 299 scripts 2.3k 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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10.65 score 470 stars 3 dependents 89 scripts 911 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://docs.openalex.org>.

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bibliographic-databibliographic-databasebibliometricsbibliometrixscience-mapping

10.56 score 120 stars 7 dependents 289 scripts 9.1k 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

10.53 score 93 stars 142 scripts 4.0k downloads

geojson - 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

10.49 score 32 stars 14 dependents 173 scripts 3.3k 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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peer-reviewed

10.49 score 106 stars 1 dependents 1.5k scripts 1.5k downloads

rnaturalearthdata - 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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10.48 score 13 stars 7 dependents 5.0k scripts 17k downloads

av - 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

10.45 score 94 stars 17 dependents 868 scripts 8.5k 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

10.41 score 150 stars 5 dependents 712 scripts 774 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

10.31 score 105 stars 6 dependents 186 scripts 1.9k downloads

googleLanguageR - Call Google's 'Natural Language' API, 'Cloud Translation' API, 'Cloud Speech' API and 'Cloud Text-to-Speech' API

Call 'Google Cloud' machine learning APIs for text and speech tasks. Call the 'Cloud Translation' API <https://cloud.google.com/translate> for detection and translation of text, the 'Natural Language' API <https://cloud.google.com/natural-language> to analyse text for sentiment, entities or syntax, the 'Cloud Speech' API <https://cloud.google.com/speech-to-text> to transcribe sound files to text and the 'Cloud Text-to-Speech' API <https://cloud.google.com/text-to-speech> to turn text into sound files.

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cloud-speech-apicloud-translation-apigoogle-api-clientgoogle-cloudgoogle-cloud-speechgoogle-nlpgoogleauthrnatural-language-processingpeer-reviewedsentiment-analysisspeech-apitranslation-api

10.26 score 198 stars 2 dependents 274 scripts 1.4k 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

10.25 score 177 stars 432 scripts 2.2k downloads

tsbox - 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

10.19 score 150 stars 4 dependents 560 scripts 2.1k downloads

jsonvalidate - 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

10.17 score 51 stars 44 dependents 35 scripts 8.4k downloads

spatsoc - Group Animal Relocation Data by Spatial and Temporal Relationship

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 In addition, the randomizations function provides data-stream randomization methods suitable for GPS data.

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animalgpsnetworksocialspatial

10.11 score 24 stars 3 dependents 143 scripts 620 downloads

git2rdata - Store and Retrieve Data.frames in a Git Repository

The git2rdata package is an R package for writing and reading dataframes as plain text files. A metadata file stores important information. 1) Storing metadata allows to maintain the classes of variables. By default, git2rdata optimizes the data for file storage. The optimization is most effective on data containing factors. The optimization makes the data less human readable. The user can turn this off when they prefer a human readable format over smaller files. Details on the implementation are available in vignette("plain_text", package = "git2rdata"). 2) Storing metadata also allows smaller row based diffs between two consecutive commits. This is a useful feature when storing data as plain text files under version control. Details on this part of the implementation are available in vignette("version_control", package = "git2rdata"). Although we envisioned git2rdata with a git workflow in mind, you can use it in combination with other version control systems like subversion or mercurial. 3) git2rdata is a useful tool in a reproducible and traceable workflow. vignette("workflow", package = "git2rdata") gives a toy example. 4) vignette("efficiency", package = "git2rdata") provides some insight into the efficiency of file storage, git repository size and speed for writing and reading.

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reproducible-researchversion-control

10.07 score 103 stars 4 dependents 227 scripts 864 downloads

worrms - 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

10.07 score 27 stars 25 dependents 436 scripts 5.3k 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

10.03 score 90 stars 5 dependents 90 scripts 2.2k downloads

robotstxt - 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

10.00 score 68 stars 6 dependents 416 scripts 1.2k 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

9.98 score 13 stars 19 dependents 100 scripts 4.6k downloads

dataset - Create Data Frames for Exchange and Reuse

The 'dataset' package helps create semantically rich, machine-readable, and interoperable datasets in R. It extends tidy data frames with metadata that preserves meaning, improves interoperability, and makes datasets easier to publish, exchange, and reuse in line with ISO and W3C standards.

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datasetmetadata-management

9.94 score 19 stars 1 dependents 108 scripts 7.0k 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

9.92 score 147 stars 1 dependents 290 scripts 1.0k 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 (<https://dd.weather.gc.ca/hydrometric/csv/> and <https://collaboration.cmc.ec.gc.ca/cmc/hydrometrics/www/>) and then applies tidy data principles.

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citzgovernment-datahydrologyhydrometricstidy-datawater-resources

9.88 score 71 stars 3 dependents 264 scripts 428 downloads

jqr - 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

9.85 score 145 stars 34 dependents 93 scripts 5.7k 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

9.82 score 120 stars 2 dependents 872 scripts 911 downloads

prism - 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.

Last updated

9.81 score 60 stars 394 scripts 512 downloads

cffr - Generate Citation File Format ('cff') Metadata for R Packages

The Citation File Format version 1.2.0 <doi:10.5281/zenodo.5171937> is a human and machine readable file format which provides citation metadata for software. This package provides core utilities to generate and validate this metadata.

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attributioncitationcreditcitation-filescffmetadatacitation-file-formatropensci

9.80 score 26 stars 3 dependents 167 scripts 1.9k downloads

lingtypology - 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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abvdafboatlasautotypebivaltypclldglottolog-databaselinguistic-mapslinguisticsphoiblesailstypologywals

9.79 score 51 stars 1.5k scripts 554 downloads

charlatan - 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

9.78 score 303 stars 1 dependents 184 scripts 641 downloads

bibtex - Bibtex Parser

Utility to parse a bibtex file.

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bibtexparser

9.78 score 38 stars 19 dependents 564 scripts 7.0k downloads

rdflib - Tools to Manipulate and Query Semantic Data

The Resource Description Framework, or 'RDF' is a widely used data representation model that forms the cornerstone of the Semantic Web. 'RDF' represents data as a graph rather than the familiar data table or rectangle of relational databases. The 'rdflib' package provides a friendly and concise user interface for performing common tasks on 'RDF' data, such as reading, writing and converting between the various serializations of 'RDF' data, including 'rdfxml', 'turtle', 'nquads', 'ntriples', and 'json-ld'; creating new 'RDF' graphs, and performing graph queries using 'SPARQL'. This package wraps the low level 'redland' R package which provides direct bindings to the 'redland' C library. Additionally, the package supports the newer and more developer friendly 'JSON-LD' format through the 'jsonld' package. The package interface takes inspiration from the Python 'rdflib' library.

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peer-reviewed

9.74 score 59 stars 7 dependents 141 scripts 1.5k 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

9.63 score 560 stars 1 dependents 163 scripts 1.3k downloads

frictionless - Read and Write Frictionless Data Packages

Read and write Frictionless Data Packages. A 'Data Package' (<https://specs.frictionlessdata.io/data-package/>) 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.go-fair.org/fair-principles/>) and open datasets.

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frictionlessdataoscibio

9.60 score 31 stars 5 dependents 79 scripts 1.2k downloads

parzer - 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

9.56 score 63 stars 3 dependents 177 scripts 885 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

9.56 score 121 stars 4 dependents 556 scripts 3.2k downloads

wdman - '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

9.53 score 30 stars 11 dependents 268 scripts 3.6k downloads

tidync - A 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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9.46 score 93 stars 2 dependents 732 scripts 721 downloads

rnoaa - '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

9.43 score 338 stars 4 dependents 844 scripts 435 downloads

bib2df - 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

9.34 score 102 stars 6 dependents 220 scripts 1.1k 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

9.21 score 109 stars 1 dependents 249 scripts 1.7k downloads

codemetar - 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

9.16 score 67 stars 7 dependents 51 scripts 797 downloads

iheatmapr - 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

9.12 score 269 stars 1 dependents 108 scripts 624 downloads

elastic - General Purpose Interface to 'Elasticsearch'

Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java' Virtual Machine. Interacts with the 'Elasticsearch' 'HTTP' API (<https://www.elastic.co/elasticsearch/>), including functions for setting connection details to 'Elasticsearch' instances, loading bulk data, searching for documents with both 'HTTP' query variables and 'JSON' based body requests. In addition, 'elastic' provides functions for interacting with API's for 'indices', documents, nodes, clusters, an interface to the cat API, and more.

