commonmark - High Performance CommonMark and Github Markdown Rendering in R
The CommonMark specification 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.
Last updated 6 months ago
cmarkcmark-gfmgfmmarkdown
88 stars 14.64 score 0 dependencies 2065 dependents
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/>.
Last updated 9 days ago
data-sciencedrakehigh-performance-computingmakefilepeer-reviewedpipelinereproducibilityreproducible-researchropensciworkflow
1.3k stars 9.89 score 20 dependencies 1 dependents
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.
Last updated 7 days ago
142 stars 9.85 score 8 dependencies 352 dependentsmagick - 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. The latest version of the package includes a native graphics device for creating in-memory graphics or drawing onto images using pixel coordinates.
Last updated 7 days ago
image-magickimage-manipulationimage-processingimagemagickimagemagick-wrappermagick
453 stars 9.79 score 3 dependencies 225 dependents
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.
Last updated 11 months ago
gitpasswordssh
71 stars 9.69 score 5 dependencies 359 dependents
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.
Last updated 2 years ago
peer-reviewedropenscisummary-statisticsunconfunconf17
1.1k stars 9.59 score 32 dependencies 10 dependents
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/>).
Last updated 4 days ago
httphttpsapiweb-servicescurldownloadlibcurlasyncmockingcaching
102 stars 9.26 score 8 dependencies 302 dependents
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>).
Last updated 18 hours ago
data-sciencehigh-performance-computingmakepeer-reviewedpipeliner-targetopiareproducibilityreproducible-researchtargetsworkflow
891 stars 9.02 score 31 dependencies 15 dependentswritexl - 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.
Last updated 6 months ago
excellibxlsxwriterxlsx
206 stars 8.88 score 0 dependencies 190 dependents
rtweet - Collecting Twitter Data
An implementation of calls designed to collect and organize Twitter data via Twitter's REST and stream Application Program Interfaces (API), which can be found at the following URL: <https://developer.twitter.com/en/docs>.
Last updated 3 months ago
pdftools - Text Extraction, Rendering and Converting of PDF Documents
Utilities based on 'libpoppler' 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.
Last updated 10 months ago
pdf-filespdf-formatpdftoolspopplerpoppler-librarytext-extraction
509 stars 7.97 score 5 dependencies 39 dependents
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.
Last updated 2 months ago
javapdfpdf-documentpeer-reviewedropenscitabulatabular-data
539 stars 7.55 score 27 dependenciesassertr - 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.
Last updated 4 months ago
analysis-pipelineassertion-libraryassertion-methodsassertionspeer-reviewedpredicate-functions
467 stars 7.43 score 17 dependencies 11 dependents
visdat - Preliminary Visualisation of Data
Create preliminary exploratory data visualisations of an entire dataset to identify problems or unexpected features using 'ggplot2'.
Last updated 9 days ago
exploratory-data-analysismissingnesspeer-reviewedropenscivisualisation
449 stars 7.34 score 47 dependencies 8 dependentsrentrez - '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.
Last updated 4 years ago
194 stars 7.32 score 9 dependencies 59 dependents
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.
Last updated 5 months ago
peer-reviewed
214 stars 7.26 score 22 dependencies 37 dependentstaxize - Taxonomic Information from Around the Web
Interacts with a suite of web 'APIs' 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.
Last updated 2 months ago
taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperbiodiversitydarwincoredatataxize
264 stars 7.24 score 120 dependencies 29 dependents
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.
Last updated 2 months ago
453 stars 7.23 score 42 dependencies 3 dependents
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>.
Last updated 3 months ago
cyclecyclingdesire-linesorigin-destinationpeer-reviewedpubic-transportroute-networkroutesroutingspatialtransporttransport-planningtransportationwalking
414 stars 7.11 score 47 dependencies 2 dependents
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.
Last updated 22 hours ago
bioconductor-packageexporterparserphylogenetic-trees
95 stars 7.10 score 34 dependencies 111 dependentstokenizers - 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'.
Last updated 4 months ago
nlppeer-reviewedtext-miningtokenizer
184 stars 7.05 score 3 dependencies 74 dependentsgit2r - 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.
Last updated 1 months ago
gitgit-clientlibgit2libgit2-library
214 stars 7.00 score 0 dependencies 51 dependentsRSelenium - 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.
Last updated 1 years ago
rseleniumseleniumwebdriver
341 stars 6.81 score 22 dependencies 10 dependentssodium - 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.
Last updated 3 months ago
69 stars 6.81 score 0 dependencies 90 dependents
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'.
Last updated 2 days ago
open0street0mapopenstreetmapoverpass0apiosmcpposm-dataoverpass-apipeer-reviewed
310 stars 6.76 score 37 dependencies 9 dependentselastic - 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.
Last updated 1 years ago
databaseelasticsearchhttpapisearchnosqljavajsondocumentsdata-sciencedatabase-wrapperetl
245 stars 6.69 score 9 dependencies 1 dependents
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.
Last updated 2 months ago
gbifspecimensapiweb-servicesoccurrencesspeciestaxonomybiodiversitydatalifewatchoscibiospocc
151 stars 6.66 score 49 dependencies 20 dependentsrnoaa - '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.
Last updated 1 years ago
earthscienceclimateprecipitationtemperaturestormbuoyncdcnoaatornadoesea iceisdnoaa-data
328 stars 6.66 score 56 dependencies 4 dependentsprism - 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 8 months ago
56 stars 6.63 score 55 dependencies
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.
Last updated 2 months ago
data-storegit-lfspeer-reviewed
179 stars 6.31 score 24 dependencies 12 dependentscharlatan - 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.
Last updated 3 months ago
datadatasetfake-datafakerpeer-reviewed
291 stars 6.26 score 13 dependencies 1 dependentsqpdf - 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++ API 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.
Last updated 4 months ago
57 stars 6.21 score 4 dependencies 66 dependentsiheatmapr - 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.
Last updated 1 years ago
heatmapplotlyinteractive-visualizationsdata-visualizationhtmlwidgetspeer-reviewed
267 stars 6.11 score 52 dependencies 1 dependentshunspell - 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.
Last updated 9 months ago
hunspellspell-checkspellcheckerstemmertokenizer
108 stars 6.00 score 2 dependencies 27 dependentsbiomartr - 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.
Last updated 27 days ago
biomartgenomic-data-retrievalannotation-retrievaldatabase-retrievalncbiensemblbiological-data-retrievalensembl-serversgenomegenome-annotationgenome-retrievalgenomicsmeta-analysismetagenomicsncbi-genbankpeer-reviewedproteomesequenced-genomes
209 stars 5.97 score 79 dependencies 3 dependentstesseract - 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.
Last updated 8 months ago
ocrtesseracttesseract-ocr
240 stars 5.83 score 8 dependencies
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'.
Last updated 2 months ago
apiqualtricsqualtrics-apisurveysurvey-data
215 stars 5.77 score 44 dependencies
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.
Last updated 10 months ago
95 stars 5.74 score 0 dependencies 41 dependentsjqr - 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.
