R-universe search: open

bioc

rhdf5:R Interface to HDF5

This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

Maintained by Mike Smith. Last updated 8 days ago.

infrastructure dataimport hdf5 rhdf5 openssl curl zlib cpp

18.9 match 62 stars 15.87 score 4.2k scripts 232 dependents

ropensci

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.

metadata ropensci phylogenetics independant-contrasts biodiversity peer-reviewed phylogeny taxonomy

22.9 match 40 stars 12.05 score 356 scripts 29 dependents

datastorm-open

visNetwork:Network Visualization using 'vis.js' Library

Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.

Maintained by Benoit Thieurmel. Last updated 2 years ago.

15.0 match 550 stars 15.25 score 4.1k scripts 196 dependents

openml

OpenML:Open Machine Learning and Open Data Platform

We provide an R interface to 'OpenML.org' which is an online machine learning platform where researchers can access open data, download and upload data sets, share their machine learning tasks and experiments and organize them online to work and collaborate with other researchers. The R interface allows to query for data sets with specific properties, and allows the downloading and uploading of data sets, tasks, flows and runs. See <https://www.openml.org/guide/api> for more information.

Maintained by Giuseppe Casalicchio. Last updated 10 months ago.

arff benchmarking benchmarking-suite classification data-science database dataset datasets machine-learning machine-learning-algorithms open-data open-science opendata openml openscience regression reproducible-research statistics

20.5 match 97 stars 11.04 score 7.1k scripts

thinkr-open

golem:A Framework for Robust Shiny Applications

An opinionated framework for building a production-ready 'Shiny' application. This package contains a series of tools for building a robust 'Shiny' application from start to finish.

Maintained by Colin Fay. Last updated 7 months ago.

golemverse hacktoberfest shiny shiny-apps shiny-r shinyapps

15.0 match 921 stars 14.21 score 167 scripts 63 dependents

tiledb-inc

tiledb:Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays

The modern database 'TileDB' introduces a powerful on-disk format for storing and accessing any complex data based on multi-dimensional arrays. It supports dense and sparse arrays, dataframes and key-values stores, cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression, encryption and checksum filters, uses a fully multi-threaded implementation, supports parallel I/O, data versioning ('time travel'), metadata and groups. It is implemented as an embeddable cross-platform C++ library with APIs from several languages, and integrations. This package provides the R support.

Maintained by Isaiah Norton. Last updated 5 days ago.

array hdfs s3 storage-manager tiledb cpp

15.0 match 108 stars 11.79 score 306 scripts 4 dependents

bioc

Rsamtools:Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

Maintained by Bioconductor Package Maintainer. Last updated 4 months ago.

dataimport sequencing coverage alignment qualitycontrol bioconductor-package core-package curl bzip2 xz-utils zlib cpp

11.3 match 28 stars 15.34 score 3.2k scripts 569 dependents

datastorm-open

shinymanager:Authentication Management for 'Shiny' Applications

Simple and secure authentification mechanism for single 'Shiny' applications. Credentials can be stored in an encrypted 'SQLite' database or on your own SQL Database (Postgres, MySQL, ...). Source code of main application is protected until authentication is successful.

Maintained by Benoit Thieurmel. Last updated 11 months ago.

shiny shiny-server shinyapps

15.0 match 391 stars 10.51 score 316 scripts 2 dependents

thinkr-open

attachment:Deal with Dependencies

Manage dependencies during package development. This can retrieve all dependencies that are used in ".R" files in the "R/" directory, in ".Rmd" files in "vignettes/" directory and in 'roxygen2' documentation of functions. There is a function to update the "DESCRIPTION" file of your package with 'CRAN' packages or any other remote package. All functions to retrieve dependencies of ".R" scripts and ".Rmd" or ".qmd" files can be used independently of a package development.

Maintained by Vincent Guyader. Last updated 18 days ago.

hacktoberfest

15.0 match 110 stars 10.44 score 48 scripts 5 dependents

spatstat

spatstat.geom:Geometrical Functionality of the 'spatstat' Family

Defines spatial data types and supports geometrical operations on them. Data types include point patterns, windows (domains), pixel images, line segment patterns, tessellations and hyperframes. Capabilities include creation and manipulation of data (using command line or graphical interaction), plotting, geometrical operations (rotation, shift, rescale, affine transformation), convex hull, discretisation and pixellation, Dirichlet tessellation, Delaunay triangulation, pairwise distances, nearest-neighbour distances, distance transform, morphological operations (erosion, dilation, closing, opening), quadrat counting, geometrical measurement, geometrical covariance, colour maps, calculus on spatial domains, Gaussian blur, level sets of images, transects of images, intersections between objects, minimum distance matching. (Excludes spatial data on a network, which are supported by the package 'spatstat.linnet'.)

Maintained by Adrian Baddeley. Last updated 8 days ago.

classes-and-objects distance-calculation geometry geometry-processing images mensuration plotting point-patterns spatial-data spatial-data-analysis

12.5 match 7 stars 12.14 score 241 scripts 229 dependents

dmurdoch

rgl:3D Visualization Using OpenGL

Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.

Maintained by Duncan Murdoch. Last updated 4 days ago.

graphics opengl rgl webgl libglu libglvnd libpng libx11 freetype cpp

8.6 match 91 stars 17.40 score 7.3k scripts 303 dependents

bioc

RCy3:Functions to Access and Control Cytoscape

Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.

Maintained by Alex Pico. Last updated 6 days ago.

visualization graphandnetwork thirdpartyclient network

10.8 match 52 stars 13.47 score 628 scripts 17 dependents

bioc

ORFik:Open Reading Frames in Genomics

R package for analysis of transcript and translation features through manipulation of sequence data and NGS data like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in the sense that any transcript region can be analysed, as the name hints to it was made with investigation of ribosomal patterns over Open Reading Frames (ORFs) as it's primary use case. ORFik is extremely fast through use of C++, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CAGE-Seq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more.

Maintained by Haakon Tjeldnes. Last updated 1 months ago.

immunooncology software sequencing riboseq rnaseq functionalgenomics coverage alignment dataimport cpp

13.6 match 33 stars 10.56 score 115 scripts 2 dependents

thinkr-open

fusen:Build a Package from Rmarkdown Files

Use Rmarkdown First method to build your package. Start your package with documentation, functions, examples and tests in the same unique file. Everything can be set from the Rmarkdown template file provided in your project, then inflated as a package. Inflating the template copies the relevant chunks and sections in the appropriate files required for package development.

Maintained by Vincent Guyader. Last updated 2 months ago.

hacktoberfest rmd-first

15.0 match 163 stars 9.45 score 35 scripts

thinkr-open

gitlabr:Access to the 'GitLab' API

Provides R functions to access the API of the project and repository management web application 'GitLab'. For many common tasks (repository file access, issue assignment and status, commenting) convenience wrappers are provided, and in addition the full API can be used by specifying request locations. 'GitLab' is open-source software and can be self-hosted or used on <https://about.gitlab.com>.

Maintained by Sébastien Rochette. Last updated 11 months ago.

gitlab

16.8 match 40 stars 8.40 score 69 scripts 1 dependents

datastorm-open

suncalc:Compute Sun Position, Sunlight Phases, Moon Position and Lunar Phase

Get sun position, sunlight phases (times for sunrise, sunset, dusk, etc.), moon position and lunar phase for the given location and time. Most calculations are based on the formulas given in Astronomy Answers articles about position of the sun and the planets : <https://www.aa.quae.nl/en/reken/zonpositie.html>.

Maintained by Benoit Thieurmel. Last updated 1 years ago.

15.0 match 44 stars 9.43 score 372 scripts 16 dependents

ropensci

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.

Maintained by Aaron Wolen. Last updated 9 months ago.

open-science osf reproducible-research

13.3 match 145 stars 10.18 score 588 scripts 3 dependents

pharmaverse

admiral:ADaM in R Asset Library

A toolbox for programming Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam>).

Maintained by Ben Straub. Last updated 8 days ago.

cdisc clinical-trials open-source

9.4 match 239 stars 13.97 score 486 scripts 4 dependents

open-eo

openeo:Client Interface for 'openEO' Servers

Access data and processing functionalities of 'openEO' compliant back-ends in R.

Maintained by Florian Lahn. Last updated 2 months ago.

openeo openeo-user

15.0 match 65 stars 8.65 score 128 scripts

thinkr-open

togglr:'Toggl.com' Api for 'Rstudio'

Use the <https://toggl.com> time tracker api through R.

Maintained by Vincent Guyader. Last updated 1 years ago.

hacktoberfest toggl-api toggler

18.5 match 49 stars 6.81 score 33 scripts

open-and-sustainable

prismaid:Open Science AI Tools for Systematic, Protocol-Based Literature Reviews

prismAId uses generative AI models to extract data from scientific literature. It offers simple-to-use, efficient, and replicable methods for analyzing literature when conducting systematic reviews.

Maintained by Riccardo Boero. Last updated 16 days ago.

generative-ai open-science open-source systematic-literature-reviews

32.8 match 5 stars 3.78 score 1 scripts

open-aims

bayesnec:A Bayesian No-Effect- Concentration (NEC) Algorithm

Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECx' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>), 'NSEC' (see Fisher and Fox (2023)<doi:10.1002/etc.5610>), and 'N(S)EC (see Fisher et al. 2023<doi:10.1002/ieam.4809>). A full description of this package can be found in Fisher 'et al.' (2024)<doi:10.18637/jss.v110.i05>. This package expands and supersedes an original version implemented in 'R2jags' (see Su and Yajima (2020)<https://CRAN.R-project.org/package=R2jags>; Fisher et al. (2020)<doi:10.5281/ZENODO.3966864>).

Maintained by Rebecca Fisher. Last updated 8 months ago.

bayesian-inference concentration-response ecotoxicology no-effect-concentration non-linear-decay threshold-derivation toxicology

15.0 match 13 stars 8.15 score 360 scripts

thinkr-open

remedy:'RStudio' Addins to Simplify 'Markdown' Writing

An 'RStudio' addin providing shortcuts for writing in 'Markdown'. This package provides a series of functions that allow the user to be more efficient when using 'Markdown'. For example, you can select a word, and put it in bold or in italics, or change the alignment of elements inside you Rmd. The idea is to map all the functionalities from 'remedy' on keyboard shortcuts, so that it provides an interface close to what you can find in any other text editor.

Maintained by Colin Fay. Last updated 5 years ago.

hacktoberfest

15.0 match 452 stars 7.83 score 50 scripts

datastorm-open

rAmCharts:JavaScript Charts Tool

Provides an R interface for using 'AmCharts' Library. Based on 'htmlwidgets', it provides a global architecture to generate 'JavaScript' source code for charts. Most of classes in the library have their equivalent in R with S4 classes; for those classes, not all properties have been referenced but can easily be added in the constructors. Complex properties (e.g. 'JavaScript' object) can be passed as named list. See examples at <https://datastorm-open.github.io/introduction_ramcharts/> and <https://www.amcharts.com/> for more information about the library. The package includes the free version of 'AmCharts' Library. Its only limitation is a small link to the web site displayed on your charts. If you enjoy this library, do not hesitate to refer to this page <https://www.amcharts.com/online-store/> to purchase a licence, and thus support its creators and get a period of Priority Support. See also <https://www.amcharts.com/about/> for more information about 'AmCharts' company.

Maintained by Benoit Thieurmel. Last updated 3 months ago.

15.5 match 49 stars 7.17 score 153 scripts 4 dependents

ifellows

OpenStreetMap:Access to Open Street Map Raster Images

Accesses high resolution raster maps using the OpenStreetMap protocol. Dozens of road, satellite, and topographic map servers are directly supported, including Apple, Mapnik, Bing, and stamen. Additionally raster maps may be constructed using custom tile servers. Maps can be plotted using either base graphics, or ggplot2. This package is not affiliated with the OpenStreetMap.org mapping project.

