Showing 73 of total 73 results (show query)
ropensci
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.
Maintained by Elin Waring. Last updated 2 months ago.
peer-reviewedropenscisummary-statisticsunconfunconf17
1.1k stars 16.80 score 18k scripts 14 dependentsropensci
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.
Maintained by Philippe Massicotte. Last updated 13 days ago.
234 stars 15.51 score 7.2k scripts 47 dependentsropensci
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>).
Maintained by William Michael Landau. Last updated 1 days ago.
data-sciencehigh-performance-computingmakepeer-reviewedpipeliner-targetopiareproducibilityreproducible-researchtargetsworkflow
978 stars 15.16 score 4.6k scripts 22 dependentsropensci
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'.
Maintained by Mark Padgham. Last updated 1 months ago.
open0street0mapopenstreetmapoverpass0apiosmcpposm-dataoverpass-apipeer-reviewedcpp
322 stars 14.53 score 2.8k scripts 14 dependentsropensci
tokenizers:Fast, Consistent Tokenization of Natural Language Text
Convert natural language text into tokens. Includes tokenizers for shingled n-grams, skip n-grams, words, word stems, sentences, paragraphs, characters, shingled characters, lines, Penn Treebank, regular expressions, as well as functions for counting characters, words, and sentences, and a function for splitting longer texts into separate documents, each with the same number of words. The tokenizers have a consistent interface, and the package is built on the 'stringi' and 'Rcpp' packages for fast yet correct tokenization in 'UTF-8'.
Maintained by Thomas Charlon. Last updated 1 years ago.
nlppeer-reviewedtext-miningtokenizercpp
186 stars 13.33 score 1.1k scripts 81 dependentsropensci
visdat:Preliminary Visualisation of Data
Create preliminary exploratory data visualisations of an entire dataset to identify problems or unexpected features using 'ggplot2'.
Maintained by Nicholas Tierney. Last updated 9 months ago.
exploratory-data-analysismissingnesspeer-reviewedropenscivisualisation
452 stars 13.31 score 2.1k scripts 11 dependentsropensci
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.
Maintained by Carl Boettiger. Last updated 4 months ago.
data-storegit-lfspeer-reviewed
187 stars 12.98 score 187 scripts 12 dependentsropensci
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>.
Maintained by Robin Lovelace. Last updated 7 months ago.
cyclecyclingdesire-linesorigin-destinationpeer-reviewedpubic-transportroute-networkroutesroutingspatialtransporttransport-planningtransportationwalking
427 stars 12.31 score 684 scripts 3 dependentsropensci
RefManageR:Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management
Provides tools for importing and working with bibliographic references. It greatly enhances the 'bibentry' class by providing a class 'BibEntry' which stores 'BibTeX' and 'BibLaTeX' references, supports 'UTF-8' encoding, and can be easily searched by any field, by date ranges, and by various formats for name lists (author by last names, translator by full names, etc.). Entries can be updated, combined, sorted, printed in a number of styles, and exported. 'BibTeX' and 'BibLaTeX' '.bib' files can be read into 'R' and converted to 'BibEntry' objects. Interfaces to 'NCBI Entrez', 'CrossRef', and 'Zotero' are provided for importing references and references can be created from locally stored 'PDF' files using 'Poppler'. Includes functions for citing and generating a bibliography with hyperlinks for documents prepared with 'RMarkdown' or 'RHTML'.
Maintained by Mathew W. McLean. Last updated 4 months ago.
115 stars 12.06 score 2.3k scripts 16 dependentsropensci
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.
Maintained by Francois Michonneau. Last updated 2 years ago.
metadataropensciphylogeneticsindependant-contrastsbiodiversitypeer-reviewedphylogenytaxonomy
40 stars 12.05 score 356 scripts 29 dependentsropensci
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/>.
Maintained by William Michael Landau. Last updated 4 months ago.
data-sciencedrakehigh-performance-computingmakefilepeer-reviewedpipelinereproducibilityreproducible-researchropensciworkflow
1.3k stars 11.49 score 1.7k scripts 1 dependentsropensci
assertr:Assertive Programming for R Analysis Pipelines
Provides functionality to assert conditions that have to be met so that errors in data used in analysis pipelines can fail quickly. Similar to 'stopifnot()' but more powerful, friendly, and easier for use in pipelines.