Last updated 8 months ago
jqjson
141 stars 5.74 score 2 dependencies 27 dependentsrcrossref - 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.
Last updated 1 years ago
text-mingliteraturepdfxmlpublicationscitationsfull-texttdmcrossrefapiapi-wrappercrossref-apidoimetadata
165 stars 5.64 score 60 dependencies 9 dependentsgeojsonio - 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'.
Last updated 9 months ago
geojsontopojsongeospatialconversiondatainput-outputio
151 stars 5.53 score 56 dependencies 14 dependentswebchem - 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.
Last updated 5 months ago
cas-numberchemical-informationchemspideridentifierropensciwebscraping
160 stars 5.49 score 31 dependencies 9 dependentsspelling - 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.
Last updated 5 months ago
spell-checkspell-checkerspellcheckspellcheckerspelling
105 stars 5.47 score 12 dependencies 7 dependentsgoogleLanguageR - 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 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.
Last updated 10 days ago
cloud-speech-apicloud-translation-apigoogle-api-clientgoogle-cloudgoogle-cloud-speechgoogle-nlpgoogleauthrnatural-language-processingpeer-reviewedsentiment-analysisspeech-apitranslation-api
191 stars 5.46 score 31 dependencies 3 dependentstextreuse - 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.
Last updated 2 months ago
peer-reviewed
195 stars 5.39 score 27 dependencies
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.
Last updated 1 years ago
metadataropensciphylogeneticsindependant-contrastsbiodiversitypeer-reviewedphylogenytaxonomy
39 stars 5.25 score 26 dependencies 31 dependents
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>.
Last updated 2 years ago
emleml-metadatametadata-standard
97 stars 5.23 score 46 dependencies 5 dependents
osmextract - Download and Import Open Street Map Data Extracts
Match, download, convert and import Open Street Map data extracts obtained from several providers.
Last updated 17 days ago
geogeofabrik-zoneopen-dataosmosm-pbf
166 stars 5.14 score 22 dependenciesghql - 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.
Last updated 2 years ago
httpapiweb-servicescurldatagraphqlgraphql-apigraphql-client
144 stars 5.11 score 10 dependencies 7 dependentsjsonvalidate - 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.
Last updated 4 months ago
jsonjson-validationjsonvalidate
48 stars 5.10 score 5 dependencies 35 dependents
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 'drake' R package by Will Landau (2018) <doi:10.21105/joss.00550>.
Last updated 10 days ago
data-sciencehigh-performance-computingpeer-reviewedpipeliner-targetopiareproducibilitytargetsworkflow
121 stars 5.09 score 35 dependencies 9 dependentsdataspice - 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.
Last updated 3 years ago
datadatasetmetadataschema-orgunconfunconf18
156 stars 5.04 score 87 dependencies
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.
Last updated 22 days ago
open-scienceosfreproducible-research
139 stars 5.03 score 30 dependencies 3 dependentsphylogram - 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.
Last updated 5 years ago
peer-reviewed
11 stars 5.02 score 5 dependencies 8 dependentstsbox - 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.
Last updated 10 days ago
graphicstime-series
147 stars 4.99 score 4 dependencies 3 dependentstic - 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).
Last updated 10 days ago
appveyorcontinuous-integrationdeploymentgithubactionstravis-ci
153 stars 4.99 score 37 dependencies
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.'
Last updated 1 years ago
fishfishbasetaxonomy
109 stars 4.98 score 48 dependencies 2 dependentsssh - 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.
Last updated 10 months ago
libsshsshssh-client
127 stars 4.97 score 6 dependencies 7 dependents
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>.
Last updated 9 days ago
gdalmodismodis-datamodis-land-productspeer-reviewedpreprocessingremote-sensingsatellite-imagerytime-series
154 stars 4.94 score 72 dependencies 1 dependentsreadODS - Read and Write ODS Files
Read ODS (OpenDocument Spreadsheet) into R as data frame. Also support writing data frame into ODS file.
Last updated 9 days ago
55 stars 4.93 score 18 dependencies 19 dependents
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.
Last updated 5 months ago
specimensapiweb-servicesoccurrencesspeciestaxonomygbifinatvertnetebirdidigbioobisalaantwebbisondataecoengineinaturalistoccurrencespecies-occurrencespocc
115 stars 4.89 score 62 dependencies 6 dependents
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.
Last updated 9 days ago
datasetebird
134 stars 4.82 score 40 dependenciesav - 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.
Last updated 5 months ago
91 stars 4.80 score 0 dependencies 14 dependentsrredlist - 'IUCN' Red List Client
'IUCN' Red List (<http://apiv3.iucnredlist.org/api/v3/docs>) 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.
Last updated 2 years ago
iucnbiodiversityapiweb-servicestraitshabitatspeciesconservationapi-wrapperiucn-red-listtaxize
46 stars 4.78 score 9 dependencies 30 dependentsbold - 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.
Last updated 1 months ago
biodiversitybarcodednasequencesfastaapi-wrapperbarcodestaxize
17 stars 4.76 score 14 dependencies 30 dependents
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>.
Last updated 22 days ago
bibliographic-databibliographic-databasebibliometricsbibliometrixscience-mapping
89 stars 4.74 score 23 dependencies 5 dependents
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.
Last updated 4 months ago
opencvopencv-libraryunconfunconf18
132 stars 4.73 score 2 dependencieshoardr - 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.
Last updated 6 months ago
cachingdatafilesxmlpdf
22 stars 4.73 score 3 dependencies 38 dependentsosmplotr - Bespoke Images of 'OpenStreetMap' Data
Bespoke images of 'OpenStreetMap' ('OSM') data and data visualisation using 'OSM' objects.
Last updated 10 days ago
data-visualisationhighlighting-clustersopenstreetmaposmoverpassoverpass-apipeer-reviewed
132 stars 4.68 score 86 dependenciesqcoder - 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.
Last updated 3 years ago
unconfunconf18
128 stars 4.63 score 70 dependenciesbib2df - 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.
Last updated 4 months ago
bibtexpeer-reviewed
99 stars 4.54 score 27 dependencies 6 dependentsworrms - 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.
Last updated 6 months ago
biologysciencemarineapiwebapi-clientwormsspeciesapi-wrapperbiological-datafishjerico-relevantmarine-biologymarine-speciestaxizetaxonomy
23 stars 4.53 score 21 dependencies 31 dependentsrebird - 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.
Last updated 4 months ago
birdsbirdingebirddatabasedatabiologyobservationssightingsornithologyebird-apiebird-webservicesspocc
80 stars 4.51 score 24 dependencies 7 dependents
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/>.
Last updated 1 days ago
nasameteorological-dataweatherglobalweather-datameteorologynasa-poweragroclimatologyearth-sciencedata-accessclimate-dataagroclimatology-dataweather-variables
96 stars 4.47 score 36 dependencies 3 dependentsckanr - 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.