Maintained by Ian Fellows. Last updated 1 years ago.

openjdk

13.3 match 11 stars 8.09 score 498 scripts 4 dependents

okgreece

DescriptiveStats.OBeu:Descriptive Statistics 'OpenBudgets.eu'

Estimate and return the needed parameters for visualizations designed for 'OpenBudgets.eu' <http://openbudgets.eu/> datasets. Calculate descriptive statistical measures in budget data of municipalities across Europe, according to the 'OpenBudgets.eu' data model. There are functions for measuring central tendency and dispersion of amount variables along with their distributions and correlations and the frequencies of categorical variables for a given dataset. Also, can be used generally to other datasets, to extract visualization parameters, convert them to 'JSON' format and use them as input in a different graphical interface.

Maintained by Kleanthis Koupidis. Last updated 4 years ago.

boxplot correlation descriptive-statistics estimate frequencies obeu open-budgets openbudgets

19.7 match 1 stars 5.40 score 28 scripts 1 dependents

ropensci

osmextract:Download and Import Open Street Map Data Extracts

Match, download, convert and import Open Street Map data extracts obtained from several providers.

Maintained by Andrea Gilardi. Last updated 2 months ago.

geo geofabrik-zone open-data osm osm-pbf

10.9 match 173 stars 9.73 score 342 scripts

thinkr-open

fcuk:The Ultimate Helper for Clumsy Fingers

Automatically suggests a correction when a typo occurs.

Maintained by Vincent Guyader. Last updated 1 years ago.

error fcuk

15.0 match 92 stars 7.05 score 49 scripts

apache

arrow:Integration to 'Apache' 'Arrow'

'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. This package provides an interface to the 'Arrow C++' library.

Maintained by Jonathan Keane. Last updated 2 months ago.

arrow curl openssl cpp

5.4 match 15k stars 19.25 score 10k scripts 82 dependents

thinkr-open

thinkr:Tools for Cleaning Up Messy Files

Some tools for cleaning up messy 'Excel' files to be suitable for R. People who have been working with 'Excel' for years built more or less complicated sheets with names, characters, formats that are not homogeneous. To be able to use them in R nowadays, we built a set of functions that will avoid the majority of importation problems and keep all the data at best.

Maintained by Vincent Guyader. Last updated 3 years ago.

hacktoberfest thinkr-not-maintained

15.0 match 29 stars 6.96 score 45 scripts

thinkr-open

checkhelper:Deal with Check Outputs

Deal with packages 'check' outputs and reduce the risk of rejection by 'CRAN' by following policies.

Maintained by Sebastien Rochette. Last updated 1 years ago.

15.0 match 34 stars 6.74 score 18 scripts

pythonhealthdatascience

treat.sim:Nelson's Treatment Centre Simulation in Simmer

A discrete-event simulation of a simple urgent care treatment centre simulation from Nelson (2013). Implemented in R Simmer. The model is packaged to allow for easy experimentation, summary of results, and implementation in other software such as a Shiny interface.

Maintained by Thomas Monks. Last updated 8 months ago.

computer-simulation discrete-event-simulation health open-modelling open-science open-source r-language reproducible-research simmer

22.5 match 2 stars 4.48 score 5 scripts

eguidotti

bidask:Efficient Estimation of Bid-Ask Spreads from Open, High, Low, and Close Prices

Implements the efficient estimator of bid-ask spreads from open, high, low, and close prices described in Ardia, Guidotti, & Kroencke (JFE, 2024) <doi:10.1016/j.jfineco.2024.103916>. It also provides an implementation of the estimators described in Roll (JF, 1984) <doi:10.1111/j.1540-6261.1984.tb03897.x>, Corwin & Schultz (JF, 2012) <doi:10.1111/j.1540-6261.2012.01729.x>, and Abdi & Ranaldo (RFS, 2017) <doi:10.1093/rfs/hhx084>.

Maintained by Emanuele Guidotti. Last updated 1 months ago.

finance

14.4 match 109 stars 6.99 score 6 scripts

agrocares

OBIC:Calculate the Open Bodem Index (OBI) Score

The Open Bodem Index (OBI) is a method to evaluate the quality of soils of agricultural fields in The Netherlands and the sustainability of the current agricultural practices. The OBI score is based on four main criteria: chemical, physical, biological and management, which consist of more than 21 indicators. By providing results of a soil analysis and management info the 'OBIC' package can be use to calculate he scores, indicators and derivatives that are used by the OBI. More information about the Open Bodem Index can be found at <https://openbodemindex.nl/>.

Maintained by Sven Verweij. Last updated 7 months ago.

agriculture soil

14.5 match 11 stars 6.82 score 20 scripts

ropensci

EDIutils:An API Client for the Environmental Data Initiative Repository

A client for the Environmental Data Initiative repository REST API. The 'EDI' data repository <https://portal.edirepository.org/nis/home.jsp> is for publication and reuse of ecological data with emphasis on metadata accuracy and completeness. It is built upon the 'PASTA+' software stack <https://pastaplus-core.readthedocs.io/en/latest/index.html#> and was developed in collaboration with the US 'LTER' Network <https://lternet.edu/>. 'EDIutils' includes functions to search and access existing data, evaluate and upload new data, and assist other data management tasks common to repository users.

Maintained by Colin Smith. Last updated 1 years ago.

ecology eml-metadata open-access open-data research-data-management research-data-repository

15.0 match 10 stars 6.47 score 117 scripts

thinkr-open

shinipsum:Lorem-Ipsum-like Helpers for fast Shiny Prototyping

Prototype your shiny apps quickly with these Lorem-Ipsum-like Helpers.

Maintained by Colin Fay. Last updated 1 years ago.

dygraph ggplot golemverse hacktoberfest lorem-ipsum

15.0 match 125 stars 6.45 score 50 scripts 1 dependents

ethanbass

chromConverter:Chromatographic File Converter

Reads chromatograms from binary formats into R objects. Currently supports conversion of 'Agilent ChemStation', 'Agilent MassHunter', 'Shimadzu LabSolutions', 'ThermoRaw', and 'Varian Workstation' files as well as various text-based formats. In addition to its internal parsers, chromConverter contains bindings to parsers in external libraries, such as 'Aston' <https://github.com/bovee/aston>, 'Entab' <https://github.com/bovee/entab>, 'rainbow' <https://rainbow-api.readthedocs.io/>, and 'ThermoRawFileParser' <https://github.com/compomics/ThermoRawFileParser>.

Maintained by Ethan Bass. Last updated 2 days ago.

cheminformatics chromatography fair-data gc-fid hplc hplc-dad hplc-uv metabolomics metabolomics-data open-data open-science

15.0 match 34 stars 6.44 score 16 scripts 2 dependents

murrayefford

openCR:Open Population Capture-Recapture

Non-spatial and spatial open-population capture-recapture analysis.

Maintained by Murray Efford. Last updated 5 months ago.

cpp

16.0 match 4 stars 5.98 score 53 scripts

tpisel

openmeteo:Retrieve Weather Data from the Open-Meteo API

A client for the Open-Meteo API that retrieves Open-Meteo weather data in a tidy format. No API key is required. The API specification is located at <https://open-meteo.com/en/docs>.

Maintained by Tom Pisel. Last updated 1 years ago.

19.4 match 20 stars 4.93 score 86 scripts

ethanbass

chromatographR:Chromatographic Data Analysis Toolset

Tools for high-throughput analysis of HPLC-DAD/UV chromatograms (or similar data). Includes functions for preprocessing, alignment, peak-finding and fitting, peak-table construction, data-visualization, etc. Preprocessing and peak-table construction follow the rough formula laid out in 'alsace' (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C., 2015. <doi:10.1093/bioinformatics/btv299>. Alignment of chromatograms is available using parametric time warping (as implemented in the 'ptw' package) (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C. 2015. <doi:10.1093/bioinformatics/btv299>) or variable penalty dynamic time warping (as implemented in 'VPdtw') (Clifford, D., & Stone, G. 2012. <doi:10.18637/jss.v047.i08>). Peak-finding uses the algorithm by Tom O'Haver <https://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm>. Peaks are then fitted to a gaussian or exponential-gaussian hybrid peak shape using non-linear least squares (Lan, K. & Jorgenson, J. W. 2001. <doi:10.1016/S0021-9673(01)00594-5>). See the vignette for more details and suggested workflow.

Maintained by Ethan Bass. Last updated 16 days ago.

bioinformatics cheminformatics chromatography gc-fid hplc hplc-dad hplc-pda hplv-uv metabolomics open-data open-science reproducibility reproducible-research

15.0 match 18 stars 6.36 score 8 scripts 1 dependents

epiforecasts

EpiNow2:Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters

Estimates the time-varying reproduction number, rate of spread, and doubling time using a range of open-source tools (Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>), and current best practices (Gostic et al. (2020) <doi:10.1101/2020.06.18.20134858>). It aims to help users avoid some of the limitations of naive implementations in a framework that is informed by community feedback and is actively supported.

Maintained by Sebastian Funk. Last updated 1 months ago.

backcalculation covid-19 gaussian-processes open-source reproduction-number stan cpp

8.0 match 123 stars 11.86 score 210 scripts

rostools

prodigenr:Research Project Directory Generator

Create a project directory structure, along with typical files for that project. This allows projects to be quickly and easily created, as well as for them to be standardized. Designed specifically with scientists in mind (mainly bio-medical researchers, but likely applies to other fields).

Maintained by Luke Johnston. Last updated 4 months ago.

devtools open-science open-source project-management reproducibility reproducible-research reproducible-science rstudio usethis

15.0 match 43 stars 6.33 score 25 scripts

thinkr-open

fakir:Generate Fake Datasets for Prototyping and Teaching

Create fake datasets that can be used for prototyping and teaching. This package provides a set of functions to generate fake data for a variety of data types, such as dates, addresses, and names. It can be used for prototyping (notably in 'shiny') or as a tool to teach data manipulation and data visualization.

Maintained by Colin Fay. Last updated 7 months ago.

charlatan fake-datasets golemverse hacktoberfest

15.0 match 133 stars 6.24 score 26 scripts

thinkr-open

gitdown:Turn Your Git Commit Messages into a HTML Book

Read all commit messages of your local git repository and sort them according to tags or specific text pattern into chapters of a HTML book using 'bookdown'. The git history book presentation helps organisms required to testify for every changes in their source code, in relation to features requests.

Maintained by Sébastien Rochette. Last updated 1 years ago.

bookdown git gitbook

15.0 match 34 stars 6.01 score 15 scripts

ajwills72

catlearn:Formal Psychological Models of Categorization and Learning

Formal psychological models of categorization and learning, independently-replicated data sets against which to test them, and simulation archives.

Maintained by Andy Wills. Last updated 2 days ago.

categorization cognitive-science formal-models learning learning-theory open-models open-science psychology openblas cpp

15.0 match 26 stars 5.86 score 46 scripts

ropensci

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.

altmetrics code4lib oadoi open-access peer-reviewed unpaywall webclient

11.9 match 65 stars 7.25 score 69 scripts

ironholds

olctools:Open Location Code Handling in R

'Open Location Codes' (https://openlocationcode.com/) are a Google- created standard for identifying geographic locations. olctools provides utilities for validating, encoding and decoding entries that follow this standard.

Maintained by Oliver Keyes. Last updated 9 years ago.

cpp

16.6 match 13 stars 5.16 score 11 scripts

r-dbi

DBI:R Database Interface

A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.

Maintained by Kirill Müller. Last updated 15 days ago.

database interface

4.1 match 302 stars 20.87 score 19k scripts 2.9k dependents

shikokuchuo

nanonext:NNG (Nanomsg Next Gen) Lightweight Messaging Library

R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is a socket library for reliable, high-performance messaging over in-process, IPC, TCP, WebSocket and secure TLS transports. Implements 'Scalability Protocols', a standard for common communications patterns including publish/subscribe, request/reply and service discovery. As its own threaded concurrency framework, provides a toolkit for asynchronous programming and distributed computing. Intuitive 'aio' objects resolve automatically when asynchronous operations complete, and synchronisation primitives allow R to wait upon events signalled by concurrent threads.