Maintained by Tony Fischetti. Last updated 12 months ago.
analysis-pipelineassertion-libraryassertion-methodsassertionspeer-reviewedpredicate-functions
478 stars 11.39 score 452 scripts 12 dependentsropensci
biomartr:Genomic Data Retrieval
Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. with only one command.
Maintained by Hajk-Georg Drost. Last updated 2 months ago.
biomartgenomic-data-retrievalannotation-retrievaldatabase-retrievalncbiensemblbiological-data-retrievalensembl-serversgenomegenome-annotationgenome-retrievalgenomicsmeta-analysismetagenomicsncbi-genbankpeer-reviewedproteomesequenced-genomes
218 stars 11.35 score 129 scripts 3 dependentsropensci
tarchetypes:Archetypes for Targets
Function-oriented Make-like declarative pipelines for Statistics and data science are supported in the 'targets' R package. As an extension to 'targets', the 'tarchetypes' package provides convenient user-side functions to make 'targets' easier to use. By establishing reusable archetypes for common kinds of targets and pipelines, these functions help express complicated reproducible pipelines concisely and compactly. The methods in this package were influenced by the 'targets' R package. by Will Landau (2018) <doi:10.21105/joss.00550>.
Maintained by William Michael Landau. Last updated 1 days ago.
data-sciencehigh-performance-computingpeer-reviewedpipeliner-targetopiareproducibilitytargetsworkflow
142 stars 11.27 score 1.7k scripts 10 dependentsropensci
rix:Reproducible Data Science Environments with 'Nix'
Simplifies the creation of reproducible data science environments using the 'Nix' package manager, as described in Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()` function generates a complete description of the environment as a `default.nix` file, which can then be built using 'Nix'. This results in project specific software environments with pinned versions of R, packages, linked system dependencies, and other tools. Additional helpers make it easy to run R code in 'Nix' software environments for testing and production.
Maintained by Bruno Rodrigues. Last updated 5 days ago.
nixpeer-reviewedreproducibilityreproducible-research
238 stars 10.54 score 67 scriptsropensci
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.
Maintained by Jon Harmon. Last updated 3 months ago.
105 stars 10.50 score 1.1k scripts 1 dependentsropensci
robotstxt:A 'robots.txt' Parser and 'Webbot'/'Spider'/'Crawler' Permissions Checker
Provides functions to download and parse 'robots.txt' files. Ultimately the package makes it easy to check if bots (spiders, crawler, scrapers, ...) are allowed to access specific resources on a domain.
Maintained by Jordan Bradford. Last updated 4 months ago.
crawlerpeer-reviewedrobotstxtscraperspiderwebscraping
68 stars 10.43 score 414 scripts 7 dependentsropensci
googleLanguageR:Call Google's 'Natural Language' API, 'Cloud Translation' API, 'Cloud Speech' API and 'Cloud Text-to-Speech' API
Call 'Google Cloud' machine learning APIs for text and speech tasks. Call the 'Cloud Translation' API <https://cloud.google.com/translate/> for detection and translation of text, the 'Natural Language' API <https://cloud.google.com/natural-language/> to analyse text for sentiment, entities or syntax, the 'Cloud Speech' API <https://cloud.google.com/speech/> to 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.
Maintained by Mark Edmondson. Last updated 9 months ago.
cloud-speech-apicloud-translation-apigoogle-api-clientgoogle-cloudgoogle-cloud-speechgoogle-nlpgoogleauthrnatural-language-processingpeer-reviewedsentiment-analysisspeech-apitranslation-api
196 stars 10.36 score 268 scripts 3 dependentsropensci
rdhs:API Client and Dataset Management for the Demographic and Health Survey (DHS) Data
Provides a client for (1) querying the DHS API for survey indicators and metadata (<https://api.dhsprogram.com/#/index.html>), (2) identifying surveys and datasets for analysis, (3) downloading survey datasets from the DHS website, (4) loading datasets and associate metadata into R, and (5) extracting variables and combining datasets for pooled analysis.
