R-universe search: public

usdaforestservice

FIESTA:Forest Inventory Estimation and Analysis

A research estimation tool for analysts that work with sample-based inventory data from the U.S. Department of Agriculture, Forest Service, Forest Inventory and Analysis (FIA) Program.

Maintained by Grayson White. Last updated 3 days ago.

38.8 match 30 stars 7.24 score 62 scripts

neotomadb

neotoma2:Working with the Neotoma Paleoecology Database

Access and manipulation of data using the Neotoma Paleoecology Database. <https://api.neotomadb.org/api-docs/>.

Maintained by Dominguez Vidana Socorro. Last updated 8 months ago.

earthcube neotoma nsf paleoecology

49.6 match 8 stars 5.35 score 56 scripts

bioc

GLAD:Gain and Loss Analysis of DNA

Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.

Maintained by Philippe Hupe. Last updated 5 months ago.

microarray copynumbervariation gsl cpp

35.6 match 5.86 score 61 scripts 2 dependents

elipousson

bcpss:Baltimore City Public Schools

Provides access to demographic, enrollment, and survey data on Baltimore City Public School System (BCPSS).

Maintained by Eli Pousson. Last updated 1 years ago.

baltimore

59.9 match 3 stars 3.48 score 5 scripts

r-transit

tidytransit:Read, Validate, Analyze, and Map GTFS Feeds

Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <https://gtfs.org/>.

Maintained by Flavio Poletti. Last updated 1 months ago.

gtfs public public-transport tidyverse transit transit-data transport transportation

18.5 match 151 stars 10.47 score 272 scripts 1 dependents

immunomind

immunarch:Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq) and single-cell sequencing (scRNAseq). Immunarch implements most of the widely used AIRR analysis methods, such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor databases and clonotype tracking in vaccination and cancer studies. A successor to our previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.

Maintained by Vadim I. Nazarov. Last updated 12 months ago.

airr-analysis b-cell-receptor bcr bcr-repertoire bioinformatics ig ig-repertoire immune-repertoire immune-repertoire-analysis immune-repertoire-data immunoglobulin immunoinformatics immunology rep-seq repertoire-analysis single-cell single-cell-analysis t-cell-receptor tcr tcr-repertoire cpp

20.3 match 315 stars 9.49 score 203 scripts

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 11 months ago.

84.3 match 2.28 score 38 scripts

rempsyc

rempsyc:Convenience Functions for Psychology

Make your workflow faster and easier. Easily customizable plots (via 'ggplot2'), nice APA tables (following the style of the *American Psychological Association*) exportable to Word (via 'flextable'), easily run statistical tests or check assumptions, and automatize various other tasks.

Maintained by Rémi Thériault. Last updated 1 months ago.

convenience-functions ggplot2 psychology statistics visualization

17.3 match 43 stars 10.68 score 214 scripts 2 dependents

ctn-0094

public.ctn0094data:De-Identified Data from CTN-0094

These are harmonized datasets produced as part of the Clinical Trials Network (CTN) protocol number 0094. This is a US National Institute of Drug Abuse (NIDA) funded project; to learn more go to <https://ctnlibrary.org/protocol/ctn0094/>. These are datasets which have the data harmonized from CTN-0027 (<https://ctnlibrary.org/protocol/ctn0027/>), CTN-0030 (<https://ctnlibrary.org/protocol/ctn0030/>), and CTN-0051 (<https://ctnlibrary.org/protocol/ctn0051/>).

Maintained by Raymond Balise. Last updated 1 years ago.

37.5 match 4.86 score 24 scripts 1 dependents

ctn-0094

public.ctn0094extra:Helper Files for the CTN-0094 Relational Database

Engineered features and "helper" functions ancillary to the 'public.ctn0094data' package, extending this package for ease of use (see <https://CRAN.R-project.org/package=public.ctn0094data>). This 'public.ctn0094data' package contains harmonized datasets from some of the National Institute of Drug Abuse's Clinical Trials Network (NIDA's CTN) projects. Specifically, the CTN-0094 project is to harmonize and de-identify clinical trials data from the CTN-0027, CTN-0030, and CTN-51 studies for opioid use disorder. This current version is built from 'public.ctn0094data' v. 1.0.6.

Maintained by Gabriel Odom. Last updated 1 years ago.

38.5 match 3.88 score 15 scripts

public-health-scotland

phsmethods:Standard Methods for Use in Public Health Scotland

A collection of methods for commonly undertaken analytical tasks, primarily developed for Public Health Scotland (PHS) analysts, but the package is also generally useful to others working in the healthcare space, particularly since it has functions for working with Community Health Index (CHI) numbers. The package can help to make data manipulation and analysis more efficient and reproducible.

Maintained by Tina Fu. Last updated 4 months ago.

18.3 match 55 stars 7.71 score 85 scripts

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

17.8 match 96 stars 7.89 score 268 scripts 1 dependents

ropensci

europepmc:R Interface to the Europe PubMed Central RESTful Web Service

An R Client for the Europe PubMed Central RESTful Web Service (see <https://europepmc.org/RestfulWebService> for more information). It gives access to both metadata on life science literature and open access full texts. Europe PMC indexes all PubMed content and other literature sources including Agricola, a bibliographic database of citations to the agricultural literature, or Biological Patents. In addition to bibliographic metadata, the client allows users to fetch citations and reference lists. Links between life-science literature and other EBI databases, including ENA, PDB or ChEMBL are also accessible. No registration or API key is required. See the vignettes for usage examples.

Maintained by Najko Jahn. Last updated 1 years ago.

bibliometrics europe-pmc pubmed pubmedcentral scientific-literature scientific-publications

17.6 match 27 stars 7.94 score 122 scripts 2 dependents

yulab-smu

scholar:Analyse Citation Data from Google Scholar

Provides functions to extract citation data from Google Scholar. Convenience functions are also provided for comparing multiple scholars and predicting future h-index values.

Maintained by Guangchuang Yu. Last updated 1 years ago.

14.1 match 43 stars 9.63 score 468 scripts 3 dependents

massimoaria

dimensionsR:Gathering Bibliographic Records from 'Digital Science Dimensions' Using 'DSL' API

A set of tools to extract bibliographic content from 'Digital Science Dimensions' using 'DSL' API <https://www.dimensions.ai/dimensions-apis/>.

Maintained by Massimo Aria. Last updated 1 years ago.

bibliographic-database bibliography bibliometrics bibliometrix clinical-trials ds-dimensions dsl-api gathering-bibliographic-records grant grants grants-search patents policy-documents publications publications-search

17.5 match 42 stars 7.23 score 7 scripts 3 dependents

bioc

Maaslin2:"Multivariable Association Discovery in Population-scale Meta-omics Studies"

MaAsLin2 is comprehensive R package for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. MaAsLin2 is the next generation of MaAsLin.

Maintained by Lauren McIver. Last updated 5 months ago.

metagenomics software microbiome normalization biobakery bioconductor differential-abundance-analysis false-discovery-rate multiple-covariates public repeated-measures tools

11.0 match 133 stars 11.03 score 532 scripts 3 dependents

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 2 days ago.

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

11.8 match 44 stars 9.45 score 472 scripts

jhstaudacher

CoopGame:Important Concepts of Cooperative Game Theory

The theory of cooperative games with transferable utility offers useful insights into the way parties can share gains from cooperation and secure sustainable agreements, see e.g. one of the books by Chakravarty, Mitra and Sarkar (2015, ISBN:978-1107058798) or by Driessen (1988, ISBN:978-9027727299) for more details. A comprehensive set of tools for cooperative game theory with transferable utility is provided. Users can create special families of cooperative games, like e.g. bankruptcy games, cost sharing games and weighted voting games. There are functions to check various game properties and to compute five different set-valued solution concepts for cooperative games. A large number of point-valued solution concepts is available reflecting the diverse application areas of cooperative game theory. Some of these point-valued solution concepts can be used to analyze weighted voting games and measure the influence of individual voters within a voting body. There are routines for visualizing both set-valued and point-valued solutions in the case of three or four players.

Maintained by Jochen Staudacher. Last updated 4 years ago.

26.3 match 4.10 score 424 scripts 1 dependents

pablobarbera

Rfacebook:Access to Facebook API via R

Provides an interface to the Facebook API.

Maintained by Pablo Barbera. Last updated 5 years ago.

13.5 match 351 stars 7.75 score 268 scripts

ropensci

rcrossref:Client for Various 'CrossRef' 'APIs'

Client for various 'CrossRef' 'APIs', including 'metadata' search with their old and newer search 'APIs', get 'citations' in various formats (including 'bibtex', 'citeproc-json', 'rdf-xml', etc.), convert 'DOIs' to 'PMIDs', and 'vice versa', get citations for 'DOIs', and get links to full text of articles when available.

Maintained by Najko Jahn. Last updated 2 years ago.

text-ming literature pdf xml publications citations full-text tdm crossref api api-wrapper crossref-api doi metadata

10.0 match 172 stars 10.18 score 404 scripts 10 dependents

brownandcaldwell-public

tidywater:Water Quality Models for Drinking Water Treatment Processes

Provides multiple water chemistry-based models and published empirical models in one standard format. Functions can be chained together to model a complete treatment process and are designed to work in a 'tidyverse' workflow. Models are primarily based on these sources: Benjamin, M. M. (2002, ISBN:147862308X), Crittenden, J. C., Trussell, R., Hand, D., Howe, J. K., & Tchobanoglous, G., Borchardt, J. H. (2012, ISBN:9781118131473), USEPA. (2001) <https://www.epa.gov/sites/default/files/2017-03/documents/wtp_model_v._2.0_manual_508.pdf>.