Last updated 1 years ago
databaseopen-datackanapidatadatasetapi-wrapperckan-api
99 stars 4.47 score 32 dependencies 3 dependentsgistr - Work with 'GitHub' 'Gists'
Work with 'GitHub' 'gists' from 'R' (e.g., <https://en.wikipedia.org/wiki/GitHub#Gist>, <https://docs.github.com/en/github/writing-on-github/creating-gists/>). A 'gist' is simply one or more files with code/text/images/etc. This package allows the user to create new 'gists', update 'gists' with new files, rename files, delete files, get and delete 'gists', star and 'un-star' 'gists', fork 'gists', open a 'gist' in your default browser, get embed code for a 'gist', list 'gist' 'commits', and get rate limit information when 'authenticated'. Some requests require authentication and some do not. 'Gists' website: <https://gist.github.com/>.
Last updated 2 years ago
httphttpsapiweb-servicesgithubgithub apigistgistscodescriptsnippetapi-wrappergithub-apigithub-gist
103 stars 4.41 score 48 dependencies 2 dependentsezknitr - 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.
Last updated 11 months ago
knitrpeer-reviewedreproducibilityrmarkdownrmd
112 stars 4.40 score 10 dependencies
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.
Last updated 7 months ago
api-clientbioinformaticsccledownloadericgctcgatoiltreehouseucscucsc-xena
100 stars 4.38 score 35 dependencies 1 dependentswikitaxa - 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.
Last updated 2 years ago
taxonomyspeciesapiweb-serviceswikipediavernacularwikispecieswikicommonstaxizewikipedia-api
21 stars 4.36 score 99 dependencies 30 dependentsgeonames - 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.
Last updated 5 years ago
37 stars 4.32 score 1 dependencies 21 dependentsgeojson - 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.
Last updated 12 months ago
geojsongeospatialconversiondatainput-outputbboxpolygongeobufcrsndgeojsonspatial
32 stars 4.30 score 8 dependencies 15 dependents
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.
Last updated 8 months ago
peer-reviewed
99 stars 4.29 score 34 dependencies
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>).
Last updated 2 years ago
taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperitistaxize
16 stars 4.28 score 28 dependencies 30 dependentsnodbi - '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'.
Last updated 1 days ago
databasemongodbelasticsearchcouchdbsqlitepostgresqlduckdbnosqljsondocuments
76 stars 4.25 score 13 dependencies 1 dependentscyphr - 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.
Last updated 11 months ago
encryptionopensslpeer-reviewedsodium
93 stars 4.24 score 6 dependencies 2 dependentscodemetar - 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.
Last updated 22 days ago
metadatacodemetaropenscicitationcreditlinked-datajson-ldpeer-reviewed
66 stars 4.21 score 41 dependencies 5 dependentsnatserv - 'NatureServe' Interface
Interface to 'NatureServe' (<https://www.natureserve.org/>). Includes methods to get data, image metadata, search taxonomic names, and make maps.
Last updated 6 months ago
taxonomyspeciesapiweb-servicesnatureservemetadatamapstaxize
10 stars 4.21 score 20 dependencies 30 dependentsweathercan - 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.
Last updated 10 months ago
environment-canadapeer-reviewedweather-dataweather-downloader
102 stars 4.18 score 47 dependenciestidync - 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().
Last updated 9 months ago
89 stars 4.15 score 26 dependencies 2 dependentsfingertipsR - 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.
Last updated 5 months ago
api-wrapperfingertipshealthopen-datapeer-reviewedpublic-healthpublic-health-england
91 stars 4.13 score 67 dependencies 1 dependents
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>.
Last updated 2 days ago
us-nceimeteorological-dataglobal-weatherweatherweather-datameteorologystation-datasurface-weatherdata-accessus-ncdcdaily-datadaily-weatherglobal-datagsodhistorical-datahistorical-weatherncdcnceiweather-informationweather-stations
88 stars 4.10 score 6 dependenciesbibtex - Bibtex Parser
Utility to parse a bibtex file.
Last updated 8 months ago
bibtexparser
35 stars 4.10 score 1 dependencies 15 dependentsvcr - 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 hooking into the 'webmockr' R package for matching 'HTTP' requests by various rules ('HTTP' method, 'URL', query parameters, headers, body, etc.), and then caching real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests matching any previous requests in the same 'cassette' use a cached 'HTTP' response.
Last updated 3 hours ago
httphttpsapiweb-servicescurlmockmockinghttp-mockingtestingtesting-toolstddunit-testingvcr
78 stars 4.10 score 28 dependenciesopencage - 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>.
Last updated 1 years ago
geocodegeocoderopencageopencage-apiopencage-geocoderpeer-reviewedplacenamesrspatial
87 stars 4.09 score 38 dependenciesrzmq - R Bindings for 'ZeroMQ'
Interface to the 'ZeroMQ' lightweight messaging kernel (see <https://zeromq.org/> for more information).
Last updated 3 months ago
zeromqzmq
83 stars 4.03 score 0 dependencies
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.
Last updated 8 days ago
mapsscanspatial
88 stars 4.02 score 48 dependencies
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'.
Last updated 2 years ago
data-accessoai-pmhpeer-reviewedscholarly-api
14 stars 4.02 score 24 dependencies 24 dependentsredland - 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.
Last updated 5 months ago
17 stars 4.02 score 30 dependencies 22 dependentsrobotstxt - 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.
Last updated 2 years ago
crawlerpeer-reviewedrobotstxtscraperspiderwebscraping
69 stars 3.98 score 25 dependencies 5 dependents
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).
Last updated 3 months ago
dataisochronesjavaopentripplannerotppublic-transportroutingtransporttransportation-planning
78 stars 3.94 score 32 dependencies
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.
Last updated 3 months ago
metadatanexmlphylogeneticslinked-data
13 stars 3.94 score 38 dependencies 20 dependents
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.
Last updated 7 months ago
citzgovernment-datahydrologyhydrometricstidy-datawater-resources
69 stars 3.92 score 49 dependencies 3 dependents
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.
Last updated 10 days ago
data-sciencedata-version-controldata-versioningreproducibilityreproducible-researchtargetsworkflow
83 stars 3.90 score 42 dependencies
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.
Last updated 6 months ago
archivingdatabasedbipeer-reviewed
78 stars 3.87 score 1 dependenciesbikedata - 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.
Last updated 6 months ago
bicycle-hire-systemsbike-hire-systemsbike-hirebicycle-hiredatabasebike-datapeer-reviewed
81 stars 3.84 score 47 dependencies
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.
Last updated 6 months ago
agent-based-modelingindividual-based-modellingnetlogopeer-reviewed
75 stars 3.82 score 126 dependencieshistorydata - 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.
Last updated 3 years ago
82 stars 3.82 score 0 dependencies
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>.
Last updated 22 days ago
data-scienceobliquerandom-forestsurvival
50 stars 3.79 score 9 dependencies 1 dependents
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.
Last updated 25 days ago
apicomtradepeer-reviewedsupply-chain
63 stars 3.77 score 42 dependencies
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'.