Maintained by OJ Watson. Last updated 30 days ago.
datasetdhsdhs-apiextractpeer-reviewedsurvey-data
37 stars 10.16 score 286 scripts 4 dependentsropensci
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.
Maintained by Mauricio Vargas Sepulveda. Last updated 3 months ago.
javapdfpdf-documentpeer-reviewedropenscitabulatabular-dataopenjdk
552 stars 10.07 score 159 scripts 1 dependentsropensci
charlatan:Make Fake Data
Make fake data that looks realistic, supporting addresses, person names, dates, times, colors, coordinates, currencies, digital object identifiers ('DOIs'), jobs, phone numbers, 'DNA' sequences, doubles and integers from distributions and within a range.
Maintained by Roel M. Hogervorst. Last updated 2 months ago.
datadatasetfake-datafakerpeer-reviewed
296 stars 10.06 score 180 scripts 1 dependentsropensci
bib2df:Parse a BibTeX File to a Data Frame
Parse a BibTeX file to a data.frame to make it accessible for further analysis and visualization.
Maintained by Gianluca Baio. Last updated 8 months ago.
101 stars 9.82 score 212 scripts 6 dependentsropensci
rdflib:Tools to Manipulate and Query Semantic Data
The Resource Description Framework, or 'RDF' is a widely used data representation model that forms the cornerstone of the Semantic Web. 'RDF' represents data as a graph rather than the familiar data table or rectangle of relational databases. The 'rdflib' package provides a friendly and concise user interface for performing common tasks on 'RDF' data, such as reading, writing and converting between the various serializations of 'RDF' data, including 'rdfxml', 'turtle', 'nquads', 'ntriples', and 'json-ld'; creating new 'RDF' graphs, and performing graph queries using 'SPARQL'. This package wraps the low level 'redland' R package which provides direct bindings to the 'redland' C library. Additionally, the package supports the newer and more developer friendly 'JSON-LD' format through the 'jsonld' package. The package interface takes inspiration from the Python 'rdflib' library.
Maintained by Carl Boettiger. Last updated 8 months ago.
57 stars 9.59 score 123 scripts 7 dependentsropensci
DataPackageR:Construct Reproducible Analytic Data Sets as R Packages
A framework to help construct R data packages in a reproducible manner. Potentially time consuming processing of raw data sets into analysis ready data sets is done in a reproducible manner and decoupled from the usual 'R CMD build' process so that data sets can be processed into R objects in the data package and the data package can then be shared, built, and installed by others without the need to repeat computationally costly data processing. The package maintains data provenance by turning the data processing scripts into package vignettes, as well as enforcing documentation and version checking of included data objects. Data packages can be version controlled on 'GitHub', and used to share data for manuscripts, collaboration and reproducible research.
Maintained by Dave Slager. Last updated 6 months ago.
156 stars 9.38 score 72 scriptsropensci
textreuse:Detect Text Reuse and Document Similarity
Tools for measuring similarity among documents and detecting passages which have been reused. Implements shingled n-gram, skip n-gram, and other tokenizers; similarity/dissimilarity functions; pairwise comparisons; minhash and locality sensitive hashing algorithms; and a version of the Smith-Waterman local alignment algorithm suitable for natural language.
Maintained by Yaoxiang Li. Last updated 1 months ago.
200 stars 9.28 score 226 scriptsropensci
iheatmapr:Interactive, Complex Heatmaps
Make complex, interactive heatmaps. 'iheatmapr' includes a modular system for iteratively building up complex heatmaps, as well as the iheatmap() function for making relatively standard heatmaps.
Maintained by Alan OCallaghan. Last updated 8 months ago.
heatmapplotlyinteractive-visualizationsdata-visualizationhtmlwidgetspeer-reviewed
267 stars 9.08 score 99 scripts 1 dependentsropensci
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.