Maintained by Sierra Johnson. Last updated 2 months ago.

15.0 match 11 stars 6.66 score 14 scripts

hannahcomiskey

mcmsupply:Estimating Public and Private Sector Contraceptive Market Supply Shares

Family Planning programs and initiatives typically use nationally representative surveys to estimate key indicators of a country’s family planning progress. However, in recent years, routinely collected family planning services data (Service Statistics) have been used as a supplementary data source to bridge gaps in the surveys. The use of service statistics comes with the caveat that adjustments need to be made for missing private sector contributions to the contraceptive method supply chain. Evaluating the supply source of modern contraceptives often relies on Demographic Health Surveys (DHS), where many countries do not have recent data beyond 2015/16. Fortunately, in the absence of recent surveys we can rely on statistical model-based estimates and projections to fill the knowledge gap. We present a Bayesian, hierarchical, penalized-spline model with multivariate-normal spline coefficients, to account for across method correlations, to produce country-specific,annual estimates for the proportion of modern contraceptive methods coming from the public and private sectors. This package provides a quick and convenient way for users to access the DHS modern contraceptive supply share data at national and subnational administration levels, estimate, evaluate and plot annual estimates with uncertainty for a sample of low- and middle-income countries. Methods for the estimation of method supply shares at the national level are described in Comiskey, Alkema, Cahill (2022) <arXiv:2212.03844>.

Maintained by Hannah Comiskey. Last updated 12 months ago.

jags cpp

19.3 match 2 stars 5.15 score 20 scripts

kassambara

ggpubr:'ggplot2' Based Publication Ready Plots

The 'ggplot2' package is excellent and flexible for elegant data visualization in R. However the default generated plots requires some formatting before we can send them for publication. Furthermore, to customize a 'ggplot', the syntax is opaque and this raises the level of difficulty for researchers with no advanced R programming skills. 'ggpubr' provides some easy-to-use functions for creating and customizing 'ggplot2'- based publication ready plots.

Maintained by Alboukadel Kassambara. Last updated 2 years ago.

5.8 match 1.2k stars 16.68 score 65k scripts 409 dependents

crunch-io

crunch:Crunch.io Data Tools

The Crunch.io service <https://crunch.io/> provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.

Maintained by Greg Freedman Ellis. Last updated 11 days ago.

9.1 match 9 stars 10.53 score 200 scripts 2 dependents

bioc

EnhancedVolcano:Publication-ready volcano plots with enhanced colouring and labeling

Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many point labels in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read. Other functionality allows the user to identify up to 4 different types of attributes in the same plot space via colour, shape, size, and shade parameter configurations.

Maintained by Kevin Blighe. Last updated 5 months ago.

rnaseq geneexpression transcription differentialexpression immunooncology

7.9 match 422 stars 11.68 score 2.7k scripts

enblacar

SCpubr:Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

A system that provides a streamlined way of generating publication ready plots for known Single-Cell transcriptomics data in a “publication ready” format. This is, the goal is to automatically generate plots with the highest quality possible, that can be used right away or with minimal modifications for a research article.

Maintained by Enrique Blanco-Carmona. Last updated 1 months ago.

software singlecell visualization data-visualization ggplot2 publication-quality-plots seurat single-cell single-cell-genomics single-cell-rna-seq

10.3 match 178 stars 8.71 score 194 scripts

bschneidr

svrep:Tools for Creating, Updating, and Analyzing Survey Replicate Weights

Provides tools for creating and working with survey replicate weights, extending functionality of the 'survey' package from Lumley (2004) <doi:10.18637/jss.v009.i08>. Implements bootstrap methods for complex surveys, including the generalized survey bootstrap as described by Beaumont and Patak (2012) <doi:10.1111/j.1751-5823.2011.00166.x>. Methods are provided for applying nonresponse adjustments to both full-sample and replicate weights as described by Rust and Rao (1996) <doi:10.1177/096228029600500305>. Implements methods for sample-based calibration described by Opsomer and Erciulescu (2021) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2021002/article/00006-eng.htm>. Diagnostic functions are included to compare weights and weighted estimates from different sets of replicate weights.

Maintained by Ben Schneider. Last updated 7 days ago.

10.8 match 8 stars 8.12 score 54 scripts 3 dependents

ropensci

sodium:A Modern and Easy-to-Use Crypto Library

Bindings to 'libsodium' <https://doc.libsodium.org/>: a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. Sodium uses curve25519, a state-of-the-art Diffie-Hellman function by Daniel Bernstein, which has become very popular after it was discovered that the NSA had backdoored Dual EC DRBG.

Maintained by Jeroen Ooms. Last updated 3 months ago.

libsodium

6.8 match 70 stars 12.43 score 175 scripts 103 dependents

fbartos

RoBMA:Robust Bayesian Meta-Analyses

A framework for estimating ensembles of meta-analytic and meta-regression models (assuming either presence or absence of the effect, heterogeneity, publication bias, and moderators). The RoBMA framework uses Bayesian model-averaging to combine the competing meta-analytic models into a model ensemble, weights the posterior parameter distributions based on posterior model probabilities and uses Bayes factors to test for the presence or absence of the individual components (e.g., effect vs. no effect; Bartoš et al., 2022, <doi:10.1002/jrsm.1594>; Maier, Bartoš & Wagenmakers, 2022, <doi:10.1037/met0000405>). Users can define a wide range of prior distributions for + the effect size, heterogeneity, publication bias (including selection models and PET-PEESE), and moderator components. The package provides convenient functions for summary, visualizations, and fit diagnostics.

Maintained by František Bartoš. Last updated 1 months ago.

meta-analysis model-averaging publication-bias jags openblas cpp

12.1 match 9 stars 6.97 score 53 scripts

ipeagit

gtfs2emis:Estimating Public Transport Emissions from General Transit Feed Specification (GTFS) Data

A bottom up model to estimate the emission levels of public transport systems based on General Transit Feed Specification (GTFS) data. The package requires two main inputs: i) Public transport data in the GTFS standard format; and ii) Some basic information on fleet characteristics such as fleet age, technology, fuel and Euro stage. As it stands, the package estimates several pollutants at high spatial and temporal resolutions. Pollution levels can be calculated for specific transport routes, trips, time of the day or for the transport system as a whole. The output with emission estimates can be extracted in different formats, supporting analysis on how emission levels vary across space, time and by fleet characteristics. A full description of the methods used in the 'gtfs2emis' model is presented in Vieira, J. P. B.; Pereira, R. H. M.; Andrade, P. R. (2022) <doi:10.31219/osf.io/8m2cy>.

Maintained by Joao Bazzo. Last updated 2 months ago.

emissions environmental-modelling gtfs public-transport rspatial transport

11.0 match 28 stars 7.47 score 29 scripts

ropensci

opentripplanner:Setup and connect to 'OpenTripPlanner'

Setup and connect to 'OpenTripPlanner' (OTP) <http://www.opentripplanner.org/>. OTP is an open source platform for multi-modal and multi-agency journey planning written in 'Java'. The package allows you to manage a local version or connect to remote OTP server to find walking, cycling, driving, or transit routes. This package has been peer-reviewed by rOpenSci (v. 0.2.0.0).

Maintained by Malcolm Morgan. Last updated 3 months ago.

data isochrones java opentripplanner otp public-transport routing transport transportation-planning

8.8 match 83 stars 8.94 score 147 scripts

openintrostat

openintro:Datasets and Supplemental Functions from 'OpenIntro' Textbooks and Labs

Supplemental functions and data for 'OpenIntro' resources, which includes open-source textbooks and resources for introductory statistics (<https://www.openintro.org/>). The package contains datasets used in our open-source textbooks along with custom plotting functions for reproducing book figures. Note that many functions and examples include color transparency; some plotting elements may not show up properly (or at all) when run in some versions of Windows operating system.

Maintained by Mine Çetinkaya-Rundel. Last updated 3 months ago.

data openintro

6.9 match 240 stars 11.39 score 6.0k scripts

ironholds

urltools:Vectorised Tools for URL Handling and Parsing

A toolkit for all URL-handling needs, including encoding and decoding, parsing, parameter extraction and modification. All functions are designed to be both fast and entirely vectorised. It is intended to be useful for people dealing with web-related datasets, such as server-side logs, although may be useful for other situations involving large sets of URLs.

Maintained by Os Keyes. Last updated 4 years ago.

access-logs data-import url cpp

5.9 match 131 stars 13.43 score 968 scripts 264 dependents

ropenspain

mapSpain:Administrative Boundaries of Spain

Administrative Boundaries of Spain at several levels (Autonomous Communities, Provinces, Municipalities) based on the 'GISCO' 'Eurostat' database <https://ec.europa.eu/eurostat/web/gisco> and 'CartoBase SIANE' from 'Instituto Geografico Nacional' <https://www.ign.es/>. It also provides a 'leaflet' plugin and the ability of downloading and processing static tiles.

Maintained by Diego Hernangómez. Last updated 1 months ago.

ropenspain tiles maps spatial municipalities spain gisco provinces ign administrative-boundaries ccaa static-tiles ggplot2 gis

8.8 match 42 stars 8.83 score 244 scripts 2 dependents

igorlaltuf

ispdata:Access Data from the Public Security Institute of the State of Rio De Janeiro

Allows access to data from the Rio de Janeiro Public Security Institute (ISP), such as criminal statistics, data on gun seizures and femicide. The package also contains the spatial data of Pacifying Police Units (UPPs) and Integrated Public Safety Regions, Areas and Circumscriptions.