Last updated 9 days ago
59 stars 3.75 score 22 dependenciesantiword - 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.
Last updated 3 months ago
antiwordextract-text
56 stars 3.73 score 1 dependencies 5 dependentstradestatistics - Open Trade Statistics API Wrapper and Utility Program
Access 'Open Trade Statistics' API from R to download international trade data.
Last updated 1 years ago
api-wrapperdata-tableinternational-tradejsonliteopen-trade-statistics
75 stars 3.73 score 15 dependencies
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.
Last updated 1 years ago
geospatialdatalatitudelongitudeparsercoordinatesgeo
63 stars 3.70 score 2 dependencies 3 dependents
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/>.
Last updated 22 days ago
datasetsdemsmapmap-tilesmappingnational-mapnhdorthoimagerypeer-reviewedprogressrretrieve-dataterrainrunityunity-rendering-engineusgs
71 stars 3.69 score 52 dependencies
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.
Last updated 1 months ago
commonmarkxmlxpath
57 stars 3.69 score 13 dependencies 3 dependentstraits - Species Trait Data from Around the Web
Species trait data from many different sources, including sequence data from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>), plant trait data from 'BETYdb', data from 'EOL' 'Traitbank', 'Birdlife' International, and more.
Last updated 2 months ago
traitsapiweb-servicesspeciestaxonomyapi-client
39 stars 3.68 score 124 dependencies 9 dependentsrnaturalearthdata - 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'.
Last updated 6 months ago
11 stars 3.66 score 0 dependencies 6 dependentsrerddap - 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>.
Last updated 7 months ago
earthscienceclimateprecipitationtemperaturestormbuoynoaaapi-clienterddapnoaa-data
40 stars 3.64 score 33 dependencies 6 dependentssmapr - 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.
Last updated 1 years ago
acquisitionextract-datanasapeer-reviewedrastersmap-datasoil-mappingsoil-moisturesoil-moisture-sensor
79 stars 3.64 score 30 dependenciesroadoi - 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.
Last updated 2 years ago
altmetricscode4liboadoiopen-accesspeer-reviewedunpaywallwebclient
64 stars 3.63 score 51 dependencieswdman - '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.
Last updated 10 months ago
rseleniumseleniumwebdriverwebdriver-manager
29 stars 3.62 score 19 dependencies 11 dependentsgraphql - A GraphQL Query Parser
Bindings to the 'libgraphqlparser' C++ library. Parses GraphQL syntax and exports the AST in JSON format.
Last updated 2 years ago
graphqllibgraphql
37 stars 3.61 score 2 dependencies 9 dependents
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.
Last updated 13 days ago
brazilexchange-datafinancefinancial-datafinancial-servicesmarket-data
69 stars 3.59 score 55 dependencies
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.
Last updated 3 months ago
landscape-ecologyneutral-landscape-modelpeer-reviewedspatial
64 stars 3.58 score 43 dependencies
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.
Last updated 5 months ago
arxivarxiv-analyticsarxiv-apiarxiv-org
60 stars 3.53 score 9 dependenciesjsonld - JSON for Linking Data
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.
Last updated 4 years ago
json-ld
34 stars 3.45 score 4 dependencies 10 dependentsbabette - 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'.
Last updated 1 months ago
bayesian-inferencebeast2phylogenetics
42 stars 3.44 score 56 dependencies 1 dependentsrdataretriever - 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.
Last updated 2 days ago
datadata-sciencedatabasedatasetsscience
44 stars 3.41 score 14 dependenciestaxa - 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.
Last updated 5 months ago
taxonomybiologyhierarchydata-cleaningtaxon
48 stars 3.39 score 20 dependenciesrinat - 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.
Last updated 2 years ago
inaturalistspocc
50 stars 3.38 score 39 dependencieslingtypology - 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.
Last updated 5 months ago
abvdafboatlasautotypebivaltypclldglottolog-databaselinguistic-mapslinguisticsphoiblesailstypologywals
50 stars 3.37 score 47 dependenciesxslt - Extensible Style-Sheet Language Transformations
An extension for the 'xml2' package to transform XML documents by applying an 'xslt' style-sheet.
Last updated 3 months ago
xmlxslt
27 stars 3.37 score 4 dependencies 10 dependentswebmockr - 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.
Last updated 3 hours ago
httphttpsapiweb-servicescurlmockmockingfakewebhttp-mockingtestingtesting-toolstddhttp-mock
49 stars 3.34 score 13 dependencies 1 dependentsfrictionless - 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.
Last updated 9 days ago
frictionlessdataoscibio
28 stars 3.32 score 36 dependencies 4 dependentsbinman - 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.
Last updated 1 years ago
15 stars 3.28 score 16 dependencies 12 dependentscld2 - 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.
Last updated 2 years ago
cldcld2language-detectionlanguage-detector
37 stars 3.27 score 1 dependencies 2 dependentslandscapetools - 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.
Last updated 2 years ago
landscapelandscape-ecologyrastervisualizationworkflow
46 stars 3.27 score 32 dependencies
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.
Last updated 4 days ago
attributioncitationcreditcitation-filescffmetadatacitation-file-formatropensci
24 stars 3.26 score 9 dependencies 2 dependentspaleobioDB - Download and Process Data from the Paleobiology Database
Includes functions to wrap most endpoints of the 'PaleobioDB' API and functions to visualize and process the fossil data. The API documentation for the Paleobiology Database can be found at <https://paleobiodb.org/data1.2/>.
Last updated 5 months ago
39 stars 3.25 score 6 dependenciesrtika - 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.
Last updated 1 years ago
extract-metadataextract-textjavaparsepdf-filespeer-reviewedtesseracttika
54 stars 3.24 score 4 dependenciesrsat - 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>).
Last updated 3 months ago
satellite-images
49 stars 3.24 score 120 dependenciesbowerbird - Keep a Collection of Sparkly Data Resources
Tools to get and maintain a data repository from third-party data providers.
Last updated 1 days ago
ropensciantarcticsouthern oceandataenvironmentalsatelliteclimatepeer-reviewed
46 stars 3.24 score 100 dependencies 1 dependentsautotest - Automatic Package Testing
Automatic testing of R packages via a simple YAML schema.
Last updated 17 days ago
54 stars 3.24 score 37 dependenciesUSAboundaries - 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.
Last updated 3 years ago
digital-historyhistoryspatial-data
56 stars 3.24 score 0 dependencies
internetarchive - An API Client for the Internet Archive
Search the Internet Archive (<https://archive.org>), retrieve metadata, and download files.
Last updated 4 years ago
58 stars 3.21 score 23 dependenciesrdhs - 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.
Last updated 4 months ago
datasetdhsdhs-apiextractpeer-reviewedsurvey-data
34 stars 3.21 score 57 dependencies 3 dependents
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.
Last updated 3 months ago
43 stars 3.21 score 37 dependencies 1 dependents
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.
Last updated 2 years ago
37 stars 3.20 score 4 dependencies 4 dependents
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.