Maintained by Rory Nolan. Last updated 7 days ago.
image-manipulationimagejpeer-reviewedtiff-filestiff-imagestiff
18 stars 9.03 score 36 scripts 7 dependentsropensci
codemetar:Generate 'CodeMeta' Metadata for R Packages
The 'Codemeta' Project defines a 'JSON-LD' format for describing software metadata, as detailed at <https://codemeta.github.io>. This package provides utilities to generate, parse, and modify 'codemeta.json' files automatically for R packages, as well as tools and examples for working with 'codemeta.json' 'JSON-LD' more generally.
Maintained by Carl Boettiger. Last updated 2 months ago.
metadatacodemetaropenscicitationcreditlinked-datajson-ldpeer-reviewed
68 stars 8.90 score 34 scripts 6 dependentsropensci
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.
Maintained by Sebastian Hanss. Last updated 7 months ago.
agent-based-modelingindividual-based-modellingnetlogopeer-reviewed
78 stars 8.86 score 195 scriptsropensci
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.
Maintained by Paul Bochtler. Last updated 4 months ago.
apicomtradepeer-reviewedsupply-chain
66 stars 8.67 score 70 scriptsropensci
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'.
Maintained by Michal Bojanowski. Last updated 2 years ago.
data-accessoai-pmhpeer-reviewedscholarly-api
15 stars 8.55 score 23 scripts 24 dependentsropensci
phylogram:Dendrograms for Evolutionary Analysis
Contains functions for developing phylogenetic trees as deeply-nested lists ("dendrogram" objects). Enables bi-directional conversion between dendrogram and "phylo" objects (see Paradis et al (2004) <doi:10.1093/bioinformatics/btg412>), and features several tools for command-line tree manipulation and import/export via Newick parenthetic text.
Maintained by Shaun Wilkinson. Last updated 5 years ago.
11 stars 8.53 score 228 scripts 9 dependentsropensci
cyphr:High Level Encryption Wrappers
Encryption wrappers, using low-level support from 'sodium' and 'openssl'. 'cyphr' tries to smooth over some pain points when using encryption within applications and data analysis by wrapping around differences in function names and arguments in different encryption providing packages. It also provides high-level wrappers for input/output functions for seamlessly adding encryption to existing analyses.
Maintained by Rich FitzJohn. Last updated 2 months ago.
encryptionopensslpeer-reviewedsodium
94 stars 8.51 score 36 scripts 2 dependentsropensci
weathercan:Download Weather Data from Environment and Climate Change Canada
Provides means for downloading historical weather data from the Environment and Climate Change Canada website (<https://climate.weather.gc.ca/historical_data/search_historic_data_e.html>). Data can be downloaded from multiple stations and over large date ranges and automatically processed into a single dataset. Tools are also provided to identify stations either by name or proximity to a location.
Maintained by Steffi LaZerte. Last updated 4 days ago.
environment-canadapeer-reviewedweather-dataweather-downloader
106 stars 8.45 score 189 scriptsropensci
opencage:Geocode with the OpenCage API
Geocode with the OpenCage API, either from place name to longitude and latitude (forward geocoding) or from longitude and latitude to the name and address of a location (reverse geocoding), see <https://opencagedata.com>.
Maintained by Daniel Possenriede. Last updated 2 months ago.
geocodegeocoderopencageopencage-apiopencage-geocoderpeer-reviewedplacenamesrspatial
86 stars 8.39 score 79 scriptsropensci
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>.
Maintained by Luigi Ranghetti. Last updated 8 months ago.
gdalmodismodis-datamodis-land-productspeer-reviewedpreprocessingremote-sensingsatellite-imagerytime-series
156 stars 8.04 score 86 scripts 1 dependentsropensci
osmplotr:Bespoke Images of 'OpenStreetMap' Data
Bespoke images of 'OpenStreetMap' ('OSM') data and data visualisation using 'OSM' objects.
Maintained by Mark Padgham. Last updated 1 months ago.
data-visualisationhighlighting-clustersopenstreetmaposmoverpassoverpass-apipeer-reviewed
139 stars 7.97 score 80 scriptsropensci
fingertipsR:Fingertips Data for Public Health
Fingertips (<http://fingertips.phe.org.uk/>) contains data for many indicators of public health in England. The underlying data is now more easily accessible by making use of the API.