Maintained by Igor Laltuf. Last updated 1 months ago.

22.1 match 4 stars 3.30 score 4 scripts

tagteam

Publish:Format Output of Various Routines in a Suitable Way for Reports and Publication

A bunch of convenience functions that transform the results of some basic statistical analyses into table format nearly ready for publication. This includes descriptive tables, tables of logistic regression and Cox regression results as well as forest plots.

Maintained by Thomas A. Gerds. Last updated 11 days ago.

7.2 match 15 stars 10.11 score 274 scripts 36 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

10.9 match 7 stars 6.53 score 48 scripts

lindbrook

cholera:Amend, Augment and Aid Analysis of John Snow's Cholera Map

Amends errors, augments data and aids analysis of John Snow's map of the 1854 London cholera outbreak.

Maintained by lindbrook. Last updated 1 days ago.

cholera data-visualization datasets epidemiology john-snow public-health triangulation-delaunay voronoi voronoi-polygons

7.5 match 136 stars 9.33 score 95 scripts

ipeagit

gtfstools:General Transit Feed Specification (GTFS) Editing and Analysing Tools

Utility functions to read, manipulate, analyse and write transit feeds in the General Transit Feed Specification (GTFS) data format.

Maintained by Daniel Herszenhut. Last updated 2 months ago.

gtfs public-transport publictransport cpp

7.5 match 40 stars 9.31 score 126 scripts 3 dependents

hrbrmstr

hrbrthemes:Additional Themes, Theme Components and Utilities for 'ggplot2'

A compilation of extra 'ggplot2' themes, scales and utilities, including a spell check function for plot label fields and an overall emphasis on typography. A copy of the 'Google' font 'Roboto Condensed' is also included.

Maintained by Bob Rudis. Last updated 2 days ago.

data-visualization datavisualization ggplot-extension ggplot2 ggplot2-scales ggplot2-themes visualization

5.0 match 1.3k stars 13.92 score 13k scripts 15 dependents

eblondel

geosapi:GeoServer REST API R Interface

Provides an R interface to the GeoServer REST API, allowing to upload and publish data in a GeoServer web-application and expose data to OGC Web-Services. The package currently supports all CRUD (Create,Read,Update,Delete) operations on GeoServer workspaces, namespaces, datastores (stores of vector data), featuretypes, layers, styles, as well as vector data upload operations. For more information about the GeoServer REST API, see <https://docs.geoserver.org/stable/en/user/rest/>.

Maintained by Emmanuel Blondel. Last updated 15 days ago.

api geoserver gis publication rest spatial

11.1 match 34 stars 6.23 score 33 scripts

rpolars

polars:Lightning-Fast 'DataFrame' Library

Lightning-fast 'DataFrame' library written in 'Rust'. Convert R data to 'Polars' data and vice versa. Perform fast, lazy, larger-than-memory and optimized data queries. 'Polars' is interoperable with the package 'arrow', as both are based on the 'Apache Arrow' Columnar Format.

Maintained by Soren Welling. Last updated 4 days ago.

arrow polars rust

5.8 match 499 stars 12.01 score 1.0k scripts 2 dependents

bioc

SC3:Single-Cell Consensus Clustering

A tool for unsupervised clustering and analysis of single cell RNA-Seq data.

Maintained by Vladimir Kiselev. Last updated 5 months ago.

immunooncology singlecell software classification clustering dimensionreduction supportvectormachine rnaseq visualization transcriptomics datarepresentation gui differentialexpression transcription bioconductor-package human-cell-atlas single-cell-rna-seq openblas cpp

6.6 match 122 stars 10.09 score 374 scripts 1 dependents

munterfi

hereR:'sf'-Based Interface to the 'HERE' REST APIs

Interface to the 'HERE' REST APIs <https://developer.here.com/develop/rest-apis>: (1) geocode and autosuggest addresses or reverse geocode POIs using the 'Geocoder' API; (2) route directions, travel distance or time matrices and isolines using the 'Routing', 'Matrix Routing' and 'Isoline Routing' APIs; (3) request real-time traffic flow and incident information from the 'Traffic' API; (4) find request public transport connections and nearby stations from the 'Public Transit' API; (5) request intermodal routes using the 'Intermodal Routing' API; (6) get weather forecasts, reports on current weather conditions, astronomical information and alerts at a specific location from the 'Destination Weather' API. Locations, routes and isolines are returned as 'sf' objects.

Maintained by Merlin Unterfinger. Last updated 24 days ago.

api geocoding gis here-technologies isoline routing rspatial traffic weather

7.7 match 90 stars 8.70 score 63 scripts

connordonegan

geostan:Bayesian Spatial Analysis

For spatial data analysis; provides exploratory spatial analysis tools, spatial regression, spatial econometric, and disease mapping models, model diagnostics, and special methods for inference with small area survey data (e.g., the America Community Survey (ACS)) and censored population health monitoring data. Models are pre-specified using the Stan programming language, a platform for Bayesian inference using Markov chain Monte Carlo (MCMC). References: Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>; Donegan (2021) <doi:10.31219/osf.io/3ey65>; Donegan (2022) <doi:10.21105/joss.04716>; Donegan, Chun and Hughes (2020) <doi:10.1016/j.spasta.2020.100450>; Donegan, Chun and Griffith (2021) <doi:10.3390/ijerph18136856>; Morris et al. (2019) <doi:10.1016/j.sste.2019.100301>.

Maintained by Connor Donegan. Last updated 3 months ago.

bayesian bayesian-inference bayesian-statistics epidemiology modeling public-health rspatial spatial stan cpp

7.5 match 80 stars 8.80 score 46 scripts

urbananalyst

gtfsrouter:Routing with 'GTFS' (General Transit Feed Specification) Data

Use 'GTFS' (General Transit Feed Specification) data for routing from nominated start and end stations, for extracting 'isochrones', and travel times from any nominated start station to all other stations.

Maintained by Mark Padgham. Last updated 28 days ago.

gtfs gtfsrouter public-transportation router cpp

7.5 match 89 stars 8.78 score 21 scripts 3 dependents

ropensci

gutenbergr:Download and Process Public Domain Works from Project Gutenberg

Download and process public domain works in the Project Gutenberg collection <https://www.gutenberg.org/>. Includes metadata for all Project Gutenberg works, so that they can be searched and retrieved.

Maintained by Jon Harmon. Last updated 2 months ago.

peer-reviewed

6.2 match 105 stars 10.50 score 1.1k scripts 1 dependents

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 9 days ago.

hades openjdk

6.0 match 190 stars 10.85 score 297 scripts

surgicalinformatics

encryptr:Easily Encrypt and Decrypt Data Frame/Tibble Columns or Files using RSA Public/Private Keys

It is important to ensure that sensitive data is protected. This straightforward package is aimed at the end-user. Strong RSA encryption using a public/private key pair is used to encrypt data frame or tibble columns. A public key can be shared to allow others to encrypt data to be sent to you. This is particularly aimed a healthcare settings so patient data can be pseudonymised.

Maintained by Ewen Harrison. Last updated 5 years ago.

13.5 match 92 stars 4.78 score 13 scripts

masiraji

tabledown:Create Publication Quality Tables and Plots

Create publication quality plots and tables for Item Response Theory and Classical Test theory based item analysis, exploratory and confirmatory factor analysis.

Maintained by Mushfiqul Anwar Siraji. Last updated 11 months ago.

psychology psychometrics table

18.6 match 6 stars 3.48 score 5 scripts

bernd-mueller

epos:Epilepsy Ontologies' Similarities

Analysis and visualization of similarities between epilepsy ontologies based on text mining results by comparing ranked lists of co-occurring drug terms in the BioASQ corpus. The ranked result lists of neurological drug terms co-occurring with terms from the epilepsy ontologies EpSO, ESSO, EPILONT, EPISEM and FENICS undergo further analysis. The source data to create the ranked lists of drug names is produced using the text mining workflows described in Mueller, Bernd and Hagelstein, Alexandra (2016) <doi:10.4126/FRL01-006408558>, Mueller, Bernd et al. (2017) <doi:10.1007/978-3-319-58694-6_22>, Mueller, Bernd and Rebholz-Schuhmann, Dietrich (2020) <doi:10.1007/978-3-030-43887-6_52>, and Mueller, Bernd et al. (2022) <doi:10.1186/s13326-021-00258-w>.

Maintained by Bernd Mueller. Last updated 1 years ago.

16.0 match 4.03 score 53 scripts

yelleknek

BUCSS:Bias and Uncertainty Corrected Sample Size

Bias- and Uncertainty-Corrected Sample Size. BUCSS implements a method of correcting for publication bias and uncertainty when planning sample sizes in a future study from an original study. See Anderson, Kelley, & Maxwell (2017; Psychological Science, 28, 1547-1562).

Maintained by Ken Kelley. Last updated 5 years ago.

18.0 match 3.51 score 32 scripts

neonscience

neonUtilities:Utilities for Working with NEON Data

NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org> or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.

Maintained by Claire Lunch. Last updated 1 months ago.

5.8 match 57 stars 10.66 score 944 scripts 15 dependents

ipeagit

gtfs2gps:Converting Transport Data from GTFS Format to GPS-Like Records

Convert general transit feed specification (GTFS) data to global positioning system (GPS) records in 'data.table' format. It also has some functions to subset GTFS data in time and space and to convert both representations to simple feature format.