Maintained by Charlie Gao. Last updated 7 hours ago.

concurrency https ipc-message messaging-library nng rpc socket-communication synchronization-primitives tcp-protocol websocket mbedtls

8.6 match 60 stars 9.78 score 28 scripts 9 dependents

truecluster

ff:Memory-Efficient Storage of Large Data on Disk and Fast Access Functions

The ff package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section (pagesize) in main memory - the effective virtual memory consumption per ff object. ff supports R's standard atomic data types 'double', 'logical', 'raw' and 'integer' and non-standard atomic types boolean (1 bit), quad (2 bit unsigned), nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned), single (4 byte float with NAs). For example 'quad' allows efficient storage of genomic data as an 'A','T','G','C' factor. The unsigned types support 'circular' arithmetic. There is also support for close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and custom close-to-atomic types. ff not only has native C-support for vectors, matrices and arrays with flexible dimorder (major column-order, major row-order and generalizations for arrays). There is also a ffdf class not unlike data.frames and import/export filters for csv files. ff objects store raw data in binary flat files in native encoding, and complement this with metadata stored in R as physical and virtual attributes. ff objects have well-defined hybrid copying semantics, which gives rise to certain performance improvements through virtualization. ff objects can be stored and reopened across R sessions. ff files can be shared by multiple ff R objects (using different data en/de-coding schemes) in the same process or from multiple R processes to exploit parallelism. A wide choice of finalizer options allows to work with 'permanent' files as well as creating/removing 'temporary' ff files completely transparent to the user. On certain OS/Filesystem combinations, creating the ff files works without notable delay thanks to using sparse file allocation. Several access optimization techniques such as Hybrid Index Preprocessing and Virtualization are implemented to achieve good performance even with large datasets, for example virtual matrix transpose without touching a single byte on disk. Further, to reduce disk I/O, 'logicals' and non-standard data types get stored native and compact on binary flat files i.e. logicals take up exactly 2 bits to represent TRUE, FALSE and NA. Beyond basic access functions, the ff package also provides compatibility functions that facilitate writing code for ff and ram objects and support for batch processing on ff objects (e.g. as.ram, as.ff, ffapply). ff interfaces closely with functionality from package 'bit': chunked looping, fast bit operations and coercions between different objects that can store subscript information ('bit', 'bitwhich', ff 'boolean', ri range index, hi hybrid index). This allows to work interactively with selections of large datasets and quickly modify selection criteria. Further high-performance enhancements can be made available upon request.

Maintained by Jens Oehlschlägel. Last updated 3 months ago.

cpp

7.0 match 27 stars 12.01 score 764 scripts 71 dependents

thinkr-open

lightparser:From 'Rmarkdown' and 'Quarto' Files to Tibble and Back

Split your 'rmarkdown' or 'quarto' files by sections into a tibble: titles, text, chunks. Rebuild the file from the tibble.

Maintained by Sebastien Rochette. Last updated 11 months ago.

15.0 match 24 stars 5.56 score 9 scripts 1 dependents

alexchristensen

SemNeT:Methods and Measures for Semantic Network Analysis

Implements several functions for the analysis of semantic networks including different network estimation algorithms, partial node bootstrapping (Kenett, Anaki, & Faust, 2014 <doi:10.3389/fnhum.2014.00407>), random walk simulation (Kenett & Austerweil, 2016 <http://alab.psych.wisc.edu/papers/files/Kenett16CreativityRW.pdf>), and a function to compute global network measures. Significance tests and plotting features are also implemented.

Maintained by Alexander P. Christensen. Last updated 2 years ago.

semantic-network-analysis

18.3 match 23 stars 4.51 score 28 scripts

statistikat

STATcubeR:R Interface for the 'STATcube' REST API and Open Government Data

Import data from the 'STATcube' REST API or from the open data portal of Statistics Austria. This package includes a client for API requests as well as parsing utilities for data which originates from 'STATcube'. Documentation about 'STATcubeR' is provided by several vignettes included in the package as well as on the public 'pkgdown' page at <https://statistikat.github.io/STATcubeR/>.

Maintained by Bernhard Meindl. Last updated 4 months ago.

api database ogd open-data sdmx

16.3 match 18 stars 5.03 score 9 scripts

thinkr-open

lozen:Management tools for missions

Management tools for missions (internal and external). Includes weekly, GL projects, etc.

Maintained by Sébastien Rochette. Last updated 12 months ago.

experimental

15.0 match 7 stars 5.42 score 14 scripts

thinkr-open

rtodoist:Create and Manage Todolist using 'Todoist.com' API

Allows you to interact with the API of the "Todoist" platform. 'Todoist' <https://todoist.com/> provides an online task manager service for teams.

Maintained by Cervan Girard. Last updated 2 years ago.

17.0 match 12 stars 4.78 score 7 scripts

r-lum

Luminescence:Comprehensive Luminescence Dating Data Analysis

A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.

Maintained by Sebastian Kreutzer. Last updated 13 hours ago.

bayesian-statistics data-science geochronology luminescence luminescence-dating open-science osl plotting radiofluorescence tl xsyg cpp

7.5 match 16 stars 10.67 score 178 scripts 8 dependents

cjvanlissa

worcs:Workflow for Open Reproducible Code in Science

Create reproducible and transparent research projects in 'R'. This package is based on the Workflow for Open Reproducible Code in Science (WORCS), a step-by-step procedure based on best practices for Open Science. It includes an 'RStudio' project template, several convenience functions, and all dependencies required to make your project reproducible and transparent. WORCS is explained in the tutorial paper by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2021). <doi:10.3233/DS-210031>.

Maintained by Caspar J. Van Lissa. Last updated 4 days ago.

8.2 match 83 stars 9.77 score 59 scripts 1 dependents

thinkr-open

papillon:Build And Highlight Package Documentation With Customized Templates

Helps creating company visual identity. Build your templates for your package vignettes, reports with {bookdown}, package presentation with {pkgdown}. Highlight your documentation in your projects. Allow for code folding.

Maintained by Sébastien Rochette. Last updated 2 years ago.

18.4 match 11 stars 4.34 score 4 scripts

cderv

pandoc:Manage and Run Universal Converter 'Pandoc' from 'R'

Provides a set of tools to install, manage and run several 'Pandoc' versions.

Maintained by Christophe Dervieux. Last updated 1 years ago.

11.0 match 27 stars 7.17 score 194 scripts 3 dependents

sharlagelfand

opendatatoronto:Access the City of Toronto Open Data Portal

Access data from the "City of Toronto Open Data Portal" (<https://open.toronto.ca>) directly from R.

Maintained by Sharla Gelfand. Last updated 3 years ago.

10.3 match 63 stars 7.49 score 486 scripts

dslc-io

tidytuesdayR:Access the Weekly 'TidyTuesday' Project Dataset

'TidyTuesday' is a project by the 'Data Science Learning Community' in which they post a weekly dataset in a public data repository (<https://github.com/rfordatascience/tidytuesday>) for people to analyze and visualize. This package provides the tools to easily download this data and the description of the source.

Maintained by Jon Harmon. Last updated 7 days ago.

7.6 match 77 stars 10.13 score 3.0k scripts

oliverehmer

act:Aligned Corpus Toolkit

The Aligned Corpus Toolkit (act) is designed for linguists that work with time aligned transcription data. It offers functions to import and export various annotation file formats ('ELAN' .eaf, 'EXMARaLDA .exb and 'Praat' .TextGrid files), create print transcripts in the style of conversation analysis, search transcripts (span searches across multiple annotations, search in normalized annotations, make concordances etc.), export and re-import search results (.csv and 'Excel' .xlsx format), create cuts for the search results (print transcripts, audio/video cuts using 'FFmpeg' and video sub titles in 'Subrib title' .srt format), modify the data in a corpus (search/replace, delete, filter etc.), interact with 'Praat' using 'Praat'-scripts, and exchange data with the 'rPraat' package. The package is itself written in R and may be expanded by other users.

Maintained by Oliver Ehmer. Last updated 2 years ago.

11.5 match 4 stars 6.65 score 184 scripts

gshs-ornl

wbstats:Programmatic Access to Data and Statistics from the World Bank API

Search and download data from the World Bank Data API.

Maintained by Jesse Piburn. Last updated 4 years ago.

open-data world-bank world-bank-api worldbank

7.5 match 126 stars 10.07 score 1.1k scripts 3 dependents

petrbouchal

statnipokladna:Use Data from the Czech Public Finance Database

Get programmatic access to data from the Czech public budgeting and accounting database, Státní pokladna <https://monitor.statnipokladna.cz/>.

Maintained by Petr Bouchal. Last updated 7 months ago.

budgeting cities czech-republic government open-data public-finance

11.8 match 7 stars 6.40 score 48 scripts

mountainmath

VancouvR:Access the 'City of Vancouver' Open Data API

Wrapper around the 'City of Vancouver' Open Data API <https://opendata.vancouver.ca/api/v2/console> to simplify and standardize access to 'City of Vancouver' open data. Functionality to list the data catalogue and access data and geographic records.

Maintained by Jens von Bergmann. Last updated 10 months ago.

12.5 match 19 stars 5.98 score 25 scripts

ropensci

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.

Maintained by Matthew Hoff. Last updated 9 months ago.

eia eia-api energy-data energy-information-administration open-data

10.3 match 47 stars 7.30 score 35 scripts

ajrgodfrey

BrailleR:Improved Access for Blind Users

Blind users do not have access to the graphical output from R without printing the content of graphics windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R. This includes the text descriptions of graphs, convenience functions to replace the functionality offered in many GUI front ends, and experimental functionality for optimising graphical content to prepare it for embossing as tactile images.

Maintained by A. Jonathan R. Godfrey. Last updated 12 months ago.

8.3 match 123 stars 8.90 score 143 scripts

thinkr-open

devindocker:Help Develop a R Project Inside a Docker Container

Help develop a R project inside a Docker container.

Maintained by Sébastien Rochette. Last updated 4 years ago.

thinkr-not-maintained

15.0 match 38 stars 4.88 score 7 scripts

hrecht

censusapi:Retrieve Data from the Census APIs

A wrapper for the U.S. Census Bureau APIs that returns data frames of Census data and metadata. Available datasets include the Decennial Census, American Community Survey, Small Area Health Insurance Estimates, Small Area Income and Poverty Estimates, Population Estimates and Projections, and more.

Maintained by Hannah Recht. Last updated 27 days ago.

census census-api census-data demographics open-data

7.5 match 174 stars 9.76 score 708 scripts 6 dependents

rstudio

rstudioapi:Safely Access the RStudio API

Access the RStudio API (if available) and provide informative error messages when it's not.

Maintained by Kevin Ushey. Last updated 5 months ago.

3.9 match 172 stars 18.81 score 3.6k scripts 2.1k dependents

ropensci

tradestatistics:Open Trade Statistics API Wrapper and Utility Program

Access 'Open Trade Statistics' API from R to download international trade data.

Maintained by Mauricio Vargas. Last updated 7 months ago.

api-wrapper data-table international-trade jsonlite open-trade-statistics

10.1 match 77 stars 7.15 score 92 scripts

wincowgerdev

OpenSpecy:Analyze, Process, Identify, and Share Raman and (FT)IR Spectra

Raman and (FT)IR spectral analysis tool for plastic particles and other environmental samples (Cowger et al. 2021, <doi:10.1021/acs.analchem.1c00123>). With read_any(), Open Specy provides a single function for reading individual, batch, or map spectral data files like .asp, .csv, .jdx, .spc, .spa, .0, and .zip. process_spec() simplifies processing spectra, including smoothing, baseline correction, range restriction and flattening, intensity conversions, wavenumber alignment, and min-max normalization. Spectra can be identified in batch using an onboard reference library (Cowger et al. 2020, <doi:10.1177/0003702820929064>) using match_spec(). A Shiny app is available via run_app() or online at <https://openanalysis.org/openspecy/>.

Maintained by Win Cowger. Last updated 1 months ago.

9.3 match 29 stars 7.55 score 22 scripts

syncrosim

rsyncrosim:The R Interface to 'SyncroSim'

'SyncroSim' is a generalized framework for managing scenario-based datasets (<https://syncrosim.com/>). 'rsyncrosim' provides an interface to 'SyncroSim'. Simulation models can be added to 'SyncroSim' in order to transform these datasets, taking advantage of general features such as defining scenarios of model inputs, running Monte Carlo simulations, and summarizing model outputs. 'rsyncrosim' requires 'SyncroSim' 2.3.5 or higher (API documentation: <https://docs.syncrosim.com/>).