Maintained by Annabel Westermann. Last updated 1 years ago.
api-wrapperfingertipshealthopen-datapeer-reviewedpublic-healthpublic-health-england
96 stars 7.89 score 268 scripts 1 dependentsropensci
ezknitr:Avoid the Typical Working Directory Pain When Using 'knitr'
An extension of 'knitr' that adds flexibility in several ways. One common source of frustration with 'knitr' is that it assumes the directory where the source file lives should be the working directory, which is often not true. 'ezknitr' addresses this problem by giving you complete control over where all the inputs and outputs are, and adds several other convenient features to make rendering markdown/HTML documents easier.
Maintained by Dean Attali. Last updated 2 years ago.
knitrpeer-reviewedreproducibilityrmarkdownrmd
115 stars 7.81 score 378 scriptsropensci
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.
Maintained by Marco Sciaini. Last updated 7 months ago.
landscape-ecologyneutral-landscape-modelpeer-reviewedspatialcpp
65 stars 7.74 score 193 scriptsropensci
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/>.
Maintained by Michael Mahoney. Last updated 9 months ago.
datasetsdemsmapmap-tilesmappingnational-mapnhdorthoimagerypeer-reviewedprogressrretrieve-dataterrainrunityunity-rendering-engineusgs
72 stars 7.40 score 87 scriptsropensci
nomisr:Access 'Nomis' UK Labour Market Data
Access UK official statistics from the 'Nomis' database. 'Nomis' includes data from the Census, the Labour Force Survey, DWP benefit statistics and other economic and demographic data from the Office for National Statistics, based around statistical geographies. See <https://www.nomisweb.co.uk/api/v01/help> for full API documentation.
Maintained by Evan Odell. Last updated 7 months ago.
api-clientcensus-datademographygeographic-datanational-statisticsofficial-statisticsofficialstatisticspeer-revieweduk
48 stars 7.34 score 115 scriptsropensci
riem:Accesses Weather Data from the Iowa Environment Mesonet
Allows to get weather data from Automated Surface Observing System (ASOS) stations (airports) in the whole world thanks to the Iowa Environment Mesonet website.
Maintained by Maëlle Salmon. Last updated 1 months ago.
airportsasosiowa-environment-mesonetmetarpeer-reviewedtemperatureweatherweather-api
45 stars 7.30 score 184 scriptsropensci
jstor:Read Data from JSTOR/DfR
Functions and helpers to import metadata, ngrams and full-texts delivered by Data for Research by JSTOR.
Maintained by Thomas Klebel. Last updated 9 months ago.
jstorpeer-reviewedtext-analysistext-mining
47 stars 7.29 score 55 scriptsropensci
roadoi:Find Free Versions of Scholarly Publications via Unpaywall
This web client interfaces Unpaywall <https://unpaywall.org/products/api>, formerly oaDOI, a service finding free full-texts of academic papers by linking DOIs with open access journals and repositories. It provides unified access to various data sources for open access full-text links including Crossref and the Directory of Open Access Journals (DOAJ). API usage is free and no registration is required.
Maintained by Najko Jahn. Last updated 6 months ago.
altmetricscode4liboadoiopen-accesspeer-reviewedunpaywallwebclient
65 stars 7.25 score 69 scriptsropensci
medrxivr:Access and Search MedRxiv and BioRxiv Preprint Data
An increasingly important source of health-related bibliographic content are preprints - preliminary versions of research articles that have yet to undergo peer review. The two preprint repositories most relevant to health-related sciences are medRxiv <https://www.medrxiv.org/> and bioRxiv <https://www.biorxiv.org/>, both of which are operated by the Cold Spring Harbor Laboratory. 'medrxivr' provides programmatic access to the 'Cold Spring Harbour Laboratory (CSHL)' API <https://api.biorxiv.org/>, allowing users to easily download medRxiv and bioRxiv preprint metadata (e.g. title, abstract, publication date, author list, etc) into R. 'medrxivr' also provides functions to search the downloaded preprint records using regular expressions and Boolean logic, as well as helper functions that allow users to export their search results to a .BIB file for easy import to a reference manager and to download the full-text PDFs of preprints matching their search criteria.