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databaseelasticsearchhttpapisearchnosqljavajsondocumentsdata-sciencedatabase-wrapperetl

9.03 score 246 stars 159 scripts 3.2k 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

8.95 score 17 stars 8 dependents 42 scripts 1.1k 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

8.91 score 59 stars 1 dependents 70 scripts 2.1k downloads

sits - 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

8.89 score 511 stars 474 scripts 741 downloads

stats19 - Work with Open Road Traffic Casualty Data from Great Britain

Tools to help download, process and analyse the UK road collision data collected using the 'STATS19' form. The datasets are provided as 'CSV' files with detailed road safety information about the circumstances of car crashes and other incidents on the roads resulting in casualties in Great Britain from 1979 to present. Tables are available on 'colissions' with the circumstances (e.g. speed limit of road), information about 'vehicles' involved (e.g. type of vehicle), and 'casualties' (e.g. age). The statistics relate only to events on public roads that were reported to the police, and subsequently recorded, using the 'STATS19' collision reporting form. See the Department for Transport website <https://www.data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-accidents-safety-data> for more information on these datasets. The package is described in a paper in the Journal of Open Source Software (Lovelace et al. 2019) <doi:10.21105/joss.01181>. See Gilardi et al. (2022) <doi:10.1111/rssa.12823>, Vidal-Tortosa et al. (2021) <doi:10.1016/j.jth.2021.101291>, and Tait et al. (2023) <doi:10.1016/j.aap.2022.106895> for examples of how the data can be used for methodological and empirical road safety research.

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stats19road-safetytransportcar-crashesropenscidata

8.85 score 63 stars 205 scripts 754 downloads

weathercan - Download Weather Data from Environment and Climate Change Canada

Provides means for downloading historical weather data from the Environment and Climate Change Canada website (<https://climate.weather.gc.ca/historical_data/search_historic_data_e.html>). Data can be downloaded from multiple stations and over large date ranges and automatically processed into a single dataset. Tools are also provided to identify stations either by name or proximity to a location.

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environment-canadapeer-reviewedweather-dataweather-downloader

8.82 score 110 stars 225 scripts 69 downloads

textreuse - 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

8.82 score 202 stars 234 scripts 725 downloads

ghql - 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

8.78 score 148 stars 4 dependents 196 scripts 1.2k downloads

beautier - '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

8.76 score 13 stars 5 dependents 198 scripts 784 downloads

datapack - A Flexible Container to Transport and Manipulate Data and Associated Resources

Provides a flexible container to transport and manipulate complex sets of data. These data may consist of multiple data files and associated meta data and ancillary files. Individual data objects have associated system level meta data, and data files are linked together using the OAI-ORE standard resource map which describes the relationships between the files. The OAI- ORE standard is described at <https://www.openarchives.org/ore/>. Data packages can be serialized and transported as structured files that have been created following the BagIt specification. The BagIt specification is described at <https://tools.ietf.org/html/draft-kunze-bagit-08>.

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8.69 score 42 stars 6 dependents 186 scripts 461 downloads

geotargets - 'targets' Extensions for Geographic Spatial Formats

Provides extensions for various geographic spatial file formats, such as shape files and rasters. Currently provides support for the 'terra' geographic spatial formats. See the vignettes for worked examples, demonstrations, and explanations of how to use the various package extensions.

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geospatialpipeliner-targetopiarasterreproducibilityreproducible-researchtargetsvectorworkflow

8.69 score 86 stars 79 scripts 397 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

8.62 score 71 stars 97 scripts 906 downloads

ckanr - Client for the Comprehensive Knowledge Archive Network ('CKAN') API

Client for 'CKAN' 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' API.

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databaseopen-datackanapidatadatasetapi-wrapperckan-api

8.61 score 100 stars 4 dependents 454 scripts 876 downloads

xslt - 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

8.61 score 29 stars 19 dependents 80 scripts 6.1k downloads

babette - 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

8.58 score 46 stars 1 dependents 55 scripts 362 downloads

nlrx - Setup, Run and Analyze 'NetLogo' Model Simulations from 'R' via 'XML'

Setup, run and analyze 'NetLogo' (<https://ccl.northwestern.edu/netlogo/>) 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

8.57 score 79 stars 196 scripts 280 downloads

cyphr - 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

8.54 score 97 stars 2 dependents 43 scripts 784 downloads

phylogram - 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

8.54 score 11 stars 8 dependents 262 scripts 629 downloads

fingertipsR - 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

8.53 score 101 stars 1 dependents 285 scripts 343 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

8.50 score 41 stars 11 dependents 83 scripts 110 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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8.50 score 37 stars 7 dependents 39 scripts 10k 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

8.49 score 84 stars 153 scripts 869 downloads

geonames - 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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8.49 score 38 stars 21 dependents 184 scripts 776 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'). 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://www1.ncdc.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

8.49 score 94 stars 136 scripts 961 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

8.48 score 15 stars 24 dependents 23 scripts 4.9k 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

8.44 score 157 stars 1 dependents 93 scripts 233 downloads

slopes - Calculate Slopes of Roads, Rivers and Trajectories

Calculates the slope (longitudinal gradient or steepness) of linear geographic features such as roads (for more details, see Ariza-López et al. (2019) <doi:10.1038/s41597-019-0147-x>) and rivers (for more details, see Cohen et al. (2018) <doi:10.1016/j.jhydrol.2018.06.066>). It can use local Digital Elevation Model (DEM) data or download DEM data via the 'ceramic' package. The package also provides functions to add elevation data to linestrings and visualize elevation profiles.

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8.44 score 71 stars 43 scripts 146 downloads

opencage - 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

8.43 score 87 stars 86 scripts 555 downloads

wikitaxa - 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

8.33 score 21 stars 22 dependents 11 scripts 4.7k downloads

DataPackageR - Construct Reproducible Analytic Data Sets as R Packages

A framework to help construct R data packages in a reproducible manner. Potentially time consuming processing of raw data sets into analysis ready data sets is done in a reproducible manner and decoupled from the usual 'R CMD build' process so that data sets can be processed into R objects in the data package and the data package can then be shared, built, and installed by others without the need to repeat computationally costly data processing. The package maintains data provenance by turning the data processing scripts into package vignettes, as well as enforcing documentation and version checking of included data objects. Data packages can be version controlled on 'GitHub', and used to share data for manuscripts, collaboration and reproducible research.

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peer-reviewedreproducibility

8.30 score 155 stars 72 scripts 339 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

8.30 score 82 stars 69 scripts 624 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 <http://www.bom.gov.au/other/copyright.shtml> for further details.

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dpirdbommeteorological-dataweather-forecastaustraliaweatherweather-datameteorologywestern-australiaaustralia-bureau-of-meteorologywestern-australia-agricultureaustralia-agricultureaustralia-climateaustralia-weatherapi-clientclimatedatarainfallweather-api

8.24 score 32 stars 49 scripts 197 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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8.20 score 62 stars 212 scripts 706 downloads

nodbi - 'NoSQL' Database Connector

Simplified JSON document database access and manipulation, providing a common API across supported 'NoSQL' databases 'Elasticsearch', 'CouchDB', 'MongoDB' as well as 'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.

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databasemongodbelasticsearchcouchdbsqlitepostgresqlduckdbnosqljsondocuments

8.19 score 76 stars 1 dependents 31 scripts 558 downloads

pkgcheck - rOpenSci Package Checks

Check whether a package is ready for submission to rOpenSci's peer review system.