Maintained by Pedro R. Andrade. Last updated 2 months ago.

gps-format gtfs gtfs-format public-transport rspatial transport cpp

7.5 match 73 stars 8.22 score 101 scripts 1 dependents

ouhscbbmc

Wats:Wrap Around Time Series Graphics

Wrap-around Time Series (WATS) plots for interrupted time series designs with seasonal patterns. Longitudinal trajectories are shown in both Cartesian and polar coordinates. In many scenarios, a WATS plot more clearly shows the existence and effect size of of an intervention. This package accompanies "Graphical Data Analysis on the Circle: Wrap-Around Time Series Plots for (Interrupted) Time Series Designs" by Rodgers, Beasley, & Schuelke (2014) <doi:10.1080/00273171.2014.946589>; see 'citation("Wats")' for details.

Maintained by Will Beasley. Last updated 20 days ago.

graphical-analysis oklahoma-city-bombing publication seasonal time-series

10.0 match 7 stars 6.14 score 44 scripts

bioc

MMUPHin:Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies

MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for: a) covariate-controlled batch- and cohort effect adjustment, b) meta-analysis differential abundance testing, c) meta-analysis unsupervised discrete structure (clustering) discovery, and d) meta-analysis unsupervised continuous structure discovery.

Maintained by Siyuan MA. Last updated 5 months ago.

metagenomics microbiome batcheffect

13.7 match 4.44 score 46 scripts

epiverse-trace

sivirep:Data Wrangling and Automated Reports from 'SIVIGILA' Source

Data wrangling, pre-processing, and generating automated reports from Colombia's epidemiological surveillance system, 'SIVIGILA' <https://portalsivigila.ins.gov.co/>. It provides a customizable R Markdown template for analysis and automatic generation of epidemiological reports that can be adapted to local, regional, and national contexts. This tool offers a standardized and reproducible workflow that helps to reduce manual labor and potential errors in report generation, improving their efficiency and consistency.

Maintained by Geraldine Gómez-Millán. Last updated 18 days ago.

colombia epidemiological-surveillance epiverse public-health

7.5 match 43 stars 8.04 score 21 scripts

lrberge

fixest:Fast Fixed-Effects Estimations

Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), generalized linear models (GLM) and the negative binomial. The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Berge (2018) <https://github.com/lrberge/fixest/blob/master/_DOCS/FENmlm_paper.pdf>. Further provides tools to export and view the results of several estimations with intuitive design to cluster the standard-errors.

Maintained by Laurent Berge. Last updated 7 months ago.

cpp openmp

4.0 match 387 stars 14.69 score 3.8k scripts 25 dependents

bioc

scmap:A tool for unsupervised projection of single cell RNA-seq data

Single-cell RNA-seq (scRNA-seq) is widely used to investigate the composition of complex tissues since the technology allows researchers to define cell-types using unsupervised clustering of the transcriptome. However, due to differences in experimental methods and computational analyses, it is often challenging to directly compare the cells identified in two different experiments. scmap is a method for projecting cells from a scRNA-seq experiment on to the cell-types or individual cells identified in a different experiment.

Maintained by Vladimir Kiselev. Last updated 5 months ago.

immunooncology singlecell software classification supportvectormachine rnaseq visualization transcriptomics datarepresentation transcription sequencing preprocessing geneexpression dataimport bioconductor-package human-cell-atlas projection-mapping single-cell-rna-seq openblas cpp

6.6 match 95 stars 8.82 score 172 scripts

hakeemwahab

cities:Clinical Trials with Intercurrent Events Simulator

Simulates clinical trials and summarizes causal effects and treatment policy estimands in the presence of intercurrent events in a transparent and intuitive manner.

Maintained by Ahmad Hakeem Abdul Wahab. Last updated 2 years ago.

22.0 match 1 stars 2.59 score 39 scripts

bnaras

homomorpheR:Homomorphic Computations in R

Homomorphic computations in R for privacy-preserving applications. Currently only the Paillier Scheme is implemented.

Maintained by Balasubramanian Narasimhan. Last updated 3 years ago.

9.8 match 4 stars 5.73 score 18 scripts 1 dependents

r-forge

sandwich:Robust Covariance Matrix Estimators

Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC) covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC) covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators); clustered covariances (one-way and multi-way); panel and panel-corrected covariances; outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted to other classes through S3 methods. Details can be found in Zeileis et al. (2020) <doi:10.18637/jss.v095.i01>, Zeileis (2004) <doi:10.18637/jss.v011.i10> and Zeileis (2006) <doi:10.18637/jss.v016.i09>.

Maintained by Achim Zeileis. Last updated 2 months ago.

3.8 match 14.92 score 11k scripts 887 dependents

easystats

report:Automated Reporting of Results and Statistical Models

The aim of the 'report' package is to bridge the gap between R’s output and the formatted results contained in your manuscript. This package converts statistical models and data frames into textual reports suited for publication, ensuring standardization and quality in results reporting.

Maintained by Rémi Thériault. Last updated 1 months ago.

anovas apa automated-report-generation automatic bayesian describe easystats hacktoberfest manuscript models report reporting reports scientific statsmodels

3.9 match 698 stars 14.48 score 1.1k scripts 3 dependents

idem-lab

conmat:Builds Contact Matrices using GAMs and Population Data

Builds contact matrices using GAMs and population data. This package incorporates data that is copyright Commonwealth of Australia (Australian Electoral Commission and Australian Bureau of Statistics) 2020.

Maintained by Nicholas Tierney. Last updated 7 days ago.

contact-matrices infectious-diseases population-data public-health

7.5 match 19 stars 7.21 score 47 scripts

cdcgov

surveytable:Formatted Survey Estimates

Short and understandable commands that generate tabulated, formatted, and rounded survey estimates. Mostly a wrapper for the 'survey' package (Lumley (2004) <doi:10.18637/jss.v009.i08> <https://CRAN.R-project.org/package=survey>) that identifies low-precision estimates using the National Center for Health Statistics (NCHS) presentation standards (Parker et al. (2017) <https://www.cdc.gov/nchs/data/series/sr_02/sr02_175.pdf>, Parker et al. (2023) <doi:10.15620/cdc:124368>).

Maintained by Alex Strashny. Last updated 4 days ago.

estimates formatted-output pretty-print survey tables

8.0 match 6 stars 6.71 score 19 scripts

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

10.6 match 30 stars 5.04 score 145 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

13.7 match 17 stars 3.85 score 14 scripts

lightbluetitan

ColombiAPI:Access Colombia's Public Data via API-Colombia

ColombiAPI provides a seamless interface to access diverse public data about Colombia through the API Colombia, a RESTful API. The package enables users to explore various aspects of Colombia, including general information, geography, and cultural insights. It includes five API-related functions to retrieve data on topics such as Colombia's general information, airports, departments, regions, and presidents. Additionally, ColombiAPI offers a built-in function to view the datasets available within the package. The package also includes curated datasets covering Bogota air stations, business and holiday dates, public schools, Colombian coffee exports, cannabis licenses, Medellin rainfall, and malls in Bogota, making it a comprehensive tool for exploring Colombia's data.

Maintained by Renzo Caceres Rossi. Last updated 2 months ago.

11.9 match 5 stars 4.40 score

connordonegan

surveil:Time Series Models for Disease Surveillance

Fits time trend models for routine disease surveillance tasks and returns probability distributions for a variety of quantities of interest, including age-standardized rates, period and cumulative percent change, and measures of health inequality. The models are appropriate for count data such as disease incidence and mortality data, employing a Poisson or binomial likelihood and the first-difference (random-walk) prior for unknown risk. Optionally add a covariance matrix for multiple, correlated time series models. Inference is completed using Markov chain Monte Carlo via the Stan modeling language. References: Donegan, Hughes, and Lee (2022) <doi:10.2196/34589>; Stan Development Team (2021) <https://mc-stan.org>; Theil (1972, ISBN:0-444-10378-3).

Maintained by Connor Donegan. Last updated 8 months ago.

bayesian-statistics cancer health-equity public-health rstan cpp

10.5 match 2 stars 4.98 score 12 scripts

gvegayon

googlePublicData:Working with Google's 'Public Data Explorer' DSPL Metadata Files

Provides a collection of functions to set up 'Google Public Data Explorer' <https://www.google.com/publicdata/> data visualization tool with your own data, building automatically the corresponding DataSet Publishing Language file, or DSPL (XML), metadata file jointly with the CSV files. All zip-up and ready to be published in 'Public Data Explorer'.

Maintained by George Vega Yon. Last updated 4 years ago.

dspl gapminder google google-public-data xml

13.7 match 8 stars 3.60 score 10 scripts

ropensci

DataSpaceR:Interface to 'the CAVD DataSpace'

Provides a convenient API interface to access immunological data within 'the CAVD DataSpace'(<https://dataspace.cavd.org>), a data sharing and discovery tool that facilitates exploration of HIV immunological data from pre-clinical and clinical HIV vaccine studies.

Maintained by Jason Taylor. Last updated 24 days ago.

cavd-dataspace

7.2 match 5 stars 6.72 score 42 scripts

vlyubchich

lawstat:Tools for Biostatistics, Public Policy, and Law

Statistical tests widely utilized in biostatistics, public policy, and law. Along with the well-known tests for equality of means and variances, randomness, and measures of relative variability, the package contains new robust tests of symmetry, omnibus and directional tests of normality, and their graphical counterparts such as robust QQ plot, robust trend tests for variances, etc. All implemented tests and methods are illustrated by simulations and real-life examples from legal statistics, economics, and biostatistics.

Maintained by Yulia R. Gel. Last updated 2 years ago.