Last updated 7 days ago
eiaeia-apienergy-dataenergy-information-administrationopen-data
46 stars 3.20 score 26 dependencies
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.
Last updated 11 months ago
44 stars 3.17 score 8 dependencies
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).
Last updated 3 days ago
name disambiguationbibliometricscoauthorshipcollaborationgeoreferencingmetasciencereferencesscientometricsscience of scienceweb of science
53 stars 3.16 score 96 dependenciesrsnps - 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.
Last updated 1 years ago
genesnpsequenceapiwebapi-clientspeciesdbsnpopensnpncbigenotypedatasnpsweb-api
52 stars 3.16 score 23 dependencies
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>.
Last updated 8 days ago
bayesian-inferencepanel-datastanstatistical-models
25 stars 3.15 score 60 dependenciesjstor - Read Data from JSTOR/DfR
Functions and helpers to import metadata, ngrams and full-texts delivered by Data for Research by JSTOR.
Last updated 10 days ago
jstorpeer-reviewedtext-analysistext-mining
46 stars 3.14 score 42 dependenciesessurvey - 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.
Last updated 3 years ago
ess
49 stars 3.14 score 39 dependenciesgendercoder - Recodes Sex/Gender Descriptions into a Standard Set
Provides functions and dictionaries for recoding of freetext gender responses into more consistent categories.
Last updated 5 months ago
gender-diversityozunconf18unconf
46 stars 3.14 score 0 dependenciesspatsoc - 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.
Last updated 22 days ago
animalgpsnetworksocialspatial
24 stars 3.12 score 33 dependencies 3 dependents
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/>.
Last updated 10 days ago
bayesianhigh-performance-computingmaker-targetopiareproducibilitystanstatisticstargets
47 stars 3.08 score 54 dependencies
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, agriculture bulletin data, and downloading and importing radar and satellite imagery files. 'DPIRD' weather data are accessed through public 'APIs' provided by 'DPIRD', <https://www.agric.wa.gov.au/weather-api-20>, 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.
Last updated 11 days ago
dpirdbommeteorological-dataweather-forecastaustraliaweatherweather-datameteorologywestern-australiaaustralia-bureau-of-meteorologywestern-australia-agricultureaustralia-agricultureaustralia-climateaustralia-weatherapi-clientclimatedatarainfallweather-api
21 stars 3.08 score 55 dependenciesriem - 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.
Last updated 20 hours ago
airportsasosiowa-environment-mesonetmetarpeer-reviewedtemperatureweatherweather-api
43 stars 3.06 score 25 dependenciescld3 - 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.
Last updated 8 months ago
cldcld3language-detectionlanguage-detector
41 stars 3.04 score 1 dependencies 1 dependents
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 <https://docs.getodk.org/central-intro/>. 'ODK Central' and its API are documented at <https://docs.getodk.org/>.
Last updated 5 days ago
databaseopen-dataopendatakitodkapidatadatasetodataodata-clientodk-central
41 stars 3.03 score 48 dependencies 1 dependents
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.
Last updated 1 years ago
52 stars 3.03 score 56 dependenciesnomisr - 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.
Last updated 2 years ago
api-clientcensus-datademographygeographic-datanational-statisticsofficial-statisticsofficialstatisticspeer-revieweduk
44 stars 3.01 score 30 dependencies
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.
Last updated 8 months ago
image-manipulationimagejpeer-reviewedtiff-filestiff-images
18 stars 3.00 score 35 dependencies 7 dependentsbeautier - '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.
Last updated 19 days ago
bayesianbeastbeast2beautiphylogenetic-inferencephylogenetics
13 stars 2.96 score 22 dependencies 5 dependentsrvertnet - 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.
Last updated 4 months ago
speciesoccurrencesbiodiversitymapsvertnetmammalsmammaliaspecimensapi-wrapperspecimenspocc
7 stars 2.96 score 40 dependencies 7 dependents
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>.
Last updated 1 years ago
api-wrappergeocodergeographic-datapeer-reviewedpostcodeuk
39 stars 2.93 score 8 dependencies
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>.
Last updated 2 years ago
data60ukgrdchydrologykgclimateclassmopexpeer-reviewedprecipitationsepa
44 stars 2.89 score 45 dependencies
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.
Last updated 1 months ago
38 stars 2.88 score 60 dependencies 1 dependentsgitignore - 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.
Last updated 4 days ago
32 stars 2.87 score 13 dependenciesplater - 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.
Last updated 2 years ago
24 stars 2.87 score 16 dependencies 2 dependentsbabelquarto - Renders a Multilingual Quarto Book
Automate rendering and cross-linking of Quarto books following a prescribed structure.
Last updated 10 days ago
31 stars 2.86 score 44 dependencies 1 dependentstidyqpcr - 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.
Last updated 3 months ago
miqeqpcrqpcr-analysistidyverse
45 stars 2.86 score 48 dependenciesmedrxivr - 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.
Last updated 2 years ago
bibliographic-databasebiorxivevidence-synthesismedrxiv-datapeer-reviewedpreprint-recordssystematic-reviews
47 stars 2.86 score 37 dependencies
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).
Last updated 2 months ago
data-qualityinitial-data-analysisreproducible-researchtemporal-datatime-series
35 stars 2.85 score 66 dependenciesquartificate - Transform Google Docs into Quarto Books
Automate the Transformation of a Google Document into a Quarto Book source.
Last updated 1 years ago
47 stars 2.83 score 53 dependencies
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.
Last updated 2 months ago
couchdbdatabasenosqldocumentscloudantcouchdb-client
33 stars 2.82 score 9 dependencieshandlr - 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.
Last updated 2 years ago
doimetadatacitationbibtexcrossrefcrosscitecodemetarisciteprocrdfxmljsoncitationsdigital-object-identifier
38 stars 2.82 score 13 dependenciesbaRcodeR - 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.
Last updated 6 months ago
34 stars 2.81 score 45 dependenciestaxizedb - Tools for Working with 'Taxonomic' Databases
Tools for working with 'taxonomic' databases, including utilities for downloading databases, loading them into various 'SQL' databases, cleaning up files, and providing a 'SQL' connection that can be used to do 'SQL' queries directly or used in 'dplyr'.
Last updated 2 months ago
itistaxizetaxonomic-databasestaxonomy
30 stars 2.80 score 44 dependencies 1 dependentseuropepmc - 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.
Last updated 8 months ago
bibliometricseurope-pmcpubmedpubmedcentralscientific-literaturescientific-publications
27 stars 2.80 score 37 dependencies 2 dependentssuppdata - 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().
Last updated 10 months ago
peer-reviewed
33 stars 2.77 score 65 dependencies
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.
Last updated 2 months ago
archaeologyradiocarbon-dates
30 stars 2.76 score 25 dependenciesrOPTRAM - 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> .
Last updated 18 days ago
2 stars 2.73 score 43 dependenciesdeposits - 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.
Last updated 5 months ago
36 stars 2.70 score 24 dependencies 1 dependentspkgreviewr - 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.