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compliance-automationsoftware-analysissoftware-checking

8.18 score 24 stars 2 dependents 37 scripts

eph - Argentina's Permanent Household Survey Data and Manipulation Utilities

Tools to download and manipulate the Permanent Household Survey from Argentina (EPH is the Spanish acronym for Permanent Household Survey). e.g: get_microdata() for downloading the datasets, get_poverty_lines() for downloading the official poverty baskets, calculate_poverty() for the calculation of stating if a household is in poverty or not, following the official methodology. organize_panels() is used to concatenate observations from different periods, and organize_labels() adds the official labels to the data. The implemented methods are based on INDEC (2016) <http://www.estadistica.ec.gba.gov.ar/dpe/images/SOCIEDAD/EPH_metodologia_22_pobreza.pdf>. As this package works with the argentinian Permanent Household Survey and its main audience is from this country, the documentation was written in Spanish.

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ephindecmercado-de-trabajorstatses

8.17 score 59 stars 310 scripts 680 downloads

rinat - 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

8.16 score 61 stars 237 scripts 1.0k downloads

dataspice - 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

8.14 score 164 stars 1 dependents 40 scripts 316 downloads

hoardr - 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

8.13 score 23 stars 35 dependents 7 scripts 2.8k downloads

binman - 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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8.12 score 16 stars 12 dependents 47 scripts 3.2k downloads

plater - 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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8.11 score 24 stars 2 dependents 59 scripts 680 downloads

rvertnet - 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

8.05 score 7 stars 5 dependents 35 scripts 2.2k downloads

FedData - Download Geospatial Data Available from Several Federated Data Sources

Download geospatial data available from several federated data sources (mainly sources maintained by the US Federal government). Currently, the package enables extraction from nine datasets: The National Elevation Dataset digital elevation models (<https://www.usgs.gov/3d-elevation-program> 1 and 1/3 arc-second; USGS); The National Hydrography Dataset (<https://www.usgs.gov/national-hydrography/national-hydrography-dataset>; USGS); The Soil Survey Geographic (SSURGO) database from the National Cooperative Soil Survey (<https://websoilsurvey.sc.egov.usda.gov/>; NCSS), which is led by the Natural Resources Conservation Service (NRCS) under the USDA; the Global Historical Climatology Network (<https://www.ncei.noaa.gov/products/land-based-station/global-historical-climatology-network-daily>; GHCN), coordinated by National Climatic Data Center at NOAA; the Daymet gridded estimates of daily weather parameters for North America, version 4, available from the Oak Ridge National Laboratory's Distributed Active Archive Center (<https://daymet.ornl.gov/>; DAAC); the International Tree Ring Data Bank; the National Land Cover Database (<https://www.mrlc.gov/>; NLCD); the Cropland Data Layer from the National Agricultural Statistics Service (<https://www.nass.usda.gov/Research_and_Science/Cropland/SARS1a.php>; NASS); and the PAD-US dataset of protected area boundaries (<https://www.usgs.gov/programs/gap-analysis-project/science/pad-us-data-overview>; USGS).

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peer-reviewed

8.03 score 103 stars 430 scripts 920 downloads

webmockr - 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

8.03 score 50 stars 136 scripts 3.0k 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 24 scripts 575 downloads

tinkr - 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

8.02 score 58 stars 4 dependents 4 scripts 660 downloads

beastier - 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

8.00 score 11 stars 4 dependents 50 scripts 593 downloads

dittodb - A Test Environment for Database Requests

Testing and documenting code that communicates with remote databases can be painful. Although the interaction with R is usually relatively simple (e.g. data(frames) passed to and from a database), because they rely on a separate service and the data there, testing them can be difficult to set up, unsustainable in a continuous integration environment, or impossible without replicating an entire production cluster. This package addresses that by allowing you to make recordings from your database interactions and then play them back while testing (or in other contexts) all without needing to spin up or have access to the database your code would typically connect to.

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7.98 score 81 stars 44 scripts 549 downloads

europepmc - 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

7.95 score 28 stars 2 dependents 132 scripts 842 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

7.90 score 16 stars 13 dependents 98 scripts 1.9k 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, 2024) <doi:10.48550/arXiv.2302.01607>.

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bayesian-inferencepanel-datastanstatistical-models

7.86 score 34 stars 24 scripts 412 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

7.82 score 9 stars 2 dependents 102 scripts 390 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

7.82 score 13 stars 2 dependents 12 scripts 1.3k 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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7.81 score 47 stars 1 dependents 131 scripts 426 downloads

emld - Ecological Metadata as Linked Data

This is a utility for transforming Ecological Metadata Language ('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a list-based representation of 'EML' in R, so that 'EML' data can easily be manipulated using standard 'R' tools. This makes this package an effective backend for other 'R'-based tools working with 'EML.' By abstracting away the complexity of 'XML' Schema, developers can build around native 'R' list objects and not have to worry about satisfying many of the additional constraints of set by the schema (such as element ordering, which is handled automatically). Additionally, the 'JSON-LD' representation enables the use of developer-friendly 'JSON' parsing and serialization that may facilitate the use of 'EML' in contexts outside of 'R,' as well as the informatics-friendly serializations such as 'RDF' and 'SPARQL' queries.

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7.80 score 14 stars 11 dependents 69 scripts 730 downloads

ezknitr - 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

7.80 score 113 stars 376 scripts 367 downloads

taxadb - A High-Performance Local Taxonomic Database Interface

Creates a local database of many commonly used taxonomic authorities and provides functions that can quickly query this data.

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7.79 score 44 stars 1 dependents 66 scripts 1.0k downloads

ritis - 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

7.73 score 16 stars 24 dependents 64 scripts 4.9k 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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7.72 score 47 stars 1 dependents 178 scripts 1.4k 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

7.70 score 140 stars 90 scripts 594 downloads

cld2 - 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

7.68 score 38 stars 1 dependents 210 scripts 939 downloads

babelquarto - Renders a Multilingual Quarto Book

Automate rendering and cross-linking of Quarto books following a prescribed structure.

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quarto

7.62 score 51 stars 1 dependents 27 scripts

allcontributors - 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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7.55 score 31 stars 1 dependents 5 scripts 519 downloads

chopin - Spatial Parallel Computing by Hierarchical Data Partitioning

Geospatial data computation is parallelized by grid, hierarchy, or raster files. Based on 'future' (Bengtsson, 2024 <doi:10.32614/CRAN.package.future>) and 'mirai' (Gao et al., 2025 <doi:10.32614/CRAN.package.mirai>) parallel back-ends, 'terra' (Hijmans et al., 2025 <doi:10.32614/CRAN.package.terra>) and 'sf' (Pebesma et al., 2024 <doi:10.32614/CRAN.package.sf>) functions as well as convenience functions in the package can be distributed over multiple threads. The simplest way of parallelizing generic geospatial computation is to start from par_pad_*() functions to par_grid(), par_hierarchy(), or par_multirasters() functions. Virtually any functions accepting classes in 'terra' or 'sf' packages can be used in the three parallelization functions. A common raster-vector overlay operation is provided as a function extract_at(), which uses 'exactextractr' (Baston, 2023 <doi:10.32614/CRAN.package.exactextractr>), with options for kernel weights for summarizing raster values at vector geometries. Other convenience functions for vector-vector operations including simple areal interpolation (summarize_aw()) and summation of exponentially decaying weights (summarize_sedc()) are also provided.

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7.53 score 26 stars 26 scripts 161 downloads

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

7.48 score 23 stars 52 scripts 308 downloads

rsat - Dealing with Multiplatform Satellite Images

Downloading, customizing, and processing time series of satellite images for a region of interest. 'rsat' functions allow a unified access to multispectral images from Landsat, MODIS and Sentinel repositories. 'rsat' also offers capabilities for customizing satellite images, such as tile mosaicking, image cropping and new variables computation. Finally, 'rsat' covers the processing, including cloud masking, compositing and gap-filling/smoothing time series of images (Militino et al., 2018 <doi:10.3390/rs10030398> and Militino et al., 2019 <doi:10.1109/TGRS.2019.2904193>).