Maintained by Yaoxiang Li. Last updated 2 months ago.
bibliographic-databasebiorxivevidence-synthesismedrxiv-datapeer-reviewedpreprint-recordssystematic-reviews
56 stars 7.17 score 44 scriptsropensci
bowerbird:Keep a Collection of Sparkly Data Resources
Tools to get and maintain a data repository from third-party data providers.
Maintained by Ben Raymond. Last updated 18 days ago.
ropensciantarcticsouthern oceandataenvironmentalsatelliteclimatepeer-reviewed
50 stars 7.16 score 16 scripts 1 dependentsropensci
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.
Maintained by Carl Boettiger. Last updated 1 years ago.
archivingdatabasedbipeer-reviewed
79 stars 6.86 score 37 scriptsropensci
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>).
Maintained by Daniel Vartanian. Last updated 3 months ago.
infrastructurepreprocessingvisualizationbiological-rhythmchronobiologychronotypecircadian-phenotypecircadian-rhythmentrainmentmctqpeer-reviewedsleeptemporal-phenotype
12 stars 6.85 score 28 scriptsropensci
getCRUCLdata:'CRU' 'CL' v. 2.0 Climatology Client
Provides functions that automate downloading and importing University of East Anglia Climate Research Unit ('CRU') 'CL' v. 2.0 climatology data, facilitates the calculation of minimum temperature and maximum temperature and formats the data into a data.table object or a list of 'terra' 'rast' objects for use. 'CRU' 'CL' v. 2.0 data are a gridded climatology of 1961-1990 monthly means released in 2002 and cover all land areas (excluding Antarctica) at 10 arc minutes (0.1666667 degree) resolution. For more information see the description of the data provided by the University of East Anglia Climate Research Unit, <https://crudata.uea.ac.uk/cru/data/hrg/tmc/readme.txt>.
Maintained by Adam H. Sparks. Last updated 24 days ago.
anglia-cruclimate-datacru-cl2temperaturerainfallelevationdata-accesswindrelative-humiditysolar-radiationdiurnal-temperaturefrostcrupeer-reviewed
18 stars 6.83 score 18 scriptsropensci
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>.
Maintained by Eryk Walczak. Last updated 2 years ago.
api-wrappergeocodergeographic-datapeer-reviewedpostcodeuk
41 stars 6.49 score 50 scriptsropensci
epubr:Read EPUB File Metadata and Text
Provides functions supporting the reading and parsing of internal e-book content from EPUB files. The 'epubr' package provides functions supporting the reading and parsing of internal e-book content from EPUB files. E-book metadata and text content are parsed separately and joined together in a tidy, nested tibble data frame. E-book formatting is not completely standardized across all literature. It can be challenging to curate parsed e-book content across an arbitrary collection of e-books perfectly and in completely general form, to yield a singular, consistently formatted output. Many EPUB files do not even contain all the same pieces of information in their respective metadata. EPUB file parsing functionality in this package is intended for relatively general application to arbitrary EPUB e-books. However, poorly formatted e-books or e-books with highly uncommon formatting may not work with this package. There may even be cases where an EPUB file has DRM or some other property that makes it impossible to read with 'epubr'. Text is read 'as is' for the most part. The only nominal changes are minor substitutions, for example curly quotes changed to straight quotes. Substantive changes are expected to be performed subsequently by the user as part of their text analysis. Additional text cleaning can be performed at the user's discretion, such as with functions from packages like 'tm' or 'qdap'.
Maintained by Matthew Leonawicz. Last updated 7 months ago.
epubepub-filesepub-formatpeer-reviewed
24 stars 6.37 score 49 scriptsropensci
patentsview:An R Client to the 'PatentsView' API
Provides functions to simplify the 'PatentsView' API (<https://patentsview.org/apis/purpose>) query language, send GET and POST requests to the API's twenty seven endpoints, and parse the data that comes back.