Maintained by Katie Birchard. Last updated 25 days ago.

9.8 match 9 stars 7.09 score 189 scripts

alexchristensen

SemNetCleaner:An Automated Cleaning Tool for Semantic and Linguistic Data

Implements several functions that automates the cleaning and spell-checking of text data. Also converges, finalizes, removes plurals and continuous strings, and puts text data in binary format for semantic network analysis. Uses the 'SemNetDictionaries' package to make the cleaning process more accurate, efficient, and reproducible.

Maintained by Alexander P. Christensen. Last updated 3 years ago.

preprocessing semantic-network-analysis

11.0 match 10 stars 6.16 score 48 scripts 1 dependents

thinkr-open

tutor:Deploy shiny_prerendered Rmds

Deploy Rmd using shiny_prerendered.

Maintained by vincent guyader. Last updated 10 months ago.

15.0 match 4 stars 4.51 score 102 scripts

openjusticeok

ojodb:Analyze Data from the Open Justice Oklahoma Database

{ojodb} provides convenient functions to query court data from the Open Justice Oklahoma database.

Maintained by Brancen Gregory. Last updated 7 days ago.

courts justice oklahoma open-data

11.0 match 8 stars 6.12 score 69 scripts

cran

queueing:Analysis of Queueing Networks and Models

It provides versatile tools for analysis of birth and death based Markovian Queueing Models and Single and Multiclass Product-Form Queueing Networks. It implements M/M/1, M/M/c, M/M/Infinite, M/M/1/K, M/M/c/K, M/M/c/c, M/M/1/K/K, M/M/c/K/K, M/M/c/K/m, M/M/Infinite/K/K, Multiple Channel Open Jackson Networks, Multiple Channel Closed Jackson Networks, Single Channel Multiple Class Open Networks, Single Channel Multiple Class Closed Networks and Single Channel Multiple Class Mixed Networks. Also it provides a B-Erlang, C-Erlang and Engset calculators. This work is dedicated to the memory of D. Sixto Rios Insua.

Maintained by Pedro Canadilla. Last updated 5 years ago.

62.9 match 1.06 score

biodiverse

unmarked:Models for Data from Unmarked Animals

Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.

Maintained by Ken Kellner. Last updated 13 days ago.

openblas cpp openmp

5.1 match 4 stars 13.02 score 652 scripts 12 dependents

petrbouchal

czso:Use Open Data from the Czech Statistical Office in R

Get programmatic access to the open data provided by the Czech Statistical Office (CZSO, <https://czso.cz>).

Maintained by Petr Bouchal. Last updated 7 months ago.

czech-republic czech-statistical-office czso dataset open-data statistics

12.7 match 11 stars 5.24 score 53 scripts

henrikbengtsson

R.devices:Unified Handling of Graphics Devices

Functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as scales and aspect ratios are controlled in a uniform way across all device types. Switching output format requires minimal changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts.

Maintained by Henrik Bengtsson. Last updated 1 years ago.

graphics

9.5 match 18 stars 6.90 score 67 scripts 13 dependents

chicago

RSocrata:Download or Upload 'Socrata' Data Sets

Provides easier interaction with 'Socrata' open data portals <https://dev.socrata.com>. Users can provide a 'Socrata' data set resource URL, or a 'Socrata' Open Data API (SODA) web query, or a 'Socrata' "human-friendly" URL, returns an R data frame. Converts dates to 'POSIX' format and manages throttling by 'Socrata'. Users can upload data to 'Socrata' portals directly from R.

Maintained by "Gene Leynes". Last updated 2 years ago.

chicago government open-data socrata soda

8.3 match 237 stars 7.88 score 864 scripts

opencasestudies

OCSdata:Download Data from the 'Open Case Studies' Repository

Provides functions to access and download data from the 'Open Case Studies' <https://www.opencasestudies.org/> repositories on 'GitHub' <https://github.com/opencasestudies>. Different functions enable users to grab the data they need at different sections in the case study, as well as download the whole case study repository. All the user needs to do is input the name of the case study being worked on. The package relies on the httr::GET() function to access files through the 'GitHub' API. The functions usethis::use_zip() and usethis::create_from_github() are used to clone and/or download the case study repositories. See <https://github.com/opencasestudies/OCSdata/blob/master/README.md> for instructions and examples. To cite an individual case study, please see the 'README' file in the respective case study repository: <https://github.com/opencasestudies/ocs-bp-rural-and-urban-obesity> <https://github.com/opencasestudies/ocs-bp-air-pollution> <https://github.com/opencasestudies/ocs-bp-vaping-case-study> <https://github.com/opencasestudies/ocs-bp-opioid-rural-urban> <https://github.com/opencasestudies/ocs-bp-RTC-wrangling> <https://github.com/opencasestudies/ocs-bp-RTC-analysis> <https://github.com/opencasestudies/ocs-bp-youth-disconnection> <https://github.com/opencasestudies/ocs-bp-youth-mental-health> <https://github.com/opencasestudies/ocs-bp-school-shootings-dashboard> <https://github.com/opencasestudies/ocs-bp-co2-emissions> <https://github.com/opencasestudies/ocs-bp-diet>.

Maintained by Carrie Wright. Last updated 9 months ago.

data-science public-health

15.5 match 1 stars 4.20 score 32 scripts

thinkr-open

arpr:Advanced R Pipes

Provides convenience functions for programming with 'magrittr' pipes. Conditional pipes, a string prefixer and a function to pipe the given object into a specific argument given by character name are currently supported. It is named after the dadaist Hans Arp, a friend of Rene Magritte.

Maintained by Sébastien Rochette. Last updated 4 years ago.

15.0 match 7 stars 4.32 score 5 scripts 2 dependents

ropensci

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

Client for 'CKAN' API (<https://ckan.org/>). Includes interface to 'CKAN' 'APIs' for search, list, show for packages, organizations, and resources. In addition, provides an interface to the 'datastore' API.

Maintained by Francisco Alves. Last updated 2 years ago.

database open-data ckan api data dataset api-wrapper ckan-api

7.5 match 98 stars 8.60 score 448 scripts 4 dependents

alexchristensen

NetworkToolbox:Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis

Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershgoren, Mantegna, & Ben-Jacob, 2010 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteristics (e.g., clustering coefficient), and various other measures associated with the reliability and reproducibility of network analysis.

Maintained by Alexander Christensen. Last updated 2 years ago.

network-analysis

9.1 match 23 stars 7.04 score 101 scripts 4 dependents

opendataformat

opendataformat:Reading and Writing Open Data Format Files

The Open Data Format (ODF) is a new, non-proprietary, multilingual, metadata enriched, and zip-compressed data format with metadata structured in the Data Documentation Initiative (DDI) Codebook standard. This package allows reading and writing of data files in the Open Data Format (ODF) in R, and displaying metadata in different languages. For further information on the Open Data Format, see <https://opendataformat.github.io/>.

Maintained by Tom Hartl. Last updated 23 days ago.

11.7 match 5.41 score 7 scripts

troyhill

NitrogenUptake2016:Data and Source Code From: Nitrogen Uptake and Allocation Estimates for Spartina Alterniflora and Distichlis Spicata

Contains data, code, and figures from Hill et al. 2018a (Journal of Experimental Marine Biology and Ecology; <DOI: 10.1016/j.jembe.2018.07.006>) and Hill et al. 2018b (Data In Brief <DOI: 10.1016/j.dib.2018.09.133>). Datasets document plant allometry, stem heights, nutrient and stable isotope content, and sediment denitrification enzyme assays. The data and analysis offer an examination of nitrogen uptake and allocation in two salt marsh plant species.

Maintained by Troy D. Hill. Last updated 6 years ago.

nitrogen open-data open-science salt-marsh

15.0 match 1 stars 4.15 score 14 scripts

kadyb

rgugik:Search and Retrieve Spatial Data from 'GUGiK'

Automatic open data acquisition from resources of Polish Head Office of Geodesy and Cartography ('Główny Urząd Geodezji i Kartografii') (<https://www.gov.pl/web/gugik>). Available datasets include various types of numeric, raster and vector data, such as orthophotomaps, digital elevation models (digital terrain models, digital surface model, point clouds), state register of borders, spatial databases, geometries of cadastral parcels, 3D models of buildings, and more. It is also possible to geocode addresses or objects using the geocodePL_get() function.

Maintained by Krzysztof Dyba. Last updated 24 days ago.

cartography geodesy gis open-data poland

8.0 match 34 stars 7.69 score 30 scripts

petzi53

repairData:Open Repair Alliance Datasets 2021

The complete data set of open repair data, full compliant with the Open Repair Data Standards (ORDS). It combines the datasets contributed by partner organizations of the Open Repair Alliance (ORA). Last updated: 2021-02-22. The package also contains via quests enriched datasets on batteries, printers, mobiles, and tablets.

Maintained by Peter Baumgartner. Last updated 3 years ago.

data open-data open-datasets repair repair-cafe repairs

22.5 match 2.70 score 1 scripts

ropensci

beautier:'BEAUti' from R

'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAUti 2' (which is part of 'BEAST2') is a GUI tool that allows users to specify the many possible setups and generates the XML file 'BEAST2' needs to run. This package provides a way to create 'BEAST2' input files without active user input, but using R function calls instead.

Maintained by Richèl J.C. Bilderbeek. Last updated 1 months ago.

bayesian beast beast2 beauti phylogenetic-inference phylogenetics

6.9 match 13 stars 8.76 score 198 scripts 5 dependents

ropensci

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-wrapper fingertips health open-data peer-reviewed public-health public-health-england

7.5 match 96 stars 7.89 score 268 scripts 1 dependents

thinkr-open

rusk:Beautiful Graphical Representation of Multiplication Tables on a Modular Circle

By placing on a circle 10 points numbered from 1 to 10, and connecting them by a straight line to the point corresponding to its multiplication by 2. (1 must be connected to 1 * 2 = 2, point 2 must be set to 2 * 2 = 4, point 3 to 3 * 2 = 6 and so on). You will obtain an amazing geometric figure that complicates and beautifies itself by varying the number of points and the multiplication table you use.

Maintained by Vincent Guyader. Last updated 6 years ago.

thinkr-not-maintained

17.0 match 6 stars 3.48 score 9 scripts

elipousson

mapbaltimore:Make maps for Baltimore City with open data

This package provides data from the Baltimore City, the state of Maryland, and other sources, functions to access additional data, and function to create and modify simple maps of Baltimore neighborhoods using sf and ggplot2.

Maintained by Eli Pousson. Last updated 4 months ago.

baltimore rspatial

15.1 match 18 stars 3.88 score 14 scripts

joachim-gassen

ExPanDaR:Explore Your Data Interactively

Provides a shiny-based front end (the 'ExPanD' app) and a set of functions for exploratory data analysis. Run as a web-based app, 'ExPanD' enables users to assess the robustness of empirical evidence without providing them access to the underlying data. You can export a notebook containing the analysis of 'ExPanD' and/or use the functions of the package to support your exploratory data analysis workflow. Refer to the vignettes of the package for more information on how to use 'ExPanD' and/or the functions of this package.

Maintained by Joachim Gassen. Last updated 4 years ago.

accounting eda exploratory-data-analysis finance open-science replication shiny shiny-apps

7.5 match 156 stars 7.80 score 203 scripts

bioc

Biobase:Biobase: Base functions for Bioconductor

Functions that are needed by many other packages or which replace R functions.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

infrastructure bioconductor-package core-package

3.5 match 9 stars 16.46 score 6.6k scripts 1.8k dependents

r-lib

ps:List, Query, Manipulate System Processes

List, query and manipulate all system processes, on 'Windows', 'Linux' and 'macOS'.

Maintained by Gábor Csárdi. Last updated 1 months ago.