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satellite-images

7.45 score 54 stars 52 scripts 220 downloads

rdataretriever - 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

7.42 score 47 stars 37 scripts 294 downloads

USAboundaries - 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

7.38 score 62 stars 1.3k scripts 94 downloads

tiler - Create Geographic and Non-Geographic Map Tiles

Creates geographic map tiles from geospatial map files or non-geographic map tiles from simple image files. This package provides a tile generator function for creating map tile sets for use with packages such as 'leaflet'. In addition to generating map tiles based on a common raster layer source, it also handles the non-geographic edge case, producing map tiles from arbitrary images. These map tiles, which have a non-geographic, simple coordinate reference system (CRS), can also be used with 'leaflet' when applying the simple CRS option. Map tiles can be created from an input file with any of the following extensions: tif, grd and nc for spatial maps and png, jpg and bmp for basic images. This package requires 'Python' and the 'gdal' library for 'Python'. 'Windows' users are recommended to install 'OSGeo4W' (<https://trac.osgeo.org/osgeo4w/>) as an easy way to obtain the required 'gdal' support for 'Python'.

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7.35 score 64 stars 2 dependents 39 scripts 305 downloads

roadoi - 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

7.32 score 66 stars 80 scripts 466 downloads

jstor - Read Data from JSTOR/DfR

Functions and helpers to import metadata, ngrams and full-texts delivered by Data for Research by JSTOR.

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jstorpeer-reviewedtext-analysistext-mining

7.30 score 47 stars 56 scripts 328 downloads

jsonld - 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

7.27 score 35 stars 14 dependents 73 scripts 1.7k downloads

tic - 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

7.26 score 153 stars 16 scripts

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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7.25 score 12 stars 2 dependents 82 scripts 177 downloads

bowerbird - 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

7.23 score 50 stars 1 dependents 19 scripts

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

7.23 score 25 stars 9 scripts 249 downloads

tradestatistics - 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

7.19 score 78 stars 99 scripts 446 downloads

riem - Accesses Weather Data from the Iowa Environment Mesonet

Allows to get weather data from Automated Surface Observing System (ASOS) stations (airports) in the whole world thanks to the Iowa Environment Mesonet website.

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airportsasosiowa-environment-mesonetmetarpeer-reviewedtemperatureweatherweather-api

7.18 score 45 stars 185 scripts 376 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

7.16 score 42 stars 58 scripts

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

7.11 score 74 stars 87 scripts 441 downloads

natserv - '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

7.08 score 11 stars 22 dependents 18 scripts 4.6k downloads

taxizedb - Offline Access to Taxonomic Databases

Download taxonomic databases, convert them into 'SQLite' format, and query them locally for fast, reliable, and reproducible access to taxonomic data.

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itistaxizetaxonomic-databasestaxonomy

7.06 score 32 stars 1 dependents 100 scripts 958 downloads

sofa - Connector to 'CouchDB'

Provides an interface to the 'NoSQL' database 'CouchDB' (<http://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' databases such as '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

7.03 score 33 stars 54 scripts 556 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

7.02 score 50 stars 105 scripts 179 downloads

rzmq - R Bindings for 'ZeroMQ'

Interface to the 'ZeroMQ' lightweight messaging kernel (see <https://zeromq.org/> for more information).

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zeromqzmqzeromq3cpp

7.01 score 87 stars 84 scripts 608 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

6.97 score 63 stars 74 scripts 764 downloads

ohun - 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

6.96 score 17 stars 1 dependents 30 scripts 178 downloads

baRcodeR - 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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6.96 score 36 stars 51 scripts 454 downloads

pkgstats - 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-analysiscpp

6.95 score 19 stars 3 dependents 2 scripts

rsi - Efficiently Retrieve and Process Satellite Imagery

Downloads spatial data from spatiotemporal asset catalogs ('STAC'), computes standard spectral indices from the Awesome Spectral Indices project (Montero et al. (2023) <doi:10.1038/s41597-023-02096-0>) against raster data, and glues the outputs together into predictor bricks. Methods focus on interoperability with the broader spatial ecosystem; function arguments and outputs use classes from 'sf' and 'terra', and data downloading functions support complex 'CQL2' queries using 'rstac'.

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6.94 score 53 stars 47 scripts 393 downloads

waywiser - Ergonomic Methods for Assessing Spatial Models

Assessing predictive models of spatial data can be challenging, both because these models are typically built for extrapolating outside the original region represented by training data and due to potential spatially structured errors, with "hot spots" of higher than expected error clustered geographically due to spatial structure in the underlying data. Methods are provided for assessing models fit to spatial data, including approaches for measuring the spatial structure of model errors, assessing model predictions at multiple spatial scales, and evaluating where predictions can be made safely. Methods are particularly useful for models fit using the 'tidymodels' framework. Methods include Moran's I ('Moran' (1950) <doi:10.2307/2332142>), Geary's C ('Geary' (1954) <doi:10.2307/2986645>), Getis-Ord's G ('Ord' and 'Getis' (1995) <doi:10.1111/j.1538-4632.1995.tb00912.x>), agreement coefficients from 'Ji' and Gallo (2006) (<doi: 10.14358/PERS.72.7.823>), agreement metrics from 'Willmott' (1981) (<doi: 10.1080/02723646.1981.10642213>) and 'Willmott' 'et' 'al'. (2012) (<doi: 10.1002/joc.2419>), an implementation of the area of applicability methodology from 'Meyer' and 'Pebesma' (2021) (<doi:10.1111/2041-210X.13650>), and an implementation of multi-scale assessment as described in 'Riemann' 'et' 'al'. (2010) (<doi:10.1016/j.rse.2010.05.010>).

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spatialspatial-analysistidymodelstidyverse

6.93 score 39 stars 24 scripts 337 downloads

essurvey - 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

6.89 score 49 stars 79 scripts 302 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

6.89 score 27 stars 1 dependents 191 scripts 301 downloads

antiword - 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

6.89 score 57 stars 8 dependents 7 scripts 5.6k 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

6.88 score 79 stars 38 scripts 437 downloads

mregions2 - 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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6.87 score 9 stars 51 scripts 250 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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6.86 score 5 stars 9 scripts 477 downloads

graphql - 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

6.85 score 39 stars 6 dependents 6 scripts 860 downloads

melt - Multiple Empirical Likelihood Tests

Performs multiple empirical likelihood tests. It offers an easy-to-use interface and flexibility in specifying hypotheses and calibration methods, extending the framework to simultaneous inferences. The core computational routines are implemented using the 'Eigen' 'C++' library and 'RcppEigen' interface, with 'OpenMP' for parallel computation. Details of the testing procedures are provided in Kim, MacEachern, and Peruggia (2023) <doi:10.1080/10485252.2023.2206919>. A companion paper by Kim, MacEachern, and Peruggia (2024) <doi:10.18637/jss.v108.i05> is available for further information. This work was supported by the U.S. National Science Foundation under Grants No. SES-1921523 and DMS-2015552.

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cppopenmp

6.83 score 17 stars 89 scripts 925 downloads

phylocomr - 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

6.83 score 15 stars 3 dependents 20 scripts 275 downloads

taxa - 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

6.83 score 49 stars 228 scripts 615 downloads

baRulho - 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

6.81 score 8 stars 16 scripts 148 downloads

historydata - 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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6.81 score 91 stars 118 scripts 260 downloads

rglobi - 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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6.79 score 18 stars 43 scripts 346 downloads

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

6.77 score 50 stars 198 scripts

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

6.76 score 48 stars 40 scripts 546 downloads

rnaturalearthhires - 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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6.74 score 27 stars 1 dependents 840 scripts

NLMR - Simulating Neutral Landscape Models

Provides neutral landscape models (<doi:10.1007/BF02275262>, <http://sci-hub.tw/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 (raster* objects from the 'raster' 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

6.73 score 65 stars 188 scripts 165 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

6.73 score 89 stars 2 scripts 307 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

6.72 score 11 stars 9 scripts 277 downloads

chirps - API Client for CHIRPS and CHIRTS

API Client for the Climate Hazards Center 'CHIRPS' and 'CHIRTS'. 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 'CHIRPS' and 'CHIRTS' data please visit its official home page <https://www.chc.ucsb.edu/data>.