6.8 match 7.17 score 484 scripts 6 dependents

topepo

AmesHousing:The Ames Iowa Housing Data

Raw and processed versions of the data from De Cock (2011) <http://ww2.amstat.org/publications/jse> are included in the package.

Maintained by Max Kuhn. Last updated 5 years ago.

6.5 match 14 stars 7.36 score 524 scripts 2 dependents

bioc

SurfR:Surface Protein Prediction and Identification

Identify Surface Protein coding genes from a list of candidates. Systematically download data from GEO and TCGA or use your own data. Perform DGE on bulk RNAseq data. Perform Meta-analysis. Descriptive enrichment analysis and plots.

Maintained by Aurora Maurizio. Last updated 2 days ago.

software sequencing rnaseq geneexpression transcription differentialexpression principalcomponent genesetenrichment pathways batcheffect functionalgenomics visualization dataimport functionalprediction geneprediction go dge enrichment-analysis metaanalysis plots proteins public-data surface surfaceome

8.8 match 3 stars 5.43 score 3 scripts

lazappi

doilinker:Link Preprints And Publications By DOI

Links preprints to publications using the method described in Cabanac G, Oikonomidi T, Boutron I. "Day-to-day discovery of preprint-publication links". Scientometrics. 2021;1–20. DOI: 10.1007/s11192-021-03900-7.

Maintained by Luke Zappia. Last updated 1 years ago.

doi preprint publication

13.9 match 5 stars 3.40 score 3 scripts

bioc

HuBMAPR:Interface to 'HuBMAP'

'HuBMAP' provides an open, global bio-molecular atlas of the human body at the cellular level. The `datasets()`, `samples()`, `donors()`, `publications()`, and `collections()` functions retrieves the information for each of these entity types. `*_details()` are available for individual entries of each entity type. `*_derived()` are available for retrieving derived datasets or samples for individual entries of each entity type. Data files can be accessed using `bulk_data_transfer()`.

Maintained by Christine Hou. Last updated 1 months ago.

software singlecell dataimport thirdpartyclient spatial infrastructure bioconductor-package client hubmap rstudio

8.0 match 3 stars 5.80 score 1 scripts

kwb-r

kwb.endnote:Helper Functions for Analysing KWB Endnote Library (Exported as .xml)

Helper Functions For Analysing KWB Endnote Library (Exported As .XML).

Maintained by Michael Rustler. Last updated 4 years ago.

endnote knowledge-repo literature-data-management project-fakin publication

15.4 match 3.00 score 2 scripts

guido-s

metasens:Statistical Methods for Sensitivity Analysis in Meta-Analysis

The following methods are implemented to evaluate how sensitive the results of a meta-analysis are to potential bias in meta-analysis and to support Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 5 'Small-Study Effects in Meta-Analysis': - Copas selection model described in Copas & Shi (2001) <DOI:10.1177/096228020101000402>; - limit meta-analysis by Rücker et al. (2011) <DOI:10.1093/biostatistics/kxq046>; - upper bound for outcome reporting bias by Copas & Jackson (2004) <DOI:10.1111/j.0006-341X.2004.00161.x>; - imputation methods for missing binary data by Gamble & Hollis (2005) <DOI:10.1016/j.jclinepi.2004.09.013> and Higgins et al. (2008) <DOI:10.1177/1740774508091600>; - LFK index test and Doi plot by Furuya-Kanamori et al. (2018) <DOI:10.1097/XEB.0000000000000141>.

Maintained by Guido Schwarzer. Last updated 13 hours ago.

adjustment meta-analysis publication-bias rstudio

7.5 match 8 stars 6.01 score 53 scripts

bioc

ReactomeGSA:Client for the Reactome Analysis Service for comparative multi-omics gene set analysis

The ReactomeGSA packages uses Reactome's online analysis service to perform a multi-omics gene set analysis. The main advantage of this package is, that the retrieved results can be visualized using REACTOME's powerful webapplication. Since Reactome's analysis service also uses R to perfrom the actual gene set analysis you will get similar results when using the same packages (such as limma and edgeR) locally. Therefore, if you only require a gene set analysis, different packages are more suited.

Maintained by Johannes Griss. Last updated 4 months ago.

genesetenrichment proteomics transcriptomics systemsbiology geneexpression reactome

5.6 match 23 stars 8.05 score 67 scripts

politicaargentina

opinAr:Argentina's Public Opinion Toolbox

A toolbox for working with public opinion data from Argentina. It facilitates access to microdata and the calculation of indicators of the Trust in Government Index (ICG), prepared by the Torcuato Di Tella University. Although we will try to document everything possible in English, by its very nature Spanish will be the main language. El paquete fue pensado como una caja de herramientas para el trabajo con datos de opinión pública de Argentina. El mismo facilita el acceso a los microdatos y el cálculos de indicadores del Índice de Confianza en el Gobierno (ICG), elaborado por la Universidad Torcuato Di Tella.

Maintained by Juan Pablo Ruiz Nicolini. Last updated 1 years ago.

argentina data political-science politics public-opinion

11.1 match 4.00 score

jameel-institute

daedalus:Model Health, Social, and Economic Costs of a Pandemic

Model the health, education, and economic costs of directly transmitted respiratory virus pandemics, under different scenarios of prior vaccine investment and reactive interventions, using the 'DAEDALUS' integrated health-economics model adapted from Haw et al. (2022) <doi.org/10.1038/s43588-022-00233-0>.

Maintained by Pratik Gupte. Last updated 7 days ago.

decision-support epidemiological-models health-economics pandemic-preparedness public-health rcpp sdg-3 cpp openmp

7.5 match 4 stars 5.92 score 8 scripts

prioritizr

prioritizr:Systematic Conservation Prioritization in R

Systematic conservation prioritization using mixed integer linear programming (MILP). It provides a flexible interface for building and solving conservation planning problems. Once built, conservation planning problems can be solved using a variety of commercial and open-source exact algorithm solvers. By using exact algorithm solvers, solutions can be generated that are guaranteed to be optimal (or within a pre-specified optimality gap). Furthermore, conservation problems can be constructed to optimize the spatial allocation of different management actions or zones, meaning that conservation practitioners can identify solutions that benefit multiple stakeholders. To solve large-scale or complex conservation planning problems, users should install the Gurobi optimization software (available from <https://www.gurobi.com/>) and the 'gurobi' R package (see Gurobi Installation Guide vignette for details). Users can also install the IBM CPLEX software (<https://www.ibm.com/products/ilog-cplex-optimization-studio/cplex-optimizer>) and the 'cplexAPI' R package (available at <https://github.com/cran/cplexAPI>). Additionally, the 'rcbc' R package (available at <https://github.com/dirkschumacher/rcbc>) can be used to generate solutions using the CBC optimization software (<https://github.com/coin-or/Cbc>). For further details, see Hanson et al. (2025) <doi:10.1111/cobi.14376>.

Maintained by Richard Schuster. Last updated 11 days ago.

biodiversity conservation conservation-planner optimization prioritization solver spatial cpp

3.8 match 124 stars 11.82 score 584 scripts 2 dependents

mlizhangx

NAIR:Network Analysis of Immune Repertoire

Pipelines for studying the adaptive immune repertoire of T cells and B cells via network analysis based on receptor sequence similarity. Relate clinical outcomes to immune repertoires based on their network properties, or to particular clusters and clones within a repertoire. Yang et al. (2023) <doi:10.3389/fimmu.2023.1181825>.

Maintained by Brian Neal. Last updated 2 months ago.

cpp openmp

6.4 match 7 stars 6.83 score 27 scripts

s-u

PKI:Public Key Infrastucture for R Based on the X.509 Standard

Public Key Infrastucture functions such as verifying certificates, RSA encription and signing which can be used to build PKI infrastructure and perform cryptographic tasks.

Maintained by Simon Urbanek. Last updated 7 months ago.

openssl

5.1 match 18 stars 8.52 score 63 scripts 8 dependents

r-forge

carData:Companion to Applied Regression Data Sets

Datasets to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage (2019).

Maintained by John Fox. Last updated 5 months ago.

3.5 match 12.41 score 944 scripts 919 dependents

paws-r

paws:Amazon Web Services Software Development Kit

Interface to Amazon Web Services <https://aws.amazon.com>, including storage, database, and compute services, such as 'Simple Storage Service' ('S3'), 'DynamoDB' 'NoSQL' database, and 'Lambda' functions-as-a-service.

Maintained by Dyfan Jones. Last updated 4 days ago.

aws aws-sdk

3.8 match 332 stars 11.25 score 177 scripts 12 dependents

svmiller

stevedata:Steve's Toy Data for Teaching About a Variety of Methodological, Social, and Political Topics

This is a collection of various kinds of data with broad uses for teaching. My students, and academics like me who teach the same topics I teach, should find this useful if their teaching workflow is also built around the R programming language. The applications are multiple but mostly cluster on topics of statistical methodology, international relations, and political economy.

Maintained by Steve Miller. Last updated 4 days ago.

7.1 match 8 stars 5.97 score 178 scripts

singmann

afex:Analysis of Factorial Experiments

Convenience functions for analyzing factorial experiments using ANOVA or mixed models. aov_ez(), aov_car(), and aov_4() allow specification of between, within (i.e., repeated-measures), or mixed (i.e., split-plot) ANOVAs for data in long format (i.e., one observation per row), automatically aggregating multiple observations per individual and cell of the design. mixed() fits mixed models using lme4::lmer() and computes p-values for all fixed effects using either Kenward-Roger or Satterthwaite approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex_plot() provides a high-level interface for interaction or one-way plots using ggplot2, combining raw data and model estimates. afex uses type 3 sums of squares as default (imitating commercial statistical software).