Maintained by Christopher Baker. Last updated 3 months ago.
patentspatentsviewpatentsview-apipeer-revieweduspto
32 stars 6.36 score 89 scriptsropensci
rtika:R Interface to 'Apache Tika'
Extract text or metadata from over a thousand file types, using Apache Tika <https://tika.apache.org/>. Get either plain text or structured XHTML content.
Maintained by Sasha Goodman. Last updated 2 years ago.
extract-metadataextract-textjavaparsepdf-filespeer-reviewedtesseracttika
55 stars 6.00 score 12 scriptsropensci
bikedata:Download and Aggregate Data from Public Hire Bicycle Systems
Download and aggregate data from all public hire bicycle systems which provide open data, currently including 'Santander' Cycles in London, U.K.; from the U.S.A., 'Ford GoBike' in San Francisco CA, 'citibike' in New York City NY, 'Divvy' in Chicago IL, 'Capital Bikeshare' in Washington DC, 'Hubway' in Boston MA, 'Metro' in Los Angeles LA, 'Indego' in Philadelphia PA, and 'Nice Ride' in Minnesota; 'Bixi' from Montreal, Canada; and 'mibici' from Guadalajara, Mexico.
Maintained by Mark Padgham. Last updated 1 years ago.
bicycle-hire-systemsbike-hire-systemsbike-hirebicycle-hiredatabasebike-datapeer-reviewedcpp
81 stars 5.96 score 28 scriptsropensci
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.
Maintained by Shixiang Wang. Last updated 8 months ago.
blastngenbankpeer-reviewedphylogeneticssequence-alignment
23 stars 5.86 score 156 scriptsropensci
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>.
Maintained by Dorothea Hug Peter. Last updated 7 months ago.
data60ukgrdchydrologykgclimateclassmopexpeer-reviewedprecipitationsepa
48 stars 5.56 score 25 scriptsropensci
EndoMineR:Functions to mine endoscopic and associated pathology datasets
This script comprises the functions that are used to clean up endoscopic reports and pathology reports as well as many of the scripts used for analysis. The scripts assume the endoscopy and histopathology data set is merged already but it can also be used of course with the unmerged datasets.
Maintained by Sebastian Zeki. Last updated 7 months ago.
endoscopygastroenterologypeer-reviewedsemi-structured-datatext-mining
13 stars 5.47 score 30 scriptsropensci
DoOR.functions:Integrating Heterogeneous Odorant Response Data into a Common Response Model: A DoOR to the Complete Olfactome
This is a function package providing functions to perform data manipulations and visualizations for DoOR.data. See the URLs for the original and the DoOR 2.0 publication.
Maintained by Daniel Münch. Last updated 1 years ago.
8 stars 5.40 score 52 scriptsropensci
smapr:Acquisition and Processing of NASA Soil Moisture Active-Passive (SMAP) Data
Facilitates programmatic access to NASA Soil Moisture Active Passive (SMAP) data with R. It includes functions to search for, acquire, and extract SMAP data.
Maintained by Maxwell Joseph. Last updated 2 years ago.
acquisitionextract-datanasapeer-reviewedrastersmap-datasoil-mappingsoil-moisturesoil-moisture-sensor
84 stars 4.97 score 22 scriptsropensci
hydroscoper:Interface to the Greek National Data Bank for Hydrometeorological Information
R interface to the Greek National Data Bank for Hydrological and Meteorological Information. It covers Hydroscope's data sources and provides functions to transliterate, translate and download them into tidy dataframes.
Maintained by Konstantinos Vantas. Last updated 8 months ago.
climategreecehydrologyhydrometeorologyhydroscopemeteorological-datameteorological-stationspeer-reviewedtidy-datatime-serieswater-resources
14 stars 4.97 score 33 scriptsropensci
outcomerate:AAPOR Survey Outcome Rates
Standardized survey outcome rate functions, including the response rate, contact rate, cooperation rate, and refusal rate. These outcome rates allow survey researchers to measure the quality of survey data using definitions published by the American Association of Public Opinion Research (AAPOR). For details on these standards, see AAPOR (2016) <https://www.aapor.org/Standards-Ethics/Standard-Definitions-(1).aspx>.