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chirpsclimatologyprecipitation-data

6.71 score 31 stars 37 scripts 657 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

6.71 score 5 stars 41 scripts 379 downloads

rsnps - 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

6.69 score 55 stars 74 scripts 100 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

6.61 score 41 stars 67 scripts 382 downloads

landscapetools - 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

6.61 score 49 stars 186 scripts 65 downloads

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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6.59 score 36 stars 31 scripts 635 downloads

rcites - 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

6.58 score 14 stars 30 scripts 327 downloads

paleobioDB - 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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6.57 score 45 stars 83 scripts 838 downloads

EDIutils - 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

6.57 score 9 stars 164 scripts 285 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

6.56 score 13 stars 31 scripts 274 downloads

fireexposuR - Compute and Visualize Wildfire Exposure

Methods for computing and visualizing wildfire igntion 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 6 stars 8 scripts 330 downloads

tracerer - 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

6.49 score 8 stars 3 dependents 85 scripts 346 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

6.45 score 11 stars 32 scripts 510 downloads

gendercoder - Recodes Sex/Gender Descriptions into a Standard Set

Provides functions and dictionaries for recoding of freetext gender responses into more consistent categories.

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gender-diversityozunconf18unconf

6.44 score 47 stars 53 scripts

patentsview - An R Client to the 'PatentsView' API

Provides functions to simplify the 'PatentsView' API (<https://patentsview.org/apis/purpose>) 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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patentspatentsviewpatentsview-apipeer-revieweduspto

6.43 score 34 stars 100 scripts 299 downloads

osmplotr - 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

6.37 score 140 stars 83 scripts 98 downloads

pangaear - 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

6.36 score 23 stars 33 scripts 757 downloads

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 <https://www.biorxiv.org/>, 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

6.36 score 57 stars 53 scripts 59 downloads

coder - Deterministic Categorization of Items Based on External Code Data

Fast categorization of items based on external code data identified by regular expressions. A typical use case considers patient with medically coded data, such as codes from the International Classification of Diseases ('ICD') or the Anatomic Therapeutic Chemical ('ATC') classification system. Functions of the package relies on a triad of objects: (1) case data with unit id:s and possible dates of interest; (2) external code data for corresponding units in (1) and with optional dates of interest and; (3) a classification scheme ('classcodes' object) with regular expressions to identify and categorize relevant codes from (2). It is easy to introduce new classification schemes ('classcodes' objects) or to use default schemes included in the package. Use cases includes patient categorization based on 'comorbidity indices' such as 'Charlson', 'Elixhauser', 'RxRisk V', or the 'comorbidity-polypharmacy' score (CPS), as well as adverse events after hip and knee replacement surgery.

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classificationicd-10

6.32 score 22 stars 24 scripts 310 downloads

karel - 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

6.31 score 10 stars 34 scripts 103 downloads

autotest - Automatic Package Testing

Automatic testing of R packages via a simple YAML schema.

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automated-testingfuzzingtesting

6.31 score 54 stars 25 scripts

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

6.29 score 7 stars 11 scripts 466 downloads

spiro - 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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6.26 score 14 stars 43 scripts 171 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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6.23 score 10 stars 17 scripts 283 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, xronos.

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archaeologyradiocarbon-dates

6.23 score 31 stars 52 scripts 36 downloads

deposits - 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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6.21 score 39 stars 1 dependents 8 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

6.17 score 15 stars 11 scripts 203 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

6.16 score 29 stars 1 dependents 11 scripts 336 downloads

epubr - Read EPUB File Metadata and Text

Provides functions supporting the reading and parsing of internal e-book content from EPUB files. The 'epubr' package provides functions supporting the reading and parsing of internal e-book content from EPUB files. E-book metadata and text content are parsed separately and joined together in a tidy, nested tibble data frame. E-book formatting is not completely standardized across all literature. It can be challenging to curate parsed e-book content across an arbitrary collection of e-books perfectly and in completely general form, to yield a singular, consistently formatted output. Many EPUB files do not even contain all the same pieces of information in their respective metadata. EPUB file parsing functionality in this package is intended for relatively general application to arbitrary EPUB e-books. However, poorly formatted e-books or e-books with highly uncommon formatting may not work with this package. There may even be cases where an EPUB file has DRM or some other property that makes it impossible to read with 'epubr'. Text is read 'as is' for the most part. The only nominal changes are minor substitutions, for example curly quotes changed to straight quotes. Substantive changes are expected to be performed subsequently by the user as part of their text analysis. Additional text cleaning can be performed at the user's discretion, such as with functions from packages like 'tm' or 'qdap'.

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epubepub-filesepub-formatpeer-reviewed

6.14 score 24 stars 58 scripts 369 downloads

treebase - 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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6.14 score 10 stars 46 scripts 332 downloads

phonfieldwork - 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

6.12 score 20 stars 22 scripts 301 downloads

cld3 - 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

6.09 score 41 stars 98 scripts 1.0k 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

6.08 score 8 stars 4 scripts 159 downloads

pangoling - Access to Large Language Model Predictions

Provides access to word predictability estimates using large language models (LLMs) based on 'transformer' architectures via integration with the 'Hugging Face' ecosystem <https://huggingface.co/>. The package interfaces with pre-trained neural networks and supports both causal/auto-regressive LLMs (e.g., 'GPT-2') and masked/bidirectional LLMs (e.g., 'BERT') to compute the probability of words, phrases, or tokens given their linguistic context. For details on GPT-2 and causal models, see Radford et al. (2019) <https://storage.prod.researchhub.com/uploads/papers/2020/06/01/language-models.pdf>, for details on BERT and masked models, see Devlin et al. (2019) <doi:10.48550/arXiv.1810.04805>. By enabling a straightforward estimation of word predictability, the package facilitates research in psycholinguistics, computational linguistics, and natural language processing (NLP).

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nlppsycholinguisticstransformers

6.08 score 12 stars 10 scripts 549 downloads

Rpolyhedra - Polyhedra Database

A polyhedra database scraped from various sources as R6 objects and 'rgl' visualizing capabilities.

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geometrypolyhedra-databasergl

6.05 score 12 stars 31 scripts 788 downloads

gbifdb - High Performance Interface to 'GBIF'

A high performance interface to the Global Biodiversity Information Facility, 'GBIF'. In contrast to 'rgbif', which can access small subsets of 'GBIF' data through web-based queries to a central server, 'gbifdb' provides enhanced performance for R users performing large-scale analyses on servers and cloud computing providers, providing full support for arbitrary 'SQL' or 'dplyr' operations on the complete 'GBIF' data tables (now over 1 billion records, and over a terabyte in size). 'gbifdb' accesses a copy of the 'GBIF' data in 'parquet' format, which is already readily available in commercial computing clouds such as the Amazon Open Data portal and the Microsoft Planetary Computer, or can be accessed directly without downloading, or downloaded to any server with suitable bandwidth and storage space. The high-performance techniques for local and remote access are described in <https://duckdb.org/why_duckdb> and <https://arrow.apache.org/docs/r/articles/fs.html> respectively.

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6.04 score 38 stars 29 scripts 142 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

6.04 score 36 stars 34 scripts

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

6.03 score 89 stars 12 scripts 535 downloads

QuadratiK - Collection of Methods Constructed using Kernel-Based Quadratic Distances

It includes test for multivariate normality, test for uniformity on the d-dimensional Sphere, non-parametric two- and k-sample tests, random generation of points from the Poisson kernel-based density and clustering algorithm for spherical data. For more information see Saraceno G., Markatou M., Mukhopadhyay R. and Golzy M. (2024) <doi:10.48550/arXiv.2402.02290> Markatou, M. and Saraceno, G. (2024) <doi:10.48550/arXiv.2407.16374>, Ding, Y., Markatou, M. and Saraceno, G. (2023) <doi:10.5705/ss.202022.0347>, and Golzy, M. and Markatou, M. (2020) <doi:10.1080/10618600.2020.1740713>.