Maintained by Henrik Singmann. Last updated 7 months ago.

2.9 match 123 stars 14.50 score 1.4k scripts 15 dependents

friendly

vcdExtra:'vcd' Extensions and Additions

Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data and the 'gnm' package for Generalized Nonlinear Models. In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of 'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer.

Maintained by Michael Friendly. Last updated 5 months ago.

categorical-data-visualization generalized-linear-models mosaic-plots

4.0 match 24 stars 10.34 score 472 scripts 3 dependents

bioc

sevenbridges:Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R

R client and utilities for Seven Bridges platform API, from Cancer Genomics Cloud to other Seven Bridges supported platforms.

Maintained by Phil Webster. Last updated 5 months ago.

software dataimport thirdpartyclient api-client bioconductor bioinformatics cloud common-workflow-language sevenbridges

5.6 match 35 stars 7.40 score 24 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 6 days ago.

api dataset open-source public-api

7.5 match 34 stars 5.47 score 43 scripts

moderndive

moderndive:Tidyverse-Friendly Introductory Linear Regression

Datasets and wrapper functions for tidyverse-friendly introductory linear regression, used in "Statistical Inference via Data Science: A ModernDive into R and the Tidyverse" available at <https://moderndive.com/>.

Maintained by Albert Y. Kim. Last updated 3 months ago.

3.6 match 88 stars 11.35 score 1.8k scripts

lcef97

SchoolDataIT:Retrieve, Harmonise and Map Open Data Regarding the Italian School System

Compiles and displays the available data sets regarding the Italian school system, with a focus on the infrastructural aspects. Input datasets are downloaded from the web, with the aim of updating everything to real time. The functions are divided in four main modules, namely 'Get', to scrape raw data from the web 'Util', various utilities needed to process raw data 'Group', to aggregate data at the municipality or province level 'Map', to visualize the output datasets.

Maintained by Leonardo Cefalo. Last updated 2 months ago.

10.1 match 3.88 score

bioc

GWENA:Pipeline for augmented co-expression analysis

The development of high-throughput sequencing led to increased use of co-expression analysis to go beyong single feature (i.e. gene) focus. We propose GWENA (Gene Whole co-Expression Network Analysis) , a tool designed to perform gene co-expression network analysis and explore the results in a single pipeline. It includes functional enrichment of modules of co-expressed genes, phenotypcal association, topological analysis and comparison of networks configuration between conditions.

Maintained by Gwenaëlle Lemoine. Last updated 5 months ago.

software geneexpression network clustering graphandnetwork genesetenrichment pathways visualization rnaseq transcriptomics mrnamicroarray microarray networkenrichment sequencing go co-expression enrichment-analysis gene network-analysis pipeline

6.8 match 24 stars 5.76 score 12 scripts

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

cjvanlissa

tidySEM:Tidy Structural Equation Modeling

A tidy workflow for generating, estimating, reporting, and plotting structural equation models using 'lavaan', 'OpenMx', or 'Mplus'. Throughout this workflow, elements of syntax, results, and graphs are represented as 'tidy' data, making them easy to customize. Includes functionality to estimate latent class analyses, and to plot 'dagitty' and 'igraph' objects.

Maintained by Caspar J. van Lissa. Last updated 7 days ago.

3.5 match 58 stars 10.69 score 330 scripts 1 dependents

kwb-r

kwb.pkgbuild:R package for standardised development at KWB

Helper functions for automating R package development at KWB to a predefined style.

Maintained by Michael Rustler. Last updated 2 years ago.

automation best-practices project-fakin publication r-package-automation

10.0 match 2 stars 3.78 score 1 scripts 1 dependents

vincentarelbundock

modelsummary:Summary Tables and Plots for Statistical Models and Data: Beautiful, Customizable, and Publication-Ready

Create beautiful and customizable tables to summarize several statistical models side-by-side. Draw coefficient plots, multi-level cross-tabs, dataset summaries, balance tables (a.k.a. "Table 1s"), and correlation matrices. This package supports dozens of statistical models, and it can produce tables in HTML, LaTeX, Word, Markdown, PDF, PowerPoint, Excel, RTF, JPG, or PNG. Tables can easily be embedded in 'Rmarkdown' or 'knitr' dynamic documents. Details can be found in Arel-Bundock (2022) <doi:10.18637/jss.v103.i01>.

Maintained by Vincent Arel-Bundock. Last updated 15 days ago.

2.8 match 926 stars 13.41 score 6.2k scripts 2 dependents

dami82

easyPubMed:Search and Retrieve Scientific Publication Records from PubMed

Query NCBI Entrez and retrieve PubMed records in XML or text format. Process PubMed records by extracting and aggregating data from selected fields. A large number of records can be easily downloaded via this simple-to-use interface to the NCBI PubMed API.

Maintained by Damiano Fantini. Last updated 1 years ago.

4.7 match 21 stars 7.83 score 178 scripts 4 dependents

yaoxiangli

ggvolcano:Publication-Ready Volcano Plots

Provides publication-ready volcano plots for visualizing differential expression results, commonly used in RNA-seq and similar analyses. This tool helps create high-quality visual representations of data using the 'ggplot2' framework Wickham (2016) <doi:10.1007/978-3-319-24277-4>.

Maintained by Yaoxiang Li. Last updated 1 months ago.

8.4 match 4.32 score 42 scripts

selesnow

rtgstat:Client for 'TGStat API'

Allow function for using 'TGStat Stat API' and 'TGStat Search API', for more details see <https://api.tgstat.ru/docs/ru/start/intro.html>. 'TGStat' provide telegram channel analytics data.

Maintained by Alexey Seleznev. Last updated 5 months ago.

10.0 match 8 stars 3.60 score 3 scripts

dpagliaccio

scipub:Summarize Data for Scientific Publication

Create and format tables and APA statistics for scientific publication. This includes making a 'Table 1' to summarize demographics across groups, correlation tables with significance indicated by stars, and extracting formatted statistical summarizes from simple tests for in-text notation. The package also includes functions for Winsorizing data based on a Z-statistic cutoff.

Maintained by David Pagliaccio. Last updated 1 years ago.

10.5 match 2 stars 3.43 score 27 scripts

villegar

trainR:An Interface to the National Rail Enquiries Systems

The goal of 'trainR' is to provide a simple interface to the National Rail Enquiries (NRE) systems. There are few data feeds available, the simplest of them is Darwin, which provides real-time arrival and departure predictions, platform numbers, delay estimates, schedule changes and cancellations. Other data feeds provide historical data, Historic Service Performance (HSP), and much more. 'trainR' simplifies the data retrieval, so that the users can focus on their analyses. For more details visit <https://www.nationalrail.co.uk/46391.aspx>.

Maintained by Roberto Villegas-Diaz. Last updated 4 years ago.

national-rail national-rail-darwin national-rail-enquiries nre uk-railway uk-trains

9.9 match 8 stars 3.60 score 8 scripts

wahani

aoos:Another Object Orientation System

Another implementation of object-orientation in R. It provides syntactic sugar for the S4 class system and two alternative new implementations. One is an experimental version built around S4 and the other one makes it more convenient to work with lists as objects.

Maintained by Sebastian Warnholz. Last updated 8 years ago.

5.3 match 5 stars 6.66 score 17 scripts 6 dependents

cidm-ph

phylepic:Combined Visualisation of Phylogenetic and Epidemiological Data

A collection of utilities and 'ggplot2' extensions to assist with visualisations in genomic epidemiology. This includes the 'phylepic' chart, a visual combination of a phylogenetic tree and a matched epidemic curve. The included 'ggplot2' extensions such as date axes binned by week are relevant for other applications in epidemiology and beyond. The approach is described in Suster et al. (2024) <doi:10.1101/2024.04.02.24305229>.

Maintained by Carl Suster. Last updated 2 months ago.

genomics genomics-visualization public-health

7.5 match 4.65 score 4 scripts

r-forge

surveillance:Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

Statistical methods for the modeling and monitoring of time series of counts, proportions and categorical data, as well as for the modeling of continuous-time point processes of epidemic phenomena. The monitoring methods focus on aberration detection in count data time series from public health surveillance of communicable diseases, but applications could just as well originate from environmetrics, reliability engineering, econometrics, or social sciences. The package implements many typical outbreak detection procedures such as the (improved) Farrington algorithm, or the negative binomial GLR-CUSUM method of Hoehle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>. A novel CUSUM approach combining logistic and multinomial logistic modeling is also included. The package contains several real-world data sets, the ability to simulate outbreak data, and to visualize the results of the monitoring in a temporal, spatial or spatio-temporal fashion. A recent overview of the available monitoring procedures is given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>. For the retrospective analysis of epidemic spread, the package provides three endemic-epidemic modeling frameworks with tools for visualization, likelihood inference, and simulation. hhh4() estimates models for (multivariate) count time series following Paul and Held (2011) <doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>. twinSIR() models the susceptible-infectious-recovered (SIR) event history of a fixed population, e.g, epidemics across farms or networks, as a multivariate point process as proposed by Hoehle (2009) <doi:10.1002/bimj.200900050>. twinstim() estimates self-exciting point process models for a spatio-temporal point pattern of infective events, e.g., time-stamped geo-referenced surveillance data, as proposed by Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>. A recent overview of the implemented space-time modeling frameworks for epidemic phenomena is given by Meyer et al. (2017) <doi:10.18637/jss.v077.i11>.