Last updated 11 months ago
reviewropensciropensci-reviewsunconfunconf18
36 stars 2.70 score 119 dependencies
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.
Last updated 3 months ago
dnaentrezgenbanksequence
25 stars 2.68 score 22 dependencies 1 dependentschirps - 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>.
Last updated 3 months ago
chirpsclimatologyprecipitation-data
30 stars 2.65 score 22 dependencies 1 dependentspatentsview - 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 seven endpoints, and parse the data that comes back.
Last updated 7 days ago
patentspatentsviewpatentsview-apipeer-revieweduspto
31 stars 2.64 score 12 dependencies
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>).
Last updated 2 days ago
open street mapopenstreetmaposmopenstreetmap-apiosmapiapi
8 stars 2.64 score 15 dependenciespkgcheck - rOpenSci Package Checks
Check whether a package is ready for submission to rOpenSci's peer review system.
Last updated 17 days ago
18 stars 2.63 score 104 dependencies 1 dependentsbeastier - 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.
Last updated 19 days ago
bayesianbeastbeast2phylogenetic-inferencephylogenetics
10 stars 2.63 score 51 dependencies 4 dependentsallodb - Tree Biomass Estimation at Extra-Tropical Forest Plots
Standardize and simplify the tree biomass estimation process across globally distributed extratropical forests.
Last updated 3 years ago
36 stars 2.60 score 29 dependenciestif - 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.
Last updated 8 months ago
corpusnatural-language-processingterm-frequencytext-processingtokenizer
35 stars 2.57 score 2 dependencies
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.
Last updated 6 months ago
unifirunityunity3dvisualization
29 stars 2.54 score 3 dependencies 1 dependents
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.
Last updated 9 days ago
pkgdown
25 stars 2.53 score 59 dependenciescolocr - 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>.
Last updated 5 years ago
colocalizationimage-analysis
26 stars 2.50 score 55 dependenciesrdryad - 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.
Last updated 1 years ago
datadoidryaddryad-apioai-pmh
25 stars 2.50 score 24 dependenciesbaRulho - Quantifying (Animal) Sound Degradation
Intended to facilitate acoustic analysis of (animal) sound transmission 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>).
Last updated 3 months ago
acoustic-signalsanimalbehaviorbioacoustics
6 stars 2.50 score 90 dependenciesallcontributors - 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.
Last updated 10 days ago
23 stars 2.48 score 23 dependenciesphylocomr - 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.
Last updated 1 years ago
phylogenyphylocomphylodiversitycommunity structurecharacter evolutionspeciescommunity-ecologyecologyevolution
14 stars 2.47 score 12 dependencies 4 dependentsMtreeRing - 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 10 days ago
dendrochronologyforestforestryshiny-appsshinyapptree-ring-widthtree-rings
28 stars 2.47 score 76 dependenciestidypmc - 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.
Last updated 5 years ago
31 stars 2.46 score 33 dependenciesneotoma - 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.
Last updated 2 years ago
neotomaneotoma-apisneotoma-databasensfpaleoecology
30 stars 2.46 score 87 dependenciesclifro - Easily Download and Visualise Climate Data from CliFlo
CliFlo is a web portal to the New Zealand National Climate Database and provides public access (via subscription) to around 6,500 various climate stations (see <https://cliflo.niwa.co.nz/> for more information). Collating and manipulating data from CliFlo (hence clifro) and importing into R for further analysis, exploration and visualisation is now straightforward and coherent. The user is required to have an internet connection, and a current CliFlo subscription (free) if data from stations, other than the public Reefton electronic weather station, is sought.
Last updated 1 years ago
openscizealandweatherclimatecliflodataapiwindroserainwindtemperatureclimate-dataclimate-stationskmlnational-climate-database
25 stars 2.44 score 47 dependencies
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.
Last updated 17 days ago
12 stars 2.44 score 83 dependencies 3 dependentscenso2017 - 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.)
Last updated 1 years ago
censocensuschiledemografiademographicsduckdbredatam
27 stars 2.43 score 24 dependencies
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).
Last updated 5 years ago
fisheriesopen-dataopenfisheries
25 stars 2.39 score 38 dependenciespangaear - 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.
Last updated 2 years ago
pangaeaenvironmental scienceearth sciencearchivepaleontologyecologychemistryatmosphereapi-clientdatapaleobiologyscientificwebservice-client
21 stars 2.37 score 33 dependenciestreebase - 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.
Last updated 5 months ago
10 stars 2.36 score 16 dependencies 2 dependentsrglobi - 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.
Last updated 10 months ago
14 stars 2.36 score 28 dependencies
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.
Last updated 2 years ago
datascholarlydatasethttpsapiweb-servicesapi-wrapperdataciteidentifiermetadataoai-pmhsolr
25 stars 2.35 score 20 dependencies
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.
Last updated 2 years ago
api-wrapperhealth-datahealthcarenpi-number
27 stars 2.35 score 31 dependenciespkgstats - 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.
Last updated 17 days ago
17 stars 2.35 score 38 dependencies 2 dependents
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.
Last updated 1 months ago
biodiversity-databiodiversity-informaticsbiodiversity-standardscitationsmuseum-collection-specimensmuseum-collectionsmuseum-metadata
21 stars 2.32 score 159 dependencies
babeldown - Helpers for Automatic Translation of Markdown-based Content
Provide workflows and guidance for automatic translation of Markdown-based R content using DeepL API.
Last updated 2 months ago
20 stars 2.31 score 69 dependenciesohun - 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>.
Last updated 3 months ago
audio-processingbioacousticssound-event-detectionspectrogramstreamline-analysis
11 stars 2.28 score 84 dependencies 1 dependents
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 'OceanInsight' (formerly 'OceanOptics') <https://www.oceaninsight.com/> brands.
Last updated 16 days ago
file-importreproducibilityreproducible-researchreproducible-sciencespectral-dataspectroscopy
13 stars 2.25 score 11 dependencies 2 dependents
chromer - Interface to Chromosome Counts Database API
A programmatic interface to the Chromosome Counts Database (<https://taux.evolseq.net/CCDB_web/>), Rice et al. (2014) <doi:10.1111/nph.13191>. This package is part of the 'ROpenSci' suite (<https://ropensci.org>).
Last updated 4 months ago
12 stars 2.24 score 23 dependenciesphonfieldwork - 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>.
Last updated 13 days ago
audacityeafelanexbexmaraldafieldworkflextextphoneticsphonologypraatsrt-subtitlestextgrid
20 stars 2.24 score 51 dependencies
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.
Last updated 10 months ago
hurricanepeer-reviewedweather
21 stars 2.22 score 66 dependencies
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.
Last updated 8 days ago
blastngenbankpeer-reviewedphylogeneticssequence-alignment
23 stars 2.14 score 69 dependenciesqualR - 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.
Last updated 3 months ago
air-pollutantsair-quality-dataair-quality-measurementsbrazilcetesbrio-de-janeirosao-pauloweather-data
23 stars 2.14 score 9 dependenciesrnaturalearthhires - 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.