Maintained by Rafael Pilliard Hellwig. Last updated 4 years ago.
aapordisposition-codespeer-reviewedstandardssurvey
5 stars 4.78 score 24 scriptsropensci
rperseus:Get Texts from the Perseus Digital Library
The Perseus Digital Library is a collection of classical texts. This package helps you get them. The available works can also be viewed here: <http://cts.perseids.org/>.
Maintained by David Ranzolin. Last updated 2 years ago.
classicsgreekgreek-biblegreek-new-testamentlatinpeer-reviewedperseusperseus-digital-librarytranslation
20 stars 4.76 score 29 scriptsropensci
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>.
Maintained by Filipe Teixeira. Last updated 7 months ago.
air-transportbtsbureau-of-transport-statisticsdb1bpeer-reviewedritaskynett100transtats
11 stars 4.67 score 43 scriptsropensci
camsRad:Client for CAMS Radiation Service
Copernicus Atmosphere Monitoring Service (CAMS) Radiation Service provides time series of global, direct, and diffuse irradiations on horizontal surface, and direct irradiation on normal plane for the actual weather conditions as well as for clear-sky conditions. The geographical coverage is the field-of-view of the Meteosat satellite, roughly speaking Europe, Africa, Atlantic Ocean, Middle East. The time coverage of data is from 2004-02-01 up to 2 days ago. Data are available with a time step ranging from 15 min to 1 month. For license terms and to create an account, please see <http://www.soda-pro.com/web-services/radiation/cams-radiation-service>.
Maintained by Lukas Lundstrom. Last updated 5 years ago.
9 stars 4.65 score 10 scriptsropensci
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.
Maintained by Elin Waring. Last updated 1 years ago.
20 stars 4.64 score 55 scriptsropensci
DoOR.data:Integrating Heterogeneous Odorant Response Data into a Common Response Model: A DoOR to the Complete Olfactome
This is a data package providing Drosophila odorant response data for DoOR.functions. See URLs for the original and the DoOR 2.0 publications.
Maintained by Daniel Münch. Last updated 3 years ago.
7 stars 4.45 score 135 scripts 1 dependentsropensci
antanym:Antarctic Geographic Place Names
Antarctic geographic names from the Composite Gazetteer of Antarctica, and functions for working with those place names.
Maintained by Ben Raymond. Last updated 3 years ago.
antarcticsouthern oceanplace namesgazetteerpeer-reviewed
7 stars 3.89 score 22 scriptsropensci
suppdata:Downloading Supplementary Data from Published Manuscripts
Downloads data supplementary materials from manuscripts, using papers' DOIs as references. Facilitates open, reproducible research workflows: scientists re-analyzing published datasets can work with them as easily as if they were stored on their own computer, and others can track their analysis workflow painlessly. The main function suppdata() returns a (temporary) location on the user's computer where the file is stored, making it simple to use suppdata() with standard functions like read.csv().
Maintained by William D. Pearse. Last updated 1 years ago.
34 stars 3.83 score 9 scriptsropensci
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.
Maintained by John Deck. Last updated 2 years ago.
3 stars 3.69 score 11 scriptsropensci
cRegulome:Obtain and Visualize Regulome-Gene Expression Correlations in Cancer
Builds a 'SQLite' database file of pre-calculated transcription factor/microRNA-gene correlations (co-expression) in cancer from the Cistrome Cancer Liu et al. (2011) <doi:10.1186/gb-2011-12-8-r83> and 'miRCancerdb' databases (in press). Provides custom classes and functions to query, tidy and plot the correlation data.
Maintained by Mahmoud Ahmed. Last updated 5 years ago.
cancer-genomicsdatabasedatasciencemicrornapeer-reviewedtcga-datatranscription-factors
3 stars 3.69 score 54 scriptsropensci
rrlite: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.".
Maintained by Rich FitzJohn. Last updated 5 months ago.
17 stars 3.23 score 1 scripts