Maintained by Sebastian Meyer. Last updated 2 days ago.

cpp

3.3 match 2 stars 10.68 score 446 scripts 3 dependents

javanderwal

readapra:Download and Tidy Data from the Australian Prudential Regulation Authority

Download the latest data from the Australian Prudential Regulation Authority <https://www.apra.gov.au/> and import it into R as a tidy data frame.

Maintained by Jarrod van der Wal. Last updated 22 days ago.

9.2 match 3.65 score

trinker

numform:Tools to Format Numbers for Publication

Format numbers and plots for publication; includes the removal of leading zeros, standardization of number of digits, addition of affixes, and a p-value formatter. These tools combine the functionality of several 'base' functions such as 'paste()', 'format()', and 'sprintf()' into specific use case functions that are named in a way that is consistent with usage, making their names easy to remember and easy to deploy.

Maintained by Tyler Rinker. Last updated 3 years ago.

number-formating

5.5 match 51 stars 6.06 score 151 scripts 1 dependents

jmanitz

NetOrigin:Origin Estimation for Propagation Processes on Complex Networks

Performs network-based source estimation. Different approaches are available: effective distance median, recursive backtracking, and centrality-based source estimation. Additionally, we provide public transportation network data as well as methods for data preparation, source estimation performance analysis and visualization.

Maintained by Juliane Manitz. Last updated 2 years ago.

12.2 match 2.74 score 11 scripts

nsaph-software

CausalGPS:Matching on Generalized Propensity Scores with Continuous Exposures

Provides a framework for estimating causal effects of a continuous exposure using observational data, and implementing matching and weighting on the generalized propensity score. Wu, X., Mealli, F., Kioumourtzoglou, M.A., Dominici, F. and Braun, D., 2022. Matching on generalized propensity scores with continuous exposures. Journal of the American Statistical Association, pp.1-29.

Maintained by Naeem Khoshnevis. Last updated 9 months ago.

cpp openmp

4.3 match 24 stars 7.67 score 39 scripts

bioc

singleCellTK:Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. SCTK allows users to seamlessly integrate tools from various packages at different stages of the analysis workflow. A general "a la carte" workflow gives users the ability access to multiple methods for data importing, calculation of general QC metrics, doublet detection, ambient RNA estimation and removal, filtering, normalization, batch correction or integration, dimensionality reduction, 2-D embedding, clustering, marker detection, differential expression, cell type labeling, pathway analysis, and data exporting. Curated workflows can be used to run Seurat and Celda. Streamlined quality control can be performed on the command line using the SCTK-QC pipeline. Users can analyze their data using commands in the R console or by using an interactive Shiny Graphical User Interface (GUI). Specific analyses or entire workflows can be summarized and shared with comprehensive HTML reports generated by Rmarkdown. Additional documentation and vignettes can be found at camplab.net/sctk.

Maintained by Joshua David Campbell. Last updated 24 days ago.

singlecell geneexpression differentialexpression alignment clustering immunooncology batcheffect normalization qualitycontrol dataimport gui

3.3 match 181 stars 10.16 score 252 scripts

omarwagih

ggseqlogo:A 'ggplot2' Extension for Drawing Publication-Ready Sequence Logos

The extensive range of functions provided by this package makes it possible to draw highly versatile sequence logos. Features include, but not limited to, modifying colour schemes and fonts used to draw the logo, generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other plots 'ggplot2' plots.

Maintained by Omar Wagih. Last updated 5 months ago.

2.9 match 211 stars 11.48 score 786 scripts 13 dependents

meirelesff

siconvr:Fetch Data from Plataforma +Brasil (SICONV)

Fetch data on targeted public investments from Plataforma +Brasil (SICONV) <http://plataformamaisbrasil.gov.br/>, the responsible system for requests, execution, and monitoring of federal discretionary transfers in Brazil.

Maintained by Fernando Meireles. Last updated 2 years ago.

brazil datasets plataforma-brasil public-data siconv

8.0 match 11 stars 4.04 score 4 scripts

umr-amap

AMAPVox:LiDAR Data Voxelisation

Read, manipulate and write voxel spaces. Voxel spaces are read from text-based output files of the 'AMAPVox' software. 'AMAPVox' is a LiDAR point cloud voxelisation software that aims at estimating leaf area through several theoretical/numerical approaches. See more in the article Vincent et al. (2017) <doi:10.23708/1AJNMP> and the technical note Vincent et al. (2021) <doi:10.23708/1AJNMP>.

Maintained by Philippe Verley. Last updated 2 months ago.

5.0 match 15 stars 6.35 score 12 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 8 months ago.

data-science public-health

7.5 match 1 stars 4.20 score 32 scripts

zsteinmetz

envalysis:Miscellaneous Functions for Environmental Analyses

Small toolbox for data analyses in environmental chemistry and ecotoxicology. Provides, for example, calibration() to calculate calibration curves and corresponding limits of detection (LODs) and limits of quantification (LOQs) according to German DIN 32645 (2008). texture() makes it easy to estimate soil particle size distributions from hydrometer measurements (ASTM D422-63, 2007).

Maintained by Zacharias Steinmetz. Last updated 5 months ago.

analytics chemistry ecotoxicology environment soil

5.0 match 8 stars 6.30 score 83 scripts

marcusyoung

otpr:An R Wrapper for the 'OpenTripPlanner' REST API

A wrapper for the 'OpenTripPlanner' <http://www.opentripplanner.org/> REST API. Queries are submitted to the relevant 'OpenTripPlanner' API resource, the response is parsed and useful R objects are returned.

Maintained by Marcus Young. Last updated 3 years ago.

access accessibility isochrones opentripplanner otp public-transport routing transport transport-api transportation-planning travel travel-planner travel-times

7.5 match 31 stars 4.19 score 10 scripts

nealrichardson

httptest:A Test Environment for HTTP Requests

Testing and documenting code that communicates with remote servers can be painful. Dealing with authentication, server state, and other complications can make testing seem too costly to bother with. But it doesn't need to be that hard. This package enables one to test all of the logic on the R sides of the API in your package without requiring access to the remote service. Importantly, it provides three contexts that mock the network connection in different ways, as well as testing functions to assert that HTTP requests were---or were not---made. It also allows one to safely record real API responses to use as test fixtures. The ability to save responses and load them offline also enables one to write vignettes and other dynamic documents that can be distributed without access to a live server.

Maintained by Neal Richardson. Last updated 1 years ago.

http mock test-framework

3.3 match 82 stars 9.47 score 276 scripts 1 dependents

bquast

HomomorphicEncryption:BFV, BGV, CKKS Schema for Fully Homomorphic Encryption

Implements the Brakerski-Fan-Vercauteren (BFV, 2012) <https://eprint.iacr.org/2012/144>, Brakerski-Gentry-Vaikuntanathan (BGV, 2014) <doi:10.1145/2633600>, and Cheon-Kim-Kim-Song (CKKS, 2016) <https://eprint.iacr.org/2016/421.pdf> schema for Fully Homomorphic Encryption. The included vignettes demonstrate the encryption procedures.

Maintained by Bastiaan Quast. Last updated 1 years ago.

5.6 match 1 stars 5.52 score 39 scripts

adriancorrendo

metrica:Prediction Performance Metrics

A compilation of more than 80 functions designed to quantitatively and visually evaluate prediction performance of regression (continuous variables) and classification (categorical variables) of point-forecast models (e.g. APSIM, DSSAT, DNDC, supervised Machine Learning). For regression, it includes functions to generate plots (scatter, tiles, density, & Bland-Altman plot), and to estimate error metrics (e.g. MBE, MAE, RMSE), error decomposition (e.g. lack of accuracy-precision), model efficiency (e.g. NSE, E1, KGE), indices of agreement (e.g. d, RAC), goodness of fit (e.g. r, R2), adjusted correlation coefficients (e.g. CCC, dcorr), symmetric regression coefficients (intercept, slope), and mean absolute scaled error (MASE) for time series predictions. For classification (binomial and multinomial), it offers functions to generate and plot confusion matrices, and to estimate performance metrics such as accuracy, precision, recall, specificity, F-score, Cohen's Kappa, G-mean, and many more. For more details visit the vignettes <https://adriancorrendo.github.io/metrica/>.

Maintained by Adrian A. Correndo. Last updated 9 months ago.

3.8 match 77 stars 8.18 score 49 scripts

ropensci

bikedata:Download and Aggregate Data from Public Hire Bicycle Systems

Download and aggregate data from all public hire bicycle systems which provide open data, currently including 'Santander' Cycles in London, U.K.; from the U.S.A., 'Ford GoBike' in San Francisco CA, 'citibike' in New York City NY, 'Divvy' in Chicago IL, 'Capital Bikeshare' in Washington DC, 'Hubway' in Boston MA, 'Metro' in Los Angeles LA, 'Indego' in Philadelphia PA, and 'Nice Ride' in Minnesota; 'Bixi' from Montreal, Canada; and 'mibici' from Guadalajara, Mexico.

Maintained by Mark Padgham. Last updated 1 years ago.

bicycle-hire-systems bike-hire-systems bike-hire bicycle-hire database bike-data peer-reviewed cpp

5.1 match 83 stars 5.97 score 28 scripts

ghislainv

hSDM:Hierarchical Bayesian Species Distribution Models

User-friendly and fast set of functions for estimating parameters of hierarchical Bayesian species distribution models (Latimer and others 2006 <doi:10.1890/04-0609>). Such models allow interpreting the observations (occurrence and abundance of a species) as a result of several hierarchical processes including ecological processes (habitat suitability, spatial dependence and anthropogenic disturbance) and observation processes (species detectability). Hierarchical species distribution models are essential for accurately characterizing the environmental response of species, predicting their probability of occurrence, and assessing uncertainty in the model results.