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cpp

6.02 score 1 stars 26 scripts 148 downloads

tidypmc - 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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5.99 score 35 stars 28 scripts 222 downloads

bikedata - 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

5.99 score 81 stars 30 scripts 104 downloads

rtika - 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

5.99 score 54 stars 12 scripts 283 downloads

allodb - Tree Biomass Estimation at Extra-Tropical Forest Plots

Standardize and simplify the tree biomass estimation process across globally distributed extratropical forests.

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5.97 score 40 stars 39 scripts

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

5.96 score 38 stars 12 scripts 741 downloads

workloopR - Analysis of Work Loops and Other Data from Muscle Physiology Experiments

Functions for the import, transformation, and analysis of data from muscle physiology experiments. The work loop technique is used to evaluate the mechanical work and power output of muscle. Josephson (1985) <doi:10.1242/jeb.114.1.493> modernized the technique for application in comparative biomechanics. Although our initial motivation was to provide functions to analyze work loop experiment data, as we developed the package we incorporated the ability to analyze data from experiments that are often complementary to work loops. There are currently three supported experiment types: work loops, simple twitches, and tetanus trials. Data can be imported directly from .ddf files or via an object constructor function. Through either method, data can then be cleaned or transformed via methods typically used in studies of muscle physiology. Data can then be analyzed to determine the timing and magnitude of force development and relaxation (for isometric trials) or the magnitude of work, net power, and instantaneous power among other things (for work loops). Although we do not provide plotting functions, all resultant objects are designed to be friendly to visualization via either base-R plotting or 'tidyverse' functions. This package has been peer-reviewed by rOpenSci (v. 1.1.0).

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ddfmuscle-forcemuscle-physiology-experimentstetanuswork-loopworkloop

5.93 score 3 stars 47 scripts 189 downloads

rgnparser - 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

5.92 score 14 stars 1 dependents 99 scripts 339 downloads

virtuoso - Interface to 'Virtuoso' using 'ODBC'

Provides users with a simple and convenient mechanism to manage and query a 'Virtuoso' database using the 'DBI' (Data-Base Interface) compatible 'ODBC' (Open Database Connectivity) interface. 'Virtuoso' is a high-performance "universal server," which can act as both a relational database, supporting standard Structured Query Language ('SQL') queries, while also supporting data following the Resource Description Framework ('RDF') model for Linked Data. 'RDF' data can be queried using 'SPARQL' ('SPARQL' Protocol and 'RDF' Query Language) queries, a graph-based query that supports semantic reasoning. This allows users to leverage the performance of local or remote 'Virtuoso' servers using popular 'R' packages such as 'DBI' and 'dplyr', while also providing a high-performance solution for working with large 'RDF' 'triplestores' from 'R.' The package also provides helper routines to install, launch, and manage a 'Virtuoso' server locally on 'Mac', 'Windows' and 'Linux' platforms using the standard interactive installers from the 'R' command-line. By automatically handling these setup steps, the package can make using 'Virtuoso' considerably faster and easier for a most users to deploy in a local environment. Managing the bulk import of triples from common serializations with a single intuitive command is another key feature of this package. Bulk import performance can be tens to hundreds of times faster than the comparable imports using existing 'R' tools, including 'rdflib' and 'redland' packages.

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5.91 score 9 stars 15 scripts 260 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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5.90 score 3 stars 22 scripts 462 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

5.90 score 9 stars 22 scripts 486 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

5.88 score 24 stars 157 scripts 10 downloads

pkgmatch - Find R Packages Matching Either Descriptions or Other R Packages

Find R packages matching either descriptions or other R packages.

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embeddingsllmsnatural-language-processingcpp

5.81 score 6 stars

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

5.81 score 36 stars 18 scripts 252 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

5.80 score 9 stars 9 scripts 195 downloads

naijR - Operations to Ease Data Analyses Specific to Nigeria

A set of convenience functions as well as geographical/political data about Nigeria, aimed at simplifying work with data and information that are specific to the country.

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5.76 score 12 stars 12 scripts 960 downloads

dendroNetwork - 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

5.75 score 7 stars 7 scripts 244 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

5.73 score 9 stars 7 scripts 228 downloads

BaseSet - 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 5 scripts 341 downloads

srr - 'rOpenSci' Review Roclets

Companion package to 'rOpenSci' statistical software review project.

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compliance-automationstatistical-softwarecpp

5.65 score 5 stars 3 dependents 3 scripts

rdryad - 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

5.65 score 26 stars 49 scripts 288 downloads

tidyqpcr - 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

5.65 score 53 stars 21 scripts

getCRUCLdata - '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 list of 'terra' 'rast' objects for use. '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

5.64 score 17 stars 17 scripts 141 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

5.64 score 6 stars 4 scripts

c3dr - Read and Write C3D Motion Capture Files

A wrapper for the 'EZC3D' library to work with C3D motion capture data.

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cpp

5.60 score 4 stars 7 scripts 488 downloads

gpg - 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

5.58 score 20 stars 32 scripts 438 downloads

bold - 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

5.57 score 21 stars 65 scripts 376 downloads

circle - 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

5.56 score 12 stars 3 scripts 325 downloads

hddtools - Hydrological Data Discovery Tools

Tools to discover hydrological data, accessing catalogues and databases from various data providers. The package is described in Vitolo (2017) "hddtools: Hydrological Data Discovery Tools" <doi:10.21105/joss.00056>.

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data60ukgrdchydrologykgclimateclassmopexpeer-reviewedprecipitationsepa

5.56 score 48 stars 25 scripts 116 downloads

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

5.54 score 6 stars 29 scripts 201 downloads

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

5.53 score 7 stars 32 scripts 265 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

5.50 score 55 stars 23 scripts

internetarchive - An API Client for the Internet Archive

Search the Internet Archive (<https://archive.org>), retrieve metadata, and download files.

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5.49 score 60 stars 26 scripts 30 downloads

DoOR.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

5.49 score 10 stars 52 scripts

EndoMineR - Functions to mine endoscopic and associated pathology datasets

This script comprises the functions that are used to clean up endoscopic reports and pathology reports as well as many of the scripts used for analysis. The scripts assume the endoscopy and histopathology data set is merged already but it can also be used of course with the unmerged datasets.

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endoscopygastroenterologypeer-reviewedsemi-structured-datatext-mining

5.47 score 13 stars 30 scripts

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

5.43 score 18 stars 7 scripts

ReLTER - An Interface for the eLTER Community

ReLTER provides access to DEIMS-SDR (https://deims.org/), and allows interaction with data and software implemented by eLTER Research Infrastructure (RI) thus improving data sharing among European LTER projects. ReLTER uses the R language to access and interact with the DEIMS-SDR archive of information shared by the Long Term Ecological Research (LTER) network. This package grew within eLTER H2020 as a major project that will help advance the development of European Long-Term Ecosystem Research Infrastructures (eLTER RI - https://elter-ri.eu). The ReLTER package functions in particular allow to: - retrieve the information about entities (e.g. sites, datasets, and activities) shared by DEIMS-SDR (see e.g. get_site_info function); - interact with the ODSEurope (maps.opendatascience.eu) starting with the dataset shared by DEIMS-SDR (https://deims.org/) (see e.g. the get_site_ODS() function); - use the eLTER site informations to download and crop geospatial data from other platforms (see e.g. get_site_ODS function()); - improve the quality of the dataset (see e.g. get_id_worms()). Functions currently implemented are derived from discussions of the needs among the eLTER users community. The ReLTER package will continue to follow the progress of eLTER-RI and evolve, adding new tools and improvements as required.