3.9 match 80 stars 15.07 score 108 scripts 1.5k dependents

thinkr-open

inca3:Donnees De L'Etude INCA 3

Données de consommations et habitudes alimentaires de l'étude INCA 3. Carine Dubuisson, Ariane Dufour, Sandrine Carrillo, Peggy Drouillet-Pinard, Sabrina Havard, Jean-Luc Volatier (2019). The Third French Individual and National Food Consumption (INCA3) Survey 2014-2015: method, design and participation rate in the framework of a European harmonization process. Public Health Nutrition: 22(4), 584–600. (doi:10.1017/S1368980018002896).

Maintained by Vincent Guyader. Last updated 3 years ago.

hacktoberfest thinkr-not-maintained

15.0 match 5 stars 3.88 score 4 scripts

ropensci

ruODK:An R Client for the ODK Central API

Access and tidy up data from the 'ODK Central' API. 'ODK Central' is a clearinghouse for digitally captured data using ODK <https://docs.getodk.org/central-intro/>. It manages user accounts and permissions, stores form definitions, and allows data collection clients like 'ODK Collect' to connect to it for form download and submission upload. The 'ODK Central' API is documented at <https://docs.getodk.org/central-api/>.

Maintained by Florian W. Mayer. Last updated 5 months ago.

database open-data odk api data dataset odata odata-client odk-central opendatakit

7.5 match 42 stars 7.73 score 57 scripts 1 dependents

opengeos

whitebox:'WhiteboxTools' R Frontend

An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. Suggested citation: Lindsay (2016) <doi:10.1016/j.cageo.2016.07.003>.

Maintained by Andrew Brown. Last updated 6 months ago.

geomorphometry geoprocessing geospatial gis hydrology remote-sensing rstudio

6.0 match 173 stars 9.65 score 203 scripts 2 dependents

momx

Momocs:Morphometrics using R

The goal of 'Momocs' is to provide a complete, convenient, reproducible and open-source toolkit for 2D morphometrics. It includes most common 2D morphometrics approaches on outlines, open outlines, configurations of landmarks, traditional morphometrics, and facilities for data preparation, manipulation and visualization with a consistent grammar throughout. It allows reproducible, complex morphometrics analyses and other morphometrics approaches should be easy to plug in, or develop from, on top of this canvas.

Maintained by Vincent Bonhomme. Last updated 1 years ago.

morphometrics

7.7 match 51 stars 7.42 score 346 scripts

mpjashby

crimedata:Access Crime Data from the Open Crime Database

Gives convenient access to publicly available police-recorded open crime data from large cities in the United States that are included in the Crime Open Database <https://osf.io/zyaqn/>.

Maintained by Matthew Ashby. Last updated 1 years ago.

crime crime-analysis crime-data

10.3 match 27 stars 5.53 score 25 scripts

ilostat

Rilostat:ILO Open Data via Ilostat Bulk Download Facility

Tools to download data from the [ilostat](<https://ilostat.ilo.org>) database together with search and manipulation utilities.

Maintained by David Bescond. Last updated 23 days ago.

api dataset open-source public-api

10.3 match 34 stars 5.47 score 43 scripts

justinmshea

wooldridge:115 Data Sets from "Introductory Econometrics: A Modern Approach, 7e" by Jeffrey M. Wooldridge

Students learning both econometrics and R may find the introduction to both challenging. The wooldridge data package aims to lighten the task by efficiently loading any data set found in the text with a single command. Data sets have been compressed to a fraction of their original size. Documentation files contain page numbers, the original source, time of publication, and notes from the author suggesting avenues for further analysis and research. If one needs an introduction to R model syntax, a vignette contains solutions to examples from chapters of the text. Data sets are from the 7th edition (Wooldridge 2020, ISBN-13 978-1-337-55886-0), and are backwards compatible with all previous versions of the text.

Maintained by Justin M. Shea. Last updated 4 months ago.

econometrics

6.0 match 203 stars 9.38 score 1.4k scripts

bioc

TCGAbiolinks:TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.

Maintained by Tiago Chedraoui Silva. Last updated 1 months ago.

dnamethylation differentialmethylation generegulation geneexpression methylationarray differentialexpression pathways network sequencing survival software bioc bioconductor gdc integrative-analysis tcga tcga-data tcgabiolinks

3.9 match 310 stars 14.47 score 1.6k scripts 6 dependents

joshuaulrich

quantmod:Quantitative Financial Modelling Framework

Specify, build, trade, and analyse quantitative financial trading strategies.

Maintained by Joshua M. Ulrich. Last updated 4 days ago.

algorithmic-trading charting data-import finance time-series

3.4 match 840 stars 16.18 score 8.1k scripts 343 dependents

felixfan

FinCal:Time Value of Money, Time Series Analysis and Computational Finance

Package for time value of money calculation, time series analysis and computational finance.

Maintained by Felix Yanhui Fan. Last updated 8 years ago.

9.0 match 23 stars 6.14 score 203 scripts 1 dependents

ropengov

eurostat:Tools for Eurostat Open Data

Tools to download data from the Eurostat database <https://ec.europa.eu/eurostat> together with search and manipulation utilities.

Maintained by Leo Lahti. Last updated 1 months ago.

ropengov eurostat eurostat-data

4.9 match 242 stars 11.07 score 892 scripts 4 dependents

serkor1

cryptoQuotes:Open Access to Cryptocurrency Market Data, Sentiment Indicators and Interactive Charts

This high-level API client provides open access to cryptocurrency market data, sentiment indicators, and interactive charting tools. The data is sourced from major cryptocurrency exchanges via 'curl' and returned in 'xts'-format. The data comes in open, high, low, and close (OHLC) format with flexible granularity, ranging from seconds to months. This flexibility makes it ideal for developing and backtesting trading strategies or conducting detailed market analysis.

Maintained by Serkan Korkmaz. Last updated 5 months ago.

binance binance-api bitmart bybit bybit-api cryptocurrencies cryptocurrency cryptocurrency-exchanges huobi huobi-api kraken-api kraken-exchange-api kucoin kucoin-api

8.2 match 39 stars 6.66 score 26 scripts

r-lib

xopen:Open System Files, 'URLs', Anything

Cross platform solution to open files, directories or 'URLs' with their associated programs.

Maintained by Gábor Csárdi. Last updated 5 months ago.

5.4 match 31 stars 10.00 score 40 scripts 161 dependents

bioc

OmnipathR:OmniPath web service client and more

A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).

Maintained by Denes Turei. Last updated 1 months ago.

graphandnetwork network pathways software thirdpartyclient dataimport datarepresentation genesignaling generegulation systemsbiology transcriptomics singlecell annotation kegg complexes enzyme-ptm networks networks-biology omnipath proteins quarto

5.5 match 130 stars 9.90 score 226 scripts 2 dependents

thinkr-open

testdown:'testhat' Results to Bookdown

Turn your 'testthat' results a Bookdown.

Maintained by Colin Fay. Last updated 2 years ago.

15.0 match 27 stars 3.61 score 3 scripts

thinkr-open

mariobox:A Framework For Packaging {plumber} APIs

A framework for building robust {plumber} APIs. This package contains a series of tools to build {plumber} APIs as packages.

Maintained by Colin Fay. Last updated 4 months ago.

15.0 match 38 stars 3.58 score 4 scripts

tbates

umx:Structural Equation Modeling and Twin Modeling in R

Quickly create, run, and report structural equation models, and twin models. See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS. Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.

Maintained by Timothy C. Bates. Last updated 17 hours ago.

behavior-genetics genetics openmx psychology sem statistics structural-equation-modeling tutorials twin-models umx

5.8 match 44 stars 9.32 score 472 scripts

brry

berryFunctions:Function Collection Related to Plotting and Hydrology

Draw horizontal histograms, color scattered points by 3rd dimension, enhance date- and log-axis plots, zoom in X11 graphics, trace errors and warnings, use the unit hydrograph in a linear storage cascade, convert lists to data.frames and arrays, fit multiple functions.

Maintained by Berry Boessenkool. Last updated 2 months ago.

5.7 match 13 stars 9.43 score 350 scripts 16 dependents

kwb-r

kwb.utils:General Utility Functions Developed at KWB

This package contains some small helper functions that aim at improving the quality of code developed at Kompetenzzentrum Wasser gGmbH (KWB).

Maintained by Hauke Sonnenberg. Last updated 1 years ago.

7.3 match 8 stars 7.33 score 12 scripts 78 dependents

bioc

MungeSumstats:Standardise summary statistics from GWAS

The *MungeSumstats* package is designed to facilitate the standardisation of GWAS summary statistics. It reformats inputted summary statisitics to include SNP, CHR, BP and can look up these values if any are missing. It also pefrorms dozens of QC and filtering steps to ensure high data quality and minimise inter-study differences.

Maintained by Alan Murphy. Last updated 4 months ago.

snp wholegenome genetics comparativegenomics genomewideassociation genomicvariation preprocessing

8.5 match 3 stars 6.23 score 91 scripts

thinkr-open

spongecake:Transform a Movie into a Synthetic Picture

Transform a Movie into a Synthetic Picture. A frame every 10 seconds is summarized into one colour, then every generated colors are stacked together.

Maintained by Vincent Guyader. Last updated 8 years ago.

15.0 match 6 stars 3.48 score 4 scripts

eblondel

ocs4R:Interface to Open Collaboration Services (OCS) REST API

Provides an Interface to Open Collaboration Services 'OCS' (<https://www.open-collaboration-services.org/>) REST API.

Maintained by Emmanuel Blondel. Last updated 2 months ago.

api collaboration nextcloud ocs open owncloud service webdav

14.7 match 6 stars 3.48 score 2 scripts

psolymos

intrval:Relational Operators for Intervals

Evaluating if values of vectors are within different open/closed intervals (`x %[]% c(a, b)`), or if two closed intervals overlap (`c(a1, b1) %[]o[]% c(a2, b2)`). Operators for negation and directional relations also implemented.

Maintained by Peter Solymos. Last updated 6 months ago.

closed-intervals interval-endpoints interval-operators negation open-intervals

8.0 match 41 stars 6.31 score 111 scripts 1 dependents

pecanproject

PEcAn.DB:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by David LeBauer. Last updated 11 hours ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

4.3 match 216 stars 11.90 score 127 scripts 27 dependents

ropensci

neotoma:Access to the Neotoma Paleoecological Database Through R

NOTE: This package is deprecated. Please use the neotoma2 package described at https://github.com/NeotomaDB/neotoma2. Access paleoecological datasets from the Neotoma Paleoecological Database using the published API (<http://wnapi.neotomadb.org/>), only containing datasets uploaded prior to June 2020. The functions in this package access various pre-built API functions and attempt to return the results from Neotoma in a usable format for researchers and the public.

Maintained by Simon J. Goring. Last updated 2 years ago.

neotoma neotoma-apis neotoma-database nsf paleoecology

10.0 match 30 stars 5.04 score 145 scripts

pbs-software

PBSmodelling:GUI Tools Made Easy: Interact with Models and Explore Data

Provides software to facilitate the design, testing, and operation of computer models. It focuses particularly on tools that make it easy to construct and edit a customized graphical user interface ('GUI'). Although our simplified 'GUI' language depends heavily on the R interface to the 'Tcl/Tk' package, a user does not need to know 'Tcl/Tk'. Examples illustrate models built with other R packages, including 'PBSmapping', 'PBSddesolve', and 'BRugs'. A complete user's guide 'PBSmodelling-UG.pdf' shows how to use this package effectively.

Maintained by Rowan Haigh. Last updated 5 months ago.

7.4 match 2 stars 6.76 score 120 scripts 4 dependents

ropengov

helsinki:R Tools for Helsinki Open Data

Tools for accessing various open data APIs in the Helsinki region in Finland. Current data sources include the Service Map API, Linked Events API, and Helsinki Region Infoshare statistics API.

Maintained by Juuso Parkkinen. Last updated 2 years ago.

ropengov finland helsinki helsinki-region

9.5 match 6 stars 5.28 score 21 scripts

ropensci

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>).