Last updated 6 months ago
21 stars 2.14 score 2 dependencies 1 dependentsmauricer - 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'.
Last updated 2 months ago
3 stars 2.12 score 52 dependencies 2 dependentsrgnparser - 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.
Last updated 8 months ago
taxonomy
11 stars 2.06 score 27 dependencies 1 dependentstracerer - 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.
Last updated 10 months ago
8 stars 2.06 score 3 dependencies 3 dependentsfellingdater - Estimate, report and combine felling dates of historical tree-ring series
fellingdater is an R package that aims to facilitate the analysis and interpretation of tree-ring data from wooden cultural heritage objects and structures. The package standardizes the process of computing and combining felling date estimates, both for individual and groups of related tree-ring series.
Last updated 2 months ago
dendrochronologysapwoodtree-rings
8 stars 2.05 score 55 dependenciesmregions - Marine Regions Data from 'Marineregions.org'
Tools to get marine regions data from <https://www.marineregions.org/>. Includes tools to get region metadata, as well as data in 'GeoJSON' format, as well as Shape files. Use cases include using data downstream to visualize 'geospatial' data by marine region, mapping variation among different regions, and more.
Last updated 5 months ago
jerico-relevantmarinepeer-reviewedspatial
15 stars 2.05 score 64 dependenciesbrranching - 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/>).
Last updated 2 years ago
phylogenytreephylomaticmolecularplantsphylogenies
18 stars 2.05 score 136 dependencies 1 dependents
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>.
Last updated 8 days ago
bayesianhigh-performance-computingjagsmaker-targetopiareproducibilityrjagsstatisticstargets
9 stars 2.03 score 59 dependencies
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 and 2021) 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.
Last updated 8 days ago
europeeuropean-unioneurostatnomenclaturenutsnuts-codesnuts-regionsregional-data
6 stars 2.01 score 16 dependenciescircle - 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.
Last updated 10 months ago
api-clientcircle-cicontinuous-deploymentcontinuous-integration
12 stars 1.97 score 9 dependencies
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>).
Last updated 7 days ago
chronobiologychronotypemctqpeer-reviewedsleep
12 stars 1.97 score 22 dependencies
GLMMcosinor - Fit a Cosinor Model Using a Generalised Mixed Modelling Framework
Allows users to fit a cosinor model using the 'glmmTMB' framework. This extends on existing cosinor modelling 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>.
Last updated 4 months ago
1 stars 1.96 score 45 dependencies
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.
Last updated 6 months ago
extract-textrtfunrtf
15 stars 1.92 score 1 dependenciesrcites - 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/>.
Last updated 1 years ago
api-clientcitesdatabaseendangered-speciestrade
12 stars 1.92 score 9 dependenciesspiro - 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.
Last updated 15 days ago
12 stars 1.92 score 45 dependenciesdendroNetwork - 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>.
Last updated 3 months ago
archaeologydendrochronologydendroprovenancenetwork-analysistree-rings
4 stars 1.91 score 73 dependenciesrdefra - Interact with the UK AIR Pollution Database from DEFRA
This packages allows to retrieve air pollution data from the Air Information Resource (UK-AIR, <https://uk-air.defra.gov.uk/>) of the Department for Environment, Food and Rural Affairs (DEFRA) in the United Kingdom. UK-AIR does not provide a public API for programmatic access to data, therefore this package scrapes the HTML pages to get relevant information. The package is described in Vitolo et al. (2016) "rdefra: Interact with the UK AIR Pollution Database from DEFRA" <doi:10.21105/joss.00051>.
Last updated 9 days ago
air-pollutionair-pollution-levelsair-qualitydefrapeer-revieweduk
16 stars 1.90 score 39 dependenciesBaseSet - 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.
Last updated 7 months ago
bioconductorbioconductor-packagesets
10 stars 1.87 score 16 dependenciesfluidsynth - 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.
Last updated 5 months ago
10 stars 1.86 score 2 dependencies 1 dependentsgetCRUCLdata - '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 frame 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>.
Last updated 4 months ago
anglia-cruclimate-datacru-cl2temperaturerainfallelevationdata-accesswindrelative-humiditysolar-radiationdiurnal-temperaturefrostcrupeer-reviewed
17 stars 1.85 score 8 dependencies
quadkeyr - Tools for converting QuadKey-identified datasets (Microsoft's Bing Maps Tile System) into raster images and analyzing Meta (Facebook) Mobility Data.
'Quadkeyr' functions generate raster images based on QuadKey-identified data, facilitating efficient integration of Tile Maps data into R workflows. In particular, 'Quadkeyr' provides support to process and analyze Facebook mobility datasets within the R environment.
Last updated 4 months ago
geospatialquadkeyrastertilemap
11 stars 1.85 score 65 dependencies
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.
Last updated 8 months ago
12 stars 1.82 score 21 dependencies
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>.
Last updated 5 days ago
10 stars 1.81 score 44 dependenciesRpolyhedra - Polyhedra Database
A polyhedra database scraped from various sources as R6 objects and 'rgl' visualizing capabilities.
Last updated 2 years ago
geometrypolyhedra-databasergl
12 stars 1.76 score 42 dependenciespostdoc - 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.
Last updated 2 months ago
12 stars 1.76 score 9 dependenciesroreviewapi - Plumber API to report package structure and function
Plumber API to report package structure and function.
Last updated 17 days ago
4 stars 1.75 score 117 dependenciessrr - 'rOpenSci' Review Roclets
Companion package to 'rOpenSci' statistical software review project.
Last updated 2 months ago
4 stars 1.75 score 41 dependencies 2 dependentsjenkins - 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 years ago
20 stars 1.75 score 2 dependencies
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>.
Last updated 2 years ago
air-transportbtsbureau-of-transport-statisticsdb1bpeer-reviewedritaskynett100transtats
10 stars 1.71 score 77 dependencieshelminthR - 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 a programmatic interface to the London Natural History Museum's host-parasite database, one of the largest host-parasite databases existing currently <https://www.nhm.ac.uk/research-curation/scientific-resources/taxonomy-systematics/host-parasites/>. The package allows the user to query by host species, parasite species, and geographic location.
Last updated 2 years ago
disease-networkshelminthopen-dataparasites
6 stars 1.71 score 123 dependencies
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/>).
Last updated 7 months ago
ecologynetworksfood websinteractionsdata publicationsopen access
12 stars 1.69 score 22 dependenciesEDIutils - 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.
Last updated 10 months ago
ecologyeml-metadataopen-accessopen-dataresearch-data-managementresearch-data-repository
10 stars 1.65 score 11 dependencies
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.
Last updated 6 months ago
datacleaningexclusionmturkqualtrics
8 stars 1.65 score 31 dependencieskarel - 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.
Last updated 7 hours ago
learningprogrammingr-language
8 stars 1.64 score 55 dependenciesrangr - Mechanistic Simulation of Species Range Dynamics
Species range dynamics simulation toolset.