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biodiversity-informaticsdata-scienceecologyelterresearch-infrastructure

5.41 score 13 stars 8 scripts

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

5.40 score 25 stars 4 scripts

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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5.38 score 14 stars 10 scripts

concstats - Market Structure, Concentration and Inequality Measures

Based on individual market shares of all participants in a market or space, the package offers a set of different structural and concentration measures frequently - and not so frequently - used in research and in practice. Measures can be calculated in groups or individually. The calculated measure or the resulting vector in table format should help practitioners make more informed decisions. Methods used in this package are from: 1. Chang, E. J., Guerra, S. M., de Souza Penaloza, R. A. & Tabak, B. M. (2005) "Banking concentration: the Brazilian case". 2. Cobham, A. and A. Summer (2013). "Is It All About the Tails? The Palma Measure of Income Inequality". 3. Garcia Alba Idunate, P. (1994). "Un Indice de dominancia para el analisis de la estructura de los mercados". 4. Ginevicius, R. and S. Cirba (2009). "Additive measurement of market concentration" <doi:10.3846/1611-1699.2009.10.191-198>. 5. Herfindahl, O. C. (1950), "Concentration in the steel industry" (PhD thesis). 6. Hirschmann, A. O. (1945), "National power and structure of foreign trade". 7. Melnik, A., O. Shy, and R. Stenbacka (2008), "Assessing market dominance" <doi:10.1016/j.jebo.2008.03.010>. 8. Palma, J. G. (2006). "Globalizing Inequality: 'Centrifugal' and 'Centripetal' Forces at Work". 9. Shannon, C. E. (1948). "A Mathematical Theory of Communication". 10. Simpson, E. H. (1949). "Measurement of Diversity" <doi:10.1038/163688a0>.

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business-analyticscompetitionconcentrationdiversityinequalitypackage-development

5.38 score 7 stars 17 scripts 130 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

5.37 score 14 stars 28 scripts

qualR - 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

5.34 score 27 stars 27 scripts

rfisheries - 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

5.31 score 26 stars 39 scripts 291 downloads

mauricer - 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 10 scripts 606 downloads

handlr - 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

5.25 score 38 stars 31 scripts 477 downloads

qcoder - 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

5.14 score 142 stars 15 scripts

treedata.table - Manipulation of Matched Phylogenies and Data using 'data.table'

An implementation that combines trait data and a phylogenetic tree (or trees) into a single object of class treedata.table. The resulting object can be easily manipulated to simultaneously change the trait- and tree-level sampling. Currently implemented functions allow users to use a 'data.table' syntax when performing operations on the trait dataset within the treedata.table object.

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5.14 score 7 stars 26 scripts 34 downloads

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

5.13 score 14 stars 32 scripts 111 downloads

chlorpromazineR - 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

5.12 score 12 stars 11 scripts 265 downloads

helminthR - 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

5.11 score 10 stars 13 scripts 92 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

5.11 score 28 stars 23 scripts 342 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

5.10 score 4 stars 53 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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5.08 score 2 stars 12 scripts 495 downloads

neotoma - 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

5.05 score 31 stars 145 scripts 180 downloads

rdatacite - 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

5.00 score 24 stars 28 scripts 284 downloads

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

5.00 score 20 stars 55 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

4.99 score 85 stars 23 scripts 69 downloads

hydroscoper - 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

4.98 score 14 stars 34 scripts 58 downloads

roreviewapi - Plumber API to report package structure and function

Plumber API to report package structure and function.

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4.95 score 3 stars

rOPTRAM - 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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4.95 score 10 stars 8 scripts

CRediTas - Generate CRediT Author Statements

A tiny package to generate CRediT author statements (<https://credit.niso.org/>). It provides three functions: create a template, read it back and generate the CRediT author statement in a text file.

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4.93 score 9 stars 19 scripts 611 downloads

epair - EPA Data Helper for R

Aid the user in making queries to the EPA API site found at https://aqs.epa.gov/aqsweb/documents/data_api. This package combines API calling methods from various web scraping packages with specific strings to retrieve data from the EPA API. It also contains easy to use loaded variables that help a user navigate services offered by the API and aid the user in determining the appropriate way to make a an API call.

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4.89 score 7 stars 11 scripts

citecorp - 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

4.87 score 11 stars 15 scripts 652 downloads

repometrics - 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

4.86 score 3 stars

wmm - World Magnetic Model

Calculate magnetic field at a given location and time according to the World Magnetic Model (WMM). Both the main field and secular variation components are returned. This functionality is useful for physicists and geophysicists who need orthogonal components from WMM. Currently, this package supports annualized time inputs between 2000-01-01 to 2029-12-31. If desired, users can specify which WMM version to use, e.g., the original WMM2015 release or the recent out-of-cycle WMM2015 release. Methods used to implement WMM, including the Gauss coefficients for each release, are described in the following publications: NOAA NCEI Geomagnetic Modeling Team and British Geological Survey (2024) <doi:10.25921/aqfd-sd83>, Chulliat et al (2020) <doi:10.25923/ytk1-yx35>, Chulliat et al (2019) <doi:10.25921/xhr3-0t19>, Chulliat et al (2015) <doi:10.7289/V5TB14V7>, Maus et al (2010) <https://www.ngdc.noaa.gov/geomag/WMM/data/WMMReports/WMM2010_Report.pdf>, McLean et al (2004) <https://www.ngdc.noaa.gov/geomag/WMM/data/WMMReports/TRWMM_2005.pdf>, and Macmillian et al (2000) <https://www.ngdc.noaa.gov/geomag/WMM/data/WMMReports/wmm2000.pdf>.

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4.85 score 7 stars 169 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

4.84 score 6 stars 23 scripts 225 downloads

eDNAjoint - Joint Modeling of Traditional and Environmental DNA Survey Data in a Bayesian Framework

Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: <https://ednajoint.netlify.app/>). Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and gear scaling coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.

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cpp

4.82 score 7 stars 10 scripts 251 downloads

mcbette - 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

4.82 score 7 stars 19 scripts 142 downloads

cde - Download Data from the Catchment Data Explorer Website

Facilitates searching, download and plotting of Water Framework Directive (WFD) reporting data for all waterbodies within the UK Environment Agency area. The types of data that can be downloaded are: WFD status classification data, Reasons for Not Achieving Good (RNAG) status, objectives set for waterbodies, measures put in place to improve water quality and details of associated protected areas. The site accessed is <https://environment.data.gov.uk/catchment-planning/>. The data are made available under the Open Government Licence v3.0 <https://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/>.

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4.82 score 5 stars 22 scripts 5 downloads

phruta - Phylogenetic Reconstruction and Time-dating

The phruta R package is designed to simplify the basic phylogenetic pipeline. Specifically, all code is run within the same program and data from intermediate steps are saved in independent folders. Furthermore, all code is run within the same environment which increases the reproducibility of your analysis. phruta retrieves gene sequences, combines newly downloaded and local gene sequences, and performs sequence alignments.

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4.81 score 9 stars 16 scripts

outcomerate - 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 of Public Opinion Research (AAPOR). For details on these standards, see AAPOR (2016) <https://www.aapor.org/Standards-Ethics/Standard-Definitions-(1).aspx>.

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aapordisposition-codespeer-reviewedstandardssurvey

4.80 score 5 stars 25 scripts 212 downloads

rperseus - Get Texts from the Perseus Digital Library

The Perseus Digital Library is a collection of classical texts. This package helps you get them. The available works can also be viewed here: <http://cts.perseids.org/>.

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classicsgreekgreek-biblegreek-new-testamentlatinpeer-reviewedperseusperseus-digital-librarytranslation

4.78 score 20 stars 30 scripts

colocr - 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

4.76 score 25 stars 23 scripts 45 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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4.74 score 1 stars 4 scripts 396 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

4.73 score 9 stars 7 scripts

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

4.72 score 8 stars 9 scripts

brranching - 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

4.68 score 20 stars 1 dependents 32 scripts 109 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

4.67 score 11 stars 43 scripts 150 downloads

camsRad - Client for CAMS Radiation Service

Copernicus Atmosphere Monitoring Service (CAMS) Radiation Service provides time series of global, direct, and diffuse irradiations on horizontal surface, and direct irradiation on normal plane for the actual weather conditions as well as for clear-sky conditions. The geographical coverage is the field-of-view of the Meteosat satellite, roughly speaking Europe, Africa, Atlantic Ocean, Middle East. The time coverage of data is from 2004-02-01 up to 2 days ago. Data are available with a time step ranging from 15 min to 1 month. For license terms and to create an account, please see <http://www.soda-pro.com/web-services/radiation/cams-radiation-service>.