Maintained by Joan Maspons. Last updated 5 months ago.

open street map openstreetmap osm openstreetmap-api osmapi api

6.7 match 22 stars 7.42 score 6 scripts

henrikbengtsson

R.utils:Various Programming Utilities

Utility functions useful when programming and developing R packages.

Maintained by Henrik Bengtsson. Last updated 1 years ago.

3.6 match 63 stars 13.74 score 5.7k scripts 814 dependents

kjhealy

gssrdoc:Document General Social Survey Variable

The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.

Maintained by Kieran Healy. Last updated 12 months ago.

21.5 match 2.28 score 38 scripts

usdaforestservice

gdalraster:Bindings to the 'Geospatial Data Abstraction Library' Raster API

Interface to the Raster API of the 'Geospatial Data Abstraction Library' ('GDAL', <https://gdal.org>). Bindings are implemented in an exposed C++ class encapsulating a 'GDALDataset' and its raster band objects, along with several stand-alone functions. These support manual creation of uninitialized datasets, creation from existing raster as template, read/set dataset parameters, low level I/O, color tables, raster attribute tables, virtual raster (VRT), and 'gdalwarp' wrapper for reprojection and mosaicing. Includes 'GDAL' algorithms ('dem_proc()', 'polygonize()', 'rasterize()', etc.), and functions for coordinate transformation and spatial reference systems. Calling signatures resemble the native C, C++ and Python APIs provided by the 'GDAL' project. Includes raster 'calc()' to evaluate a given R expression on a layer or stack of layers, with pixel x/y available as variables in the expression; and raster 'combine()' to identify and count unique pixel combinations across multiple input layers, with optional output of the pixel-level combination IDs. Provides raster display using base 'graphics'. Bindings to a subset of the 'OGR' API are also included for managing vector data sources. Bindings to a subset of the Virtual Systems Interface ('VSI') are also included to support operations on 'GDAL' virtual file systems. These are general utility functions that abstract file system operations on URLs, cloud storage services, 'Zip'/'GZip'/'7z'/'RAR' archives, and in-memory files. 'gdalraster' may be useful in applications that need scalable, low-level I/O, or prefer a direct 'GDAL' API.

Maintained by Chris Toney. Last updated 2 hours ago.

gdal geospatial raster vector cpp

5.1 match 41 stars 9.49 score 32 scripts 3 dependents

eurostat

restatapi:Search and Retrieve Data from Eurostat Database

Eurostat is the statistical office of the European Union and provides high quality statistics for Europe. Large set of the data is disseminated through the Eurostat database (<https://ec.europa.eu/eurostat/web/main/data/database>). The tools are using the REST API with the Statistical Data and Metadata eXchange (SDMX) Web Services (<https://wikis.ec.europa.eu/pages/viewpage.action?pageId=44165555>) to search and download data from the Eurostat database using the SDMX standard.

Maintained by Mátyás Mészáros. Last updated 7 hours ago.

database eurostat filter open-data retrieve-data sdmx

7.5 match 25 stars 6.34 score 146 scripts 1 dependents

bioc

ORFhunteR:Predict open reading frames in nucleotide sequences

The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules. It efficiently implements the machine learning model based on vectorization of nucleotide sequences and the random forest classification algorithm. The ORFhunteR package consists of a set of functions written in the R language in conjunction with C++. The efficiency of the package was confirmed by the examples of the analysis of RNA molecules from the NCBI RefSeq and Ensembl databases. The package can be used in basic and applied biomedical research related to the study of the transcriptome of normal as well as altered (for example, cancer) human cells.

Maintained by Vasily V. Grinev. Last updated 5 months ago.

technology statisticalmethod sequencing rnaseq classification featureextraction cpp

10.6 match 1 stars 4.48 score

epiforecasts

covidregionaldata:Subnational Data for COVID-19 Epidemiology

An interface to subnational and national level COVID-19 data sourced from both official sources, such as Public Health England in the UK, and from other COVID-19 data collections, including the World Health Organisation (WHO), European Centre for Disease Prevention and Control (ECDC), John Hopkins University (JHU), Google Open Data and others. Designed to streamline COVID-19 data extraction, cleaning, and processing from a range of data sources in an open and transparent way. This allows users to inspect and scrutinise the data, and tools used to process it, at every step. For all countries supported, data includes a daily time-series of cases. Wherever available data is also provided for deaths, hospitalisations, and tests. National level data are also supported using a range of sources.

Maintained by Sam Abbott. Last updated 3 years ago.

covid-19 data open-science r6 regional-data

8.3 match 37 stars 5.67 score 121 scripts

ropensci

gistr: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/>.

Maintained by Scott Chamberlain. Last updated 2 years ago.

http https api web-services github github api gist gists code script snippet api-wrapper github-api github-gist

5.5 match 104 stars 8.28 score 42 scripts 2 dependents

krlmlr

kimisc:Kirill's Miscellaneous Functions

A collection of useful functions not found anywhere else, mainly for programming: Pretty intervals, generalized lagged differences, checking containment in an interval, and an alternative interface to assign().

Maintained by Kirill Müller. Last updated 4 months ago.

7.0 match 18 stars 6.47 score 76 scripts 3 dependents

bioc

IsoformSwitchAnalyzeR:Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.

Maintained by Kristoffer Vitting-Seerup. Last updated 5 months ago.

geneexpression transcription alternativesplicing differentialexpression differentialsplicing visualization statisticalmethod transcriptomevariant biomedicalinformatics functionalgenomics systemsbiology transcriptomics rnaseq annotation functionalprediction geneprediction dataimport multiplecomparison batcheffect immunooncology

4.8 match 108 stars 9.26 score 125 scripts

bmaitner

S4DM:Small Sample Size Species Distribution Modeling

Implements a set of distribution modeling methods that are suited to species with small sample sizes (e.g., poorly sampled species or rare species). While these methods can also be used on well-sampled taxa, they are united by the fact that they can be utilized with relatively few data points. More details on the currently implemented methodologies can be found in Drake and Richards (2018) <doi:10.1002/ecs2.2373>, Drake (2015) <doi:10.1098/rsif.2015.0086>, and Drake (2014) <doi:10.1890/ES13-00202.1>.

Maintained by Brian S. Maitner. Last updated 2 months ago.

open-science range-modelling rare-species species-distribution-modeling species-distribution-modelling

7.5 match 4 stars 5.97 score 33 scripts

ropengov

sorvi:Functions for Finnish Open Data

Misc support functions for rOpenGov and open data downloads.

Maintained by Leo Lahti. Last updated 1 years ago.

6.7 match 13 stars 6.71 score 131 scripts

flare-forecast

ropenmeteo:Wrappers for 'Open-Meteo' API

Wrappers for the Application Programming Interface from the <https://open-meteo.com> project along with helper functions. The <https://open-meteo.com> project streamlines access to a range of publicly historical and forecast meteorology data from agencies across the world.

Maintained by Quinn Thomas. Last updated 7 months ago.

12.2 match 3.62 score 14 scripts

bioc

GenomicDistributions:GenomicDistributions: fast analysis of genomic intervals with Bioconductor

If you have a set of genomic ranges, this package can help you with visualization and comparison. It produces several kinds of plots, for example: Chromosome distribution plots, which visualize how your regions are distributed over chromosomes; feature distance distribution plots, which visualizes how your regions are distributed relative to a feature of interest, like Transcription Start Sites (TSSs); genomic partition plots, which visualize how your regions overlap given genomic features such as promoters, introns, exons, or intergenic regions. It also makes it easy to compare one set of ranges to another.

Maintained by Kristyna Kupkova. Last updated 5 months ago.

software genomeannotation genomeassembly datarepresentation sequencing coverage functionalgenomics visualization

5.9 match 26 stars 7.44 score 25 scripts

bioc

gdsfmt:R Interface to CoreArray Genomic Data Structure (GDS) Files

Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.

Maintained by Xiuwen Zheng. Last updated 18 days ago.

infrastructure dataimport bioinformatics gds-format genomics cpp

3.9 match 18 stars 11.34 score 920 scripts 29 dependents

dickoa

robotoolbox:Client for the 'KoboToolbox' API

Suite of utilities for accessing and manipulating data from the 'KoboToolbox' API. 'KoboToolbox' is a robust platform designed for field data collection in various disciplines. This package aims to simplify the process of fetching and handling data from the API. Detailed documentation for the 'KoboToolbox' API can be found at <https://support.kobotoolbox.org/api.html>.

Maintained by Ahmadou Dicko. Last updated 3 months ago.

open-data kobotoolbox odk kpi api data dataset

7.5 match 5.86 score 48 scripts

mjwoods

RNetCDF:Interface to 'NetCDF' Datasets

An interface to the 'NetCDF' file formats designed by Unidata for efficient storage of array-oriented scientific data and descriptions. Most capabilities of 'NetCDF' version 4 are supported. Optional conversions of time units are enabled by 'UDUNITS' version 2, also from Unidata.

Maintained by Milton Woods. Last updated 24 days ago.

udunits netcdf

4.3 match 24 stars 10.26 score 540 scripts 23 dependents

okgreece

Cluster.OBeu:Cluster Analysis 'OpenBudgets.eu'

Estimate and return the needed parameters for visualisations designed for 'OpenBudgets' <http://openbudgets.eu/> data. Calculate cluster analysis measures in Budget data of municipalities across Europe, according to the 'OpenBudgets' data model. It involves a set of techniques and algorithms used to find and divide the data into groups of similar observations. Also, can be used generally to extract visualisation parameters convert them to 'JSON' format and use them as input in a different graphical interface.

Maintained by Kleanthis Koupidis. Last updated 4 years ago.

cluster cluster-analysis clustering-algorithm clustering-measures estimate-clustering-parameters obeu open-budgets openbudgets

9.2 match 2 stars 4.75 score 14 scripts

brechtdv

DALY:The DALY Calculator - Graphical User Interface for Probabilistic DALY Calculation in R

The DALY Calculator is a free, open-source Graphical User Interface (GUI) for probabilistic disability-adjusted life year (DALY) calculation.

Maintained by Brecht Devleesschauwer. Last updated 8 years ago.

cpp

10.1 match 4 stars 4.30 score 9 scripts

r-causal

ggdag:Analyze and Create Elegant Directed Acyclic Graphs

Tidy, analyze, and plot directed acyclic graphs (DAGs). 'ggdag' is built on top of 'dagitty', an R package that uses the 'DAGitty' web tool (<https://dagitty.net/>) for creating and analyzing DAGs. 'ggdag' makes it easy to tidy and plot 'dagitty' objects using 'ggplot2' and 'ggraph', as well as common analytic and graphical functions, such as determining adjustment sets and node relationships.

Maintained by Malcolm Barrett. Last updated 8 months ago.

causal-inference dag ggplot-extension

3.7 match 443 stars 11.78 score 1.8k scripts 5 dependents

bioc

GeneStructureTools:Tools for spliced gene structure manipulation and analysis

GeneStructureTools can be used to create in silico alternative splicing events, and analyse potential effects this has on functional gene products.

Maintained by Beth Signal. Last updated 5 months ago.

immunooncology software differentialsplicing functionalprediction transcriptomics alternativesplicing rnaseq

9.8 match 4.32 score 21 scripts

paleolimbot

rosm:Plot Raster Map Tiles from Open Street Map and Other Sources

Download and plot Open Street Map <https://www.openstreetmap.org/>, Bing Maps <https://www.bing.com/maps> and other tiled map sources. Use to create basemaps quickly and add hillshade to vector-based maps.

Maintained by Dewey Dunnington. Last updated 2 years ago.

5.1 match 27 stars 8.23 score 130 scripts 26 dependents

rstudio

rticles:Article Formats for R Markdown

A suite of custom R Markdown formats and templates for authoring journal articles and conference submissions.

Maintained by Christophe Dervieux. Last updated 22 days ago.

article journal paper rmarkdown

3.5 match 1.5k stars 11.93 score 188 scripts 3 dependents

thinkr-open

bank:Extra Cache

More cache backends.