Last updated 21 hours ago
1 stars 1.64 score 6 dependenciesr2readthedocs - Convert R Package Documentation to a 'readthedocs' Website
Convert R package documentation to a 'readthedocs' website.
Last updated 1 months ago
14 stars 1.64 score 8 dependencies
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.
Last updated 1 years ago
14 stars 1.64 score 41 dependenciesrperseus - 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/>.
Last updated 1 years ago
classicsgreekgreek-biblegreek-new-testamentlatinpeer-reviewedperseusperseus-digital-librarytranslation
16 stars 1.64 score 44 dependenciescitecorp - 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.
Last updated 1 years ago
doimetadatacitationopencitationsbibtexcitationspmcidpmidsparql
11 stars 1.61 score 12 dependencieschlorpromazineR - 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.
Last updated 3 years ago
antipsychoticpharmacologypsychiatryschizophrenia
12 stars 1.59 score 0 dependencies
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>).
Last updated 9 months ago
cpp17matrix-marketmatrix-market-formatr-cpp11
6 stars 1.59 score 1 dependenciesmcbette - 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/>).
Last updated 4 days ago
7 stars 1.58 score 129 dependencieshydroscoper - 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.
Last updated 8 days ago
climategreecehydrologyhydrometeorologyhydroscopemeteorological-datameteorological-stationspeer-reviewedtidy-datatime-serieswater-resources
13 stars 1.58 score 28 dependenciesgitcellar - Helps Download Archives of GitHub Repositories
Provide functionality to download archives (backups) for all repositories in a GitHub organization (useful for backups!).
Last updated 2 months ago
githubgithub-backupgithub-backups
13 stars 1.58 score 25 dependencies
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.
Last updated 2 years ago
apiclimatelifewatchopen-scienceoscibioropensciwaterweather
13 stars 1.58 score 26 dependenciesrrlite - R Bindings to rlite
R bindings to rlite. rlite is a "self-contained, serverless, zero-configuration, transactional redis-compatible database engine. rlite is to Redis what SQLite is to SQL.".
Last updated 7 years ago
peer-reviewed
16 stars 1.58 score 4 dependencies
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>).
Last updated 8 days ago
database
4 stars 1.53 score 22 dependencies
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.
Last updated 1 years ago
animal-movementflydramotionmovement-dataoptitracktrajectoriestrajectory-analysisvisual-guidancevisual-perception
7 stars 1.48 score 45 dependenciesprismjs - 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.
Last updated 2 months ago
6 stars 1.47 score 7 dependencies 1 dependents
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.
Last updated 3 years ago
7 stars 1.46 score 43 dependenciestreestartr - 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.
Last updated 5 years ago
9 stars 1.46 score 35 dependenciesmregions2 - Access Data from Marineregions.org: The Marine Regions Gazetteer and the Marine Regions Data Products
Explore and retrieve marine geo-spatial data from the Marine Regions Gazetteer and the Marine Regions Data Products, including the Maritime Boundaries.
Last updated 2 days ago
4 stars 1.45 score 79 dependenciesrfema - 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.
Last updated 19 days ago
8 stars 1.45 score 28 dependenciesEndoMineR - 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.
Last updated 1 years ago
endoscopygastroenterologypeer-reviewedsemi-structured-datatext-mining
12 stars 1.45 score 133 dependencies
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.
Last updated 2 years ago
cavd-dataspace
5 stars 1.40 score 13 dependenciesonekp - 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 1 years ago
12 stars 1.38 score 54 dependencies
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>.
Last updated 2 years ago
apiexoplanetsnasa
13 stars 1.38 score 35 dependenciesCRediTas - 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.
Last updated 1 years ago
8 stars 1.36 score 0 dependencies
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.
Last updated 1 years ago
biodiversitycanape
7 stars 1.33 score 77 dependenciesDoOR.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.
Last updated 5 months ago
peer-reviewed
8 stars 1.31 score 1 dependenciespopler - Popler R Package
Browse and query the popler database.
Last updated 5 years ago
8 stars 1.24 score 67 dependenciestacmagic - 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.
Last updated 4 years ago
mrineuroimagingneuroscienceneuroscience-methodspetpet-mrpositronpositron-emission-tomographystatistics
5 stars 1.18 score 5 dependencies
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.
Last updated 22 days ago
9 stars 1.16 score 193 dependenciesDoOR.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.
Last updated 2 years ago
peer-reviewed
6 stars 1.16 score 0 dependencies 1 dependentsUSAboundariesData - 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'.
Last updated 3 years ago
9 stars 1.16 score 0 dependenciesrgpdd - R Interface to the Global Population Dynamics Database
R Interface to the Global Population Dynamics Database (<https://ecologicaldata.org/wiki/global-population-dynamics-database>)
Last updated 4 years ago
10 stars 1.16 score 0 dependenciesoutcomerate - 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>.
Last updated 4 years ago
aapordisposition-codespeer-reviewedstandardssurvey
5 stars 1.10 score 2 dependenciesramlegacy - 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>.
Last updated 5 years ago
fisheriesmarine-biologyramlegacyropenscistock-assessment
4 stars 1.09 score 28 dependenciesepair - 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.
Last updated 2 years ago
7 stars 1.00 score 21 dependencies
dataaimsr - AIMS Data Platform API Client
AIMS Data Platform API Client which provides easy access to AIMS Data Platform scientific data and information.
Last updated 1 years ago
aimsaustraliadatamarinemonitoringsstweather
4 stars 0.91 score 58 dependenciesantanym - Antarctic Geographic Place Names
Antarctic geographic names from the Composite Gazetteer of Antarctica, and functions for working with those place names.
Last updated 2 years ago
antarcticsouthern oceanplace namesgazetteerpeer-reviewed
7 stars 0.91 score 54 dependencies
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.
Last updated 1 years ago
peer-reviewed
3 stars 0.71 score 38 dependenciesbirdsize - 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.
Last updated 8 months ago
2 stars 0.61 score 1 dependenciesroblog - rOpenSci's blog guidance
It provides templates for roweb2 blogging and help for a GitHub forking workflow.
Last updated 2 years ago
5 stars 0.61 score 54 dependenciescRegulome - 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 4 years ago
cancer-genomicsdatabasedatasciencemicrornapeer-reviewedtcga-datatranscription-factors
3 stars 0.61 score 59 dependenciesicepalace - Snapshot Current Versions of CRAN-like Repositories
What the package does (one paragraph).
Last updated 2 years ago
4 stars 0.49 score 20 dependenciesSymbiotaR2 - 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 2 years ago
databaselibraryspecimen-recordssymbiotasymbiota2symbiota2-portal
2 stars 0.49 score 10 dependenciesuniverse - 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.
Last updated 1 years ago
3 stars 0.36 score 14 dependenciespixelclasser - 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 years ago
2 stars 0.36 score 2 dependenciesrrricanesdata - 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 5 years ago
weather
3 stars 0.36 score 0 dependencies