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peer-reviewed

4.65 score 9 stars 10 scripts 233 downloads

rfema - Access the openFEMA API

`rfema` allows users to access The Federal Emergency Management Agency's (FEMA) publicly available data through their API. The package provides a set of functions to easily navigate and access data from the National Flood Insurance Program along with FEMA's various disaster aid programs, including the Hazard Mitigation Grant Program, the Public Assistance Grant Program, and the Individual Assistance Grant Program.

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4.56 score 9 stars 6 scripts

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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4.56 score 12 stars 4 scripts 461 downloads

fluidsynth - 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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fluidsynthlibsdl2

4.56 score 12 stars 1 dependents 10 scripts 265 downloads

prismjs - 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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4.48 score 5 stars 1 dependents 1 scripts 252 downloads

DoOR.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

4.46 score 7 stars 1 dependents 136 scripts

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

4.43 score 15 stars 12 scripts 556 downloads

awardFindR - awardFindR

Queries a number of scientific awards databases. Collects relevant results based on keyword and date parameters, returns list of projects that fit those criteria as a data frame. Sources include: Arnold Ventures, Carnegie Corp, Federal RePORTER, Gates Foundation, MacArthur Foundation, Mellon Foundation, NEH, NIH, NSF, Open Philanthropy, Open Society Foundations, Rockefeller Foundation, Russell Sage Foundation, Robert Wood Johnson Foundation, Sloan Foundation, Social Science Research Council, John Templeton Foundation, and USASpending.gov.

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4.41 score 17 stars 3 scripts

babeldown - 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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4.28 score 24 stars 3 scripts

postdoc - 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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4.26 score 12 stars 2 scripts 282 downloads

universe - 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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4.26 score 9 stars 6 scripts

grainchanger - Moving-Window and Direct Data Aggregation

Data aggregation via moving window or direct methods. Aggregate a fine-resolution raster to a grid. The moving window method smooths the surface using a specified function within a moving window of a specified size and shape prior to aggregation. The direct method simply aggregates to the grid using the specified function.

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4.17 score 51 stars 29 scripts 10 downloads

ramlegacy - 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

4.13 score 5 stars 27 scripts 47 downloads

mbquartR - Finding Manitoba Quarter Sections

This package has four main functions: 1) download the Manitoba Original Survey Legal Descriptions data set; 2) find the coordinates of a quarter sections given the legal land description (e.g., "NE-11-33-29W"); 3) find the legal land description using coordinates (lat and long); and 4) plot these points on a map.

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4.11 score 1 stars 5 scripts

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

4.08 score 5 stars 16 scripts 16 downloads

saperlipopette - Create Example Git Messes

Holds functions creating Git messes, that users would then solve, to follow <https://ohshitgit.com/>.

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git

4.02 score 30 stars 2 scripts

USAboundariesData - 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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3.99 score 9 stars 108 scripts

antanym - 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

3.91 score 7 stars 23 scripts

photosearcher - Photo Searcher

Queries the Flick API (https://www.flickr.com/services/api/) to return photograph metadata as well as the ability to download the images as jpegs.

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3.90 score 16 stars 7 scripts

tif - 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

3.87 score 37 stars 20 scripts

treestartr - 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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3.86 score 9 stars 16 scripts 188 downloads

suppdata - 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

3.85 score 35 stars 9 scripts 67 downloads

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

3.85 score 14 stars 8 scripts 61 downloads

rgpdd - R Interface to the Global Population Dynamics Database

R Interface to the Global Population Dynamics Database (<https://ecologicaldata.org/wiki/global-population-dynamics-database>)

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3.83 score 9 stars 15 scripts

popler - Popler R Package

Browse and query the popler database.

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3.83 score 7 stars 48 scripts

birdsize - 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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3.78 score 3 stars 8 scripts

roblog - rOpenSci's blog guidance

It provides templates for roweb2 blogging and help for a GitHub forking workflow.

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3.70 score 5 stars 1 scripts

rppo - Access the Global Plant Phenology Data Portal

Search plant phenology data aggregated from several sources and available on the Global Plant Phenology Data Portal.

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peer-reviewed

3.69 score 3 stars 11 scripts 33 downloads

cRegulome - Obtain and Visualize Regulome-Gene Expression Correlations in Cancer

Builds a 'SQLite' database file of pre-calculated transcription factor/microRNA-gene correlations (co-expression) in cancer from the Cistrome Cancer Liu et al. (2011) <doi:10.1186/gb-2011-12-8-r83> and 'miRCancerdb' databases (in press). Provides custom classes and functions to query, tidy and plot the correlation data.

Last updated

cancer-genomicsdatabasedatasciencemicrornapeer-reviewedtcga-datatranscription-factors

3.69 score 3 stars 54 scripts 41 downloads

gitcellar - Helps Download Archives of GitHub Repositories

Provide functionality to download archives (backups) for all repositories in a GitHub organization (useful for backups!).

Last updated

githubgithub-backupgithub-backups

3.68 score 16 stars 7 scripts

MtreeRing - 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.

Last updated

dendrochronologyforestforestryshiny-appsshinyapptree-ring-widthtree-rings

3.68 score 34 stars 14 scripts 71 downloads

aeolus - Unleash Useful Linebreaks in Markdown Documents

Add linebreaks at the end of sentences and remove other linebreaks.

Last updated

3.54 score 14 stars 3 scripts

rusda - Interface to USDA Databases

An interface to the web service methods provided by the United States Department of Agriculture (USDA). The Agricultural Research Service (ARS) provides a large set of databases. The current version of the package holds interfaces to the Systematic Mycology and Microbiology Laboratory (SMML), which consists of four databases: Fungus-Host Distributions, Specimens, Literature and the Nomenclature database. It provides functions for querying these databases. The main function is \code{associations}, which allows searching for fungus-host combinations.

Last updated

3.51 score 13 stars 5 scripts 54 downloads

quartificate - Transform Google Docs into Quarto Books

Automate the Transformation of a Google Document into a Quarto Book source.

Last updated

3.38 score 48 stars

SymbiotaR2 - 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.

Last updated

databaselibraryspecimen-recordssymbiotasymbiota2symbiota2-portal

3.30 score 2 stars 4 scripts

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.

Last updated

3.30 score 21 stars 19 scripts 8 downloads

promoutils - Utilities for Promoting rOpenSci on Social Media

Utility functions for accessing GitHub and social media data.

Last updated

3.26 score 4 stars 2 scripts

pixelclasser - 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.

Last updated

3.00 score 2 stars 8 scripts 235 downloads

r2readthedocs - Convert R Package Documentation to a 'readthedocs' Website

Convert R package documentation to a 'readthedocs' website.

Last updated

2.90 score 16 stars 1 scripts

onekp - Retrieve Data from the 1000 Plants Initiative (1KP)

The 1000 Plants Initiative (www.onekp.com) has sequenced the transcriptomes of over 1000 plant species. This package allows these sequences and metadata to be retrieved and filtered by code, species or recursively by clade. Scientific names and NCBI taxonomy IDs are both supported.

Last updated

2.81 score 13 stars 5 scripts

rrricanesdata - 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.

Last updated

weather

2.64 score 3 stars 29 scripts

icepalace - Snapshot Current Versions of CRAN-like Repositories

What the package does (one paragraph).

Last updated

2.30 score 4 stars 3 scripts

commonmetar - Wraps Commonmeta For rOpenSci Blog's Needs

Uses the commonmeta Go library to generate random DOI strings.

Last updated

2.18 score 1 stars 3 scripts