Maintained by Colin Fay. Last updated 2 years ago.

cache golemverse shiny

15.0 match 12 stars 2.78 score 6 scripts

nx10

httpgd:A 'HTTP' Server Graphics Device

A graphics device for R that is accessible via network protocols. This package was created to make it easier to embed live R graphics in integrated development environments and other applications. The included 'HTML/JavaScript' client (plot viewer) aims to provide a better overall user experience when dealing with R graphics. The device asynchronously serves graphics via 'HTTP' and 'WebSockets'.

Maintained by Florian Rupprecht. Last updated 17 days ago.

cpp

3.8 match 428 stars 11.01 score 280 scripts 1 dependents

r-lib

fs:Cross-Platform File System Operations Based on 'libuv'

A cross-platform interface to file system operations, built on top of the 'libuv' C library.

Maintained by Gábor Csárdi. Last updated 5 months ago.

filesystem libuv cpp

2.0 match 370 stars 20.26 score 8.1k scripts 5.2k dependents

karlines

shape:Functions for Plotting Graphical Shapes, Colors

Functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...

Maintained by Karline Soetaert. Last updated 1 years ago.

3.7 match 10.95 score 984 scripts 1.4k dependents

ropensci

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.

Maintained by Stijn Van Hoey. Last updated 3 years ago.

api climate lifewatch open-science oscibio ropensci water weather

7.5 match 14 stars 5.36 score 27 scripts

edm44

hydraulics:Basic Pipe and Open Channel Hydraulics

Functions for basic hydraulic calculations related to water flow in circular pipes both flowing full (under pressure), and partially full (gravity flow), and trapezoidal open channels. For pressure flow this includes friction loss calculations by solving the Darcy-Weisbach equation for head loss, flow or diameter, plotting a Moody diagram, matching a pump characteristic curve to a system curve, and solving for flows in a pipe network using the Hardy-Cross method. The Darcy-Weisbach friction factor is calculated using the Colebrook (or Colebrook-White equation), the basis of the Moody diagram, the original citation being Colebrook (1939) <doi:10.1680/ijoti.1939.13150>. For gravity flow, the Manning equation is used, again solving for missing parameters. The derivation of and solutions using the Darcy-Weisbach equation and the Manning equation are outlined in many fluid mechanics texts such as Finnemore and Maurer (2024, ISBN:978-1-264-78729-6). Some gradually- and rapidly-varied flow functions are included. For the Manning equation solutions, this package uses modifications of original code from the 'iemisc' package by Irucka Embry.

Maintained by Ed Maurer. Last updated 5 months ago.

8.1 match 9 stars 4.95 score 8 scripts

malaria-atlas-project

malariaAtlas:An R Interface to Open-Access Malaria Data, Hosted by the 'Malaria Atlas Project'

A suite of tools to allow you to download all publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from the 'Malaria Atlas Project' <https://malariaatlas.org/> servers as well as utility functions for plotting the downloaded data.

Maintained by Mauricio van den Berg. Last updated 9 months ago.

database malaria opendata raster

4.4 match 44 stars 9.10 score 118 scripts 3 dependents

bioc

annotate:Annotation for microarrays

Using R enviroments for annotation.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

annotation pathways go

3.5 match 11.41 score 812 scripts 239 dependents

dariah-fi-survey-concept-network

finnsurveytext:Analyse Open-Ended Survey Responses in Finnish

Annotates Finnish textual survey responses into CoNLL-U format using Finnish treebanks from <https://universaldependencies.org/format.html> using UDPipe as described in Straka and Straková (2017) <doi:10.18653/v1/K17-3009>. Formatted data is then analysed using single or comparison n-gram plots, wordclouds, summary tables and Concept Network plots. The Concept Network plots use the TextRank algorithm as outlined in Mihalcea, Rada & Tarau, Paul (2004) <https://aclanthology.org/W04-3252/>.

Maintained by Adeline Clarke. Last updated 27 days ago.

dariah-fi

7.4 match 5.39 score 27 scripts

alexiosg

rugarch:Univariate GARCH Models

ARFIMA, in-mean, external regressors and various GARCH flavors, with methods for fit, forecast, simulation, inference and plotting.

Maintained by Alexios Galanos. Last updated 3 months ago.

cpp

3.3 match 26 stars 12.25 score 1.3k scripts 16 dependents

ropensci

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).

Maintained by Karthik Ram. Last updated 5 years ago.

fisheries open-data openfisheries

7.5 match 26 stars 5.31 score 39 scripts

jimbrig

jimstools:Tools for R

What the package does (one paragraph).

Maintained by Jimmy Briggs. Last updated 3 years ago.

functions personal utility

13.2 match 2 stars 3.00 score 2 scripts

christopherkenny

opengraph:Process Metadata from the 'Open Graph Protocol'

Social media sites often embed cards when links are shared, based on metadata in the 'Open Graph Protocol' (<https://ogp.me/>). This supports extracting that metadata from a website. It further allows for the creation of tags to add to a website to support the 'Open Graph Protocol' and provides a list of the standard tags and their required properties.

Maintained by Christopher T. Kenny. Last updated 4 months ago.

13.1 match 1 stars 3.00 score 5 scripts

carlos-alberto-silva

ICESat2VegR:NASA's Ice, Cloud, and Elevation Satellite (ICESat-2) Data Analysis for Land and Vegetation Applications

Set of tools for downloading, reading, visualizing, processing and exporting NASA's ICESat-2 ATL03 (Global Geolocated Photon Data) and ATL08 (Land and Vegetation Height) products for Land and Vegetation Applications.

Maintained by Caio Hamamura. Last updated 7 months ago.

gdal proj cpp

8.8 match 11 stars 4.44 score 21 scripts

bioc

miRBaseConverter:A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions

A comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. It can process a huge number of miRNAs in a short time without other depends.

Maintained by Taosheng Xu Taosheng Xu. Last updated 5 months ago.

software mirna

6.0 match 1 stars 6.50 score 70 scripts

kkholst

lava:Latent Variable Models

A general implementation of Structural Equation Models with latent variables (MLE, 2SLS, and composite likelihood estimators) with both continuous, censored, and ordinal outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>). Mixture latent variable models and non-linear latent variable models (Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>). The package also provides methods for graph exploration (d-separation, back-door criterion), simulation of general non-linear latent variable models, and estimation of influence functions for a broad range of statistical models.

Maintained by Klaus K. Holst. Last updated 3 months ago.

latent-variable-models simulation statistics structural-equation-models

3.0 match 33 stars 12.87 score 610 scripts 478 dependents

r-lib

httr:Tools for Working with URLs and HTTP

Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).

Maintained by Hadley Wickham. Last updated 1 years ago.

api curl http

1.9 match 989 stars 20.56 score 29k scripts 4.3k dependents

bioc

EBImage:Image processing and analysis toolbox for R

EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.

Maintained by Andrzej Oleś. Last updated 5 months ago.

visualization bioinformatics image-analysis image-processing cpp

3.0 match 71 stars 12.77 score 1.5k scripts 33 dependents

fishr-core-team

FSA:Simple Fisheries Stock Assessment Methods

A variety of simple fish stock assessment methods.

Maintained by Derek H. Ogle. Last updated 2 months ago.

fish fisheries fisheries-management fisheries-stock-assessment population-dynamics stock-assessment

3.4 match 69 stars 11.16 score 1.7k scripts 6 dependents

ropensci

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/>).

Maintained by Kevin Cazelles. Last updated 1 years ago.

ecology networks food webs interactions data publications open access

7.5 match 14 stars 5.07 score 28 scripts

rapporter

pander:An R 'Pandoc' Writer

Contains some functions catching all messages, 'stdout' and other useful information while evaluating R code and other helpers to return user specified text elements (like: header, paragraph, table, image, lists etc.) in 'pandoc' markdown or several type of R objects similarly automatically transformed to markdown format. Also capable of exporting/converting (the resulting) complex 'pandoc' documents to e.g. HTML, 'PDF', 'docx' or 'odt'. This latter reporting feature is supported in brew syntax or with a custom reference class with a smarty caching 'backend'.

Maintained by Gergely Daróczi. Last updated 1 months ago.

literate-programming markdown pandoc pandoc-markdown reproducible-research rmarkdown cpp

2.3 match 298 stars 16.76 score 7.6k scripts 110 dependents

martinschobben

oceanexplorer:Explore Our Planet's Oceans with NOAA

Provides tools for easy exploration of the world ocean atlas of the US agency National Oceanic and Atmospheric Administration (NOAA). It includes functions to extract NetCDF data from the repository and code to visualize several physical and chemical parameters of the ocean. A Shiny app further allows interactive exploration of the data. The methods for data collecting and quality checks are described in several papers, which can be found here: <https://www.ncei.noaa.gov/products/world-ocean-atlas>.

Maintained by Martin Schobben. Last updated 1 years ago.

earth earth-observation earth-science noaa noaa-data ocean ocean-sciences oceanography open-data shiny spatial spatial-analysis spatial-data

7.5 match 9 stars 5.01 score 23 scripts

mkoohafkan

rivr:Steady and Unsteady Open-Channel Flow Computation

A tool for undergraduate and graduate courses in open-channel hydraulics. Provides functions for computing normal and critical depths, steady-state water surface profiles (e.g. backwater curves) and unsteady flow computations (e.g. flood wave routing) as described in Koohafkan MC, Younis BA (2015). "Open-channel computation with R." The R Journal, 7(2), 249–262. <doi: 10.32614/RJ-2015-034>.

Maintained by Michael C Koohafkan. Last updated 7 months ago.

hydraulics cpp

6.6 match 20 stars 5.71 score 17 scripts

thinkr-open

w3css:W3CSS for 'shiny'

An implementation of W3 CSS <https://www.w3schools.com/w3css/> for 'shiny'.

Maintained by Colin Fay. Last updated 2 years ago.

golemverse shiny

15.0 match 6 stars 2.48 score

r-lib

pkgdown:Make Static HTML Documentation for a Package

Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.

Maintained by Hadley Wickham. Last updated 14 days ago.

documentation-tool

2.0 match 734 stars 18.46 score 588 scripts 162 dependents

bioc

interactiveDisplay:Package for enabling powerful shiny web displays of Bioconductor objects

The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects.

Maintained by Bioconductor Package Maintainer. Last updated 4 months ago.

go geneexpression microarray sequencing classification network qualitycontrol visualization genetics datarepresentation gui annotationdata shinyapps

10.6 match 3.48 score 4 scripts

bioc

affy:Methods for Affymetrix Oligonucleotide Arrays

The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.

Maintained by Robert D. Shear. Last updated 3 months ago.

microarray onechannel preprocessing

3.3 match 11.12 score 2.5k scripts 98 dependents

nik01010

openbankeR:R Client for Querying the UK 'Open Banking' ('Open Data') API

Creates a client with queries for the UK 'Open Banking' ('Open Data') API. API wrapper around <https://openbankinguk.github.io/opendata-api-docs-pub>.

Maintained by Nik Lilovski. Last updated 3 years ago.

bank client data openbanking openbanking-api opendata opendata-api

8.2 match 6 stars 4.48 score 6 scripts

danchaltiel

crosstable:Crosstables for Descriptive Analyses

Create descriptive tables for continuous and categorical variables. Apply summary statistics and counting function, with or without a grouping variable, and create beautiful reports using 'rmarkdown' or 'officer'. You can also compute effect sizes and statistical tests if needed.

Maintained by Dan Chaltiel. Last updated 2 months ago.

descriptive-statistics flextable frequency-table html-report msword officer

3.5 match 116 stars 10.40 score 340 scripts

nandp1

nser:Bhavcopy and Live Market Data from National Stock Exchange (NSE) & Bombay Stock Exchange (BSE) India

Download Current & Historical Bhavcopy. Get Live Market data from NSE India of Equities and Derivatives (F&O) segment. Data source <https://www.nseindia.com/>.

Maintained by Nandan Patil. Last updated 5 months ago.

bhav bhavcopy bhavcopy-downloader financial-data market-data national-stock-exchange nse nse-stock-data option-pricing optionchain rselenium stock-prices

4.8 match 8 stars 7.61 score 76 scripts

g-corbelli

reflectR:Automatic Scoring of the Cognitive Reflection Test

A tool for researchers and psychologists to automatically code open-ended responses to the Cognitive Reflection Test (CRT), a widely used class of tests in cognitive science and psychology for assessing an individual's propensity to override an incorrect gut response and engage in further reflection to find a correct answer. This package facilitates the standardization of Cognitive Reflection Test responses analysis across large datasets in cognitive psychology, decision-making, and related fields. By automating the coding process, it not only reduces manual effort but also aims to reduce the variability introduced by subjective interpretation of open-ended responses, contributing to a more consistent and reliable analysis. 'reflectR' supports automatic coding and machine scoring for the original English-language version of CRT (Frederick, 2005) <doi:10.1257/089533005775196732>, as well as for CRT4 and CRT7, 4- and 7-item versions, respectively (Toplak et al., 2014) <doi:10.1080/13546783.2013.844729>, for the CRT-long version built via Item Response Theory by Primi and colleagues (2016) <doi:10.1002/bdm.1883>, and for CRT-2 by Thomson & Oppenheimer (2016) <doi:10.1017/s1930297500007622>. Note: While 'reflectR' draws inspiration from the principles and scientific literature underlying the different versions of the Cognitive Reflection Test, it has been independently developed and does not hold any affiliation with any of the original authors. The development of this package benefited significantly from the kind insight and suggestion provided by Dr. Keela Thomson, whose contribution is gratefully acknowledged. Additional gratitude is extended to Dr. Paolo Giovanni Cicirelli, Prof. Marinella Paciello, Dr. Carmela Sportelli, and Prof. Francesca D'Errico, who not only contributed to the manual multi-rater coding of CRT-2 items but also profoundly influenced the understanding of the importance and practical relevance of cognitive reflection within personality, social, and cognitive psychology research. Acknowledgment is also due to the European project STERHEOTYPES (STudying European Racial Hoaxes and sterEOTYPES) for funding the data collection that produced the datasets initially used for manual multi-rater coding of CRT-2 items.

Maintained by Giuseppe Corbelli. Last updated 7 months ago.

assessment cognitive cognitive-psychology cognitive-science crt psychological-science psychological-tests psychology psychometrics reflection scoring testing

10.4 match 1 stars 3.48 score

ohdsi

PatientLevelPrediction:Develop Clinical Prediction Models Using the Common Data Model

A user friendly way to create patient level prediction models using the Observational Medical Outcomes Partnership Common Data Model. Given a cohort of interest and an outcome of interest, the package can use data in the Common Data Model to build a large set of features. These features can then be used to fit a predictive model with a number of machine learning algorithms. This is further described in Reps (2017) <doi:10.1093/jamia/ocy032>.

Maintained by Egill Fridgeirsson. Last updated 25 days ago.

hades openjdk

3.3 match 190 stars 10.85 score 297 scripts

unina-sfere

funcharts:Functional Control Charts

Provides functional control charts for statistical process monitoring of functional data, using the methods of Capezza et al. (2020) <doi:10.1002/asmb.2507>, Centofanti et al. (2021) <doi:10.1080/00401706.2020.1753581>, Capezza et al. (2024) <doi:10.1080/00401706.2024.2327346>, Capezza et al. (2024) <doi:10.1080/00224065.2024.2383674>, Centofanti et al. (2022) <doi:10.48550/arXiv.2205.06256>. The package is thoroughly illustrated in the paper of Capezza et al (2023) <doi:10.1080/00224065.2023.2219012>.

Maintained by Christian Capezza. Last updated 15 days ago.

openblas cpp

5.3 match 2 stars 6.73 score 168 scripts

arpapiemonte

OpeNoise:Environmental Noise Pollution Data Analysis

Provides analyse, interpret and understand noise pollution data. Data are typically regular time series measured with sound meter. The package is partially described in Fogola, Grasso, Masera and Scordino (2023, <DOI:10.61782/fa.2023.0063>).

Maintained by Pasquale Scordino. Last updated 4 months ago.

10.3 match 2 stars 3.48 score 5 scripts

bioc

GWASTools:Tools for Genome Wide Association Studies

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.

Maintained by Stephanie M. Gogarten. Last updated 14 days ago.

snp geneticvariability qualitycontrol microarray

3.3 match 17 stars 10.67 score 396 scripts 5 dependents

r-lib

devtools:Tools to Make Developing R Packages Easier

Collection of package development tools.

Maintained by Jennifer Bryan. Last updated 6 months ago.

package-creation

1.8 match 2.4k stars 19.55 score 51k scripts 150 dependents

r-lib

usethis:Automate Package and Project Setup

Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.

Maintained by Jennifer Bryan. Last updated 28 days ago.

github setup

2.0 match 869 stars 17.54 score 5.6k scripts 336 dependents

statnet

ergm:Fit, Simulate and Diagnose Exponential-Family Models for Networks

An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.

Maintained by Pavel N. Krivitsky. Last updated 23 days ago.

2.3 match 100 stars 15.36 score 1.4k scripts 36 dependents

cloudyr

googleComputeEngineR:R Interface with Google Compute Engine

Interact with the 'Google Compute Engine' API in R. Lets you create, start and stop instances in the 'Google Cloud'. Support for preconfigured instances, with templates for common R needs.

Maintained by Mark Edmondson. Last updated 17 days ago.

api cloud-computing cloudyr google-cloud googleauthr launching-virtual-machines

3.5 match 152 stars 9.73 score 235 scripts

skvrnami

hlidacr:Access Data from the 'Hlídač Státu' API

Provides access to datasets published by 'Hlídač státu' <https://www.hlidacstatu.cz/>, a Czech watchdog, via their API.

Maintained by Michael Škvrňák. Last updated 4 years ago.

czech-republic datasets open-data

7.5 match 8 stars 4.60 score 6 scripts

andreyshabalin

filematrix:File-Backed Matrix Class with Convenient Read and Write Access

Interface for working with large matrices stored in files, not in computer memory. Supports multiple non-character data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4 byte real values). Access to parts of the matrix is done by indexing, exactly as with usual R matrices. Supports very large matrices. Tested on multi-terabyte matrices. Allows for more than 2^32 rows or columns. Allows for quick addition of extra columns to a filematrix. Cross-platform as the package has R code only.

Maintained by Andrey A Shabalin. Last updated 6 years ago.

5.3 match 8 stars 6.51 score 45 scripts 2 dependents

erossiter

catSurv:Computerized Adaptive Testing for Survey Research

Provides methods of computerized adaptive testing for survey researchers. See Montgomery and Rossiter (2020) <doi:10.1093/jssam/smz027>. Includes functionality for data fit with the classic item response methods including the latent trait model, Birnbaum`s three parameter model, the graded response, and the generalized partial credit model. Additionally, includes several ability parameter estimation and item selection routines. During item selection, all calculations are done in compiled C++ code.

Maintained by Erin Rossiter. Last updated 11 months ago.

gsl cpp

7.3 match 12 stars 4.68 score 3 scripts

rapidsurveys

odkr:'Open Data Kit' ('ODK') R API

Utility functions for working with datasets gathered using 'Open Data Kit' ('ODK') <https://opendatakit.org/>. These include an API to interface with 'ODK Briefcase', a 'Java' application for fetching and pushing 'ODK' forms and their contents, that allows pulling of data from either a remote 'ODK Aggregate Server' or a local 'ODK' folder, a rename function to give more human readable variable names for 'ODK' datasets, a merge function to create a single dataframe from a nested 'ODK' dataset and an expand function to disaggregate multiple choice answers that have been collapsed into single code by 'ODK'.

Maintained by Ernest Guevarra. Last updated 6 months ago.

odk odk-briefcase open-data-kit openjdk

10.1 match 11 stars 3.32 score 19 scripts

harrelfe

Hmisc:Harrell Miscellaneous

Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, simulation, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, recoding variables, caching, simplified parallel computing, encrypting and decrypting data using a safe workflow, general moving window statistical estimation, and assistance in interpreting principal component analysis.

Maintained by Frank E Harrell Jr. Last updated 7 days ago.

fortran

1.9 match 209 stars 17.64 score 17k scripts 750 dependents

yonicd

details:Create Details HTML Tag for Markdown and Package Documentation

Create a details HTML tag around R objects to place in a Markdown, 'Rmarkdown' and 'roxygen2' documentation.

Maintained by Jonathan Sidi. Last updated 2 months ago.

html markdown rmarkdown

3.7 match 83 stars 8.92 score 192 scripts 3 dependents

julianfaraway

faraway:Datasets and Functions for Books by Julian Faraway

Books are "Linear Models with R" published 1st Ed. August 2004, 2nd Ed. July 2014, 3rd Ed. February 2025 by CRC press, ISBN 9781439887332, and "Extending the Linear Model with R" published by CRC press in 1st Ed. December 2005 and 2nd Ed. March 2016, ISBN 9781584884248 and "Practical Regression and ANOVA in R" contributed documentation on CRAN (now very dated).

Maintained by Julian Faraway. Last updated 2 months ago.

data

3.5 match 29 stars 9.43 score 1.7k scripts 1 dependents

robjhyndman

fma:Data Sets from "Forecasting: Methods and Applications" by Makridakis, Wheelwright & Hyndman (1998)

All data sets from "Forecasting: methods and applications" by Makridakis, Wheelwright & Hyndman (Wiley, 3rd ed., 1998) <https://robjhyndman.com/forecasting/>.

Maintained by Rob Hyndman. Last updated 1 years ago.

3.8 match 19 stars 8.74 score 336 scripts 2 dependents

ethanbass

ShinyChromViewer:Shiny Gadget for Interactive Viewing and Exploration of Chromatograms

Shiny Gadget for interactive viewing and exploration of chromatograms.

Maintained by Ethan Bass. Last updated 2 years ago.

chromatography hplc hplc-dad hplc-uv open-data open-science shiny shiny-apps

15.0 match 3 stars 2.18 score

ropengov

sotkanet:Sotkanet Open Data Access and Analysis

Access statistical information on welfare and health in Finland from the Sotkanet open data portal <https://sotkanet.fi/sotkanet/fi/index>.

Maintained by Leo Lahti. Last updated 9 months ago.

ropengov finland health sotkanet-data-portal

5.3 match 9 stars 6.15 score 26 scripts

ropensci

helminthR:Access London Natural History Museum Host-Helminth Record Database

Access to large host-parasite data is often hampered by the availability of data and difficulty in obtaining it in a programmatic way to encourage analyses. 'helminthR' provides 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.

Maintained by Tad Dallas. Last updated 2 years ago.

disease-networks helminth open-data parasites

7.5 match 7 stars 4.32 score 12 scripts

mikewlcheung

metaSEM:Meta-Analysis using Structural Equation Modeling

A collection of functions for conducting meta-analysis using a structural equation modeling (SEM) approach via the 'OpenMx' and 'lavaan' packages. It also implements various procedures to perform meta-analytic structural equation modeling on the correlation and covariance matrices, see Cheung (2015) <doi:10.3389/fpsyg.2014.01521>.

Maintained by Mike Cheung. Last updated 26 days ago.

meta-analysis meta-analytic-sem missing-data multilevel-models multivariate-analysis structural-equation-modeling structural-equation-models

3.4 match 30 stars 9.43 score 208 scripts 1 dependents

rspatial

raster:Geographic Data Analysis and Modeling

Reading, writing, manipulating, analyzing and modeling of spatial data. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.

Maintained by Robert J. Hijmans. Last updated 5 days ago.

cpp

1.9 match 163 stars 17.23 score 58k scripts 562 dependents

ycphs

openxlsx:Read, Write and Edit xlsx Files

Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages with the added benefit of removing the dependency on Java.

Maintained by Jan Marvin Garbuszus. Last updated 2 months ago.

xlsx cpp

1.7 match 232 stars 19.09 score 20k scripts 277 dependents

ropensci

tesseract:Open Source OCR Engine

Bindings to 'Tesseract': a powerful optical character recognition (OCR) engine that supports over 100 languages. The engine is highly configurable in order to tune the detection algorithms and obtain the best possible results.

Maintained by Jeroen Ooms. Last updated 10 days ago.

ocr tesseract tesseract-ocr cpp

3.1 match 247 stars 10.19 score 482 scripts