Maintained by Ghislain Vieilledent. Last updated 2 years ago.

gsl

5.0 match 9 stars 6.04 score 41 scripts

jfisher-usgs

inlpubs:USGS INL Project Office Publications

Contains bibliographic information for the U.S. Geological Survey (USGS) Idaho National Laboratory (INL) Project Office.

Maintained by Jason C. Fisher. Last updated 2 months ago.

15.0 match 2.00 score

adriancorrendo

soiltestcorr:Soil Test Correlation and Calibration

A compilation of functions designed to assist users on the correlation analysis of crop yield and soil test values. Functions to estimate crop response patterns to soil nutrient availability and critical soil test values using various approaches such as: 1) the modified arcsine-log calibration curve (Correndo et al. (2017) <doi:10.1071/CP16444>); 2) the graphical Cate-Nelson quadrants analysis (Cate & Nelson (1965)), 3) the statistical Cate-Nelson quadrants analysis (Cate & Nelson (1971) <doi:10.2136/sssaj1971.03615995003500040048x>), 4) the linear-plateau regression (Anderson & Nelson (1975) <doi:10.2307/2529422>), 5) the quadratic-plateau regression (Bullock & Bullock (1994) <doi:10.2134/agronj1994.00021962008600010033x>), and 6) the Mitscherlich-type exponential regression (Melsted & Peck (1977) <doi:10.2134/asaspecpub29.c1>). The package development stemmed from ongoing work with the Fertilizer Recommendation Support Tool (FRST) and Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification (SIIL) projects.

Maintained by Adrian A. Correndo. Last updated 9 months ago.

5.0 match 7 stars 6.04 score 31 scripts

tlverse

sl3:Pipelines for Machine Learning and Super Learning

A modern implementation of the Super Learner prediction algorithm, coupled with a general purpose framework for composing arbitrary pipelines for machine learning tasks.

Maintained by Jeremy Coyle. Last updated 4 months ago.

data-science ensemble-learning ensemble-model machine-learning model-selection regression stacking statistics

3.0 match 100 stars 9.94 score 748 scripts 7 dependents

alanarnholt

BSDA:Basic Statistics and Data Analysis

Data sets for book "Basic Statistics and Data Analysis" by Larry J. Kitchens.

Maintained by Alan T. Arnholt. Last updated 2 years ago.

3.3 match 7 stars 9.11 score 1.3k scripts 6 dependents

erictleung

pixarfilms:Pixar Films and Achievements

Data about Disney Pixar films provided by Wikipedia. This package contains data about the films, the people involved, and their awards.

Maintained by Eric Leung. Last updated 1 days ago.

data data-science datapackage disney imdb imdb-dataset pixar pixar-films web-scraping wikipedia

4.0 match 20 stars 7.42 score 23 scripts 1 dependents

centerforassessment

SGP:Student Growth Percentiles & Percentile Growth Trajectories

An analytic framework for the calculation of norm- and criterion-referenced academic growth estimates using large scale, longitudinal education assessment data as developed in Betebenner (2009) <doi:10.1111/j.1745-3992.2009.00161.x>.

Maintained by Damian W. Betebenner. Last updated 2 months ago.

percentile-growth-projections quantile-regression sgp sgp-analyses student-growth-percentiles student-growth-projections

3.0 match 20 stars 9.69 score 88 scripts

charlie86

spotifyr:R Wrapper for the 'Spotify' Web API

An R wrapper for pulling data from the 'Spotify' Web API <https://developer.spotify.com/documentation/web-api/> in bulk, or post items on a 'Spotify' user's playlist.

Maintained by Daniel Antal. Last updated 5 months ago.

music-information-retrieval spotify

3.4 match 374 stars 8.54 score 936 scripts

uclahs-cds

BoutrosLab.plotting.general:Functions to Create Publication-Quality Plots

Contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in the creation of these plots. These functions will give users great ease of use and customization options in broad use for biomedical applications, as well as general purpose plotting. Each of the functions also provides valid default settings to make plotting data more efficient and producing high quality plots with standard colour schemes simpler. All functions within this package are capable of producing plots that are of the quality to be presented in scientific publications and journals. P'ng et al.; BPG: Seamless, automated and interactive visualization of scientific data; BMC Bioinformatics 2019 <doi:10.1186/s12859-019-2610-2>.

Maintained by Paul Boutros. Last updated 5 months ago.

3.5 match 12 stars 8.36 score 414 scripts 6 dependents

abielr

pdfetch:Fetch Economic and Financial Time Series Data from Public Sources

Download economic and financial time series from public sources, including the St Louis Fed's FRED system, Yahoo Finance, the US Bureau of Labor Statistics, the US Energy Information Administration, the World Bank, Eurostat, the European Central Bank, the Bank of England, the UK's Office of National Statistics, Deutsche Bundesbank, and INSEE.

Maintained by Abiel Reinhart. Last updated 3 months ago.

5.0 match 16 stars 5.80 score 113 scripts

ukhsa-collaboration

PHEindicatormethods:Common Public Health Statistics and their Confidence Intervals

Functions to calculate commonly used public health statistics and their confidence intervals using methods approved for use in the production of Public Health England indicators such as those presented via Fingertips (<https://fingertips.phe.org.uk/>). It provides functions for the generation of proportions, crude rates, means, directly standardised rates, indirectly standardised rates, standardised mortality ratios, slope and relative index of inequality and life expectancy. Statistical methods are referenced in the following publications. Breslow NE, Day NE (1987) <doi:10.1002/sim.4780080614>. Dobson et al (1991) <doi:10.1002/sim.4780100317>. Armitage P, Berry G (2002) <doi:10.1002/9780470773666>. Wilson EB. (1927) <doi:10.1080/01621459.1927.10502953>. Altman DG et al (2000, ISBN: 978-0-727-91375-3). Chiang CL. (1968, ISBN: 978-0-882-75200-6). Newell C. (1994, ISBN: 978-0-898-62451-9). Eayres DP, Williams ES (2004) <doi:10.1136/jech.2003.009654>. Silcocks PBS et al (2001) <doi:10.1136/jech.55.1.38>. Low and Low (2004) <doi:10.1093/pubmed/fdh175>. Fingertips Public Health Technical Guide: <https://fingertips.phe.org.uk/static-reports/public-health-technical-guidance/>.

Maintained by Georgina Anderson. Last updated 3 months ago.

3.9 match 27 stars 7.41 score 80 scripts

liuyanguu

SHAPforxgboost:SHAP Plots for 'XGBoost'

Aid in visual data investigations using SHAP (SHapley Additive exPlanation) visualization plots for 'XGBoost' and 'LightGBM'. It provides summary plot, dependence plot, interaction plot, and force plot and relies on the SHAP implementation provided by 'XGBoost' and 'LightGBM'. Please refer to 'slundberg/shap' for the original implementation of SHAP in 'Python'.

Maintained by Yang Liu. Last updated 12 months ago.

3.3 match 110 stars 8.86 score 284 scripts 1 dependents

indrajeetpatil

ggstatsplot:'ggplot2' Based Plots with Statistical Details

Extension of 'ggplot2', 'ggstatsplot' creates graphics with details from statistical tests included in the plots themselves. It provides an easier syntax to generate information-rich plots for statistical analysis of continuous (violin plots, scatterplots, histograms, dot plots, dot-and-whisker plots) or categorical (pie and bar charts) data. Currently, it supports the most common types of statistical approaches and tests: parametric, nonparametric, robust, and Bayesian versions of t-test/ANOVA, correlation analyses, contingency table analysis, meta-analysis, and regression analyses. References: Patil (2021) <doi:10.21105/joss.03236>.

Maintained by Indrajeet Patil. Last updated 20 days ago.

bayes-factors datascience dataviz effect-size ggplot-extension hypothesis-testing non-parametric-statistics regression-models statistical-analysis

2.0 match 2.1k stars 14.49 score 3.0k scripts 1 dependents

fsolt

DCPO:Dynamic Comparative Public Opinion

Estimates latent variables of public opinion cross-nationally and over time from sparse and incomparable survey data. 'DCPO' uses a population-level graded response model with country-specific item bias terms. Sampling is conducted with 'Stan'. References: Solt (2020) <doi:10.31235/osf.io/d5n9p>.

Maintained by Frederick Solt. Last updated 1 years ago.

cpp

7.2 match 8 stars 3.98 score 24 scripts

algorithmiaio

algorithmia:Allows you to Easily Interact with the Algorithmia Platform

The company, Algorithmia, houses the largest marketplace of online algorithms. This package essentially holds a bunch of REST wrappers that make it very easy to call algorithms in the Algorithmia platform and access files and directories in the Algorithmia data API. To learn more about the services they offer and the algorithms in the platform visit <http://algorithmia.com>. More information for developers can be found at <https://algorithmia.com/developers>.

Maintained by Robert Fulton. Last updated 4 years ago.

4.8 match 14 stars 6.00 score 36 scripts

derekbeaton

prettyGraphs:Publication-Quality Graphics

Simple and crisp publication-quality graphics for the ExPosition family of packages. See An ExPosition of the Singular Value Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.

Maintained by Derek Beaton. Last updated 1 years ago.

5.7 match 4 stars 4.99 score 41 scripts 10 dependents

jonasmoss

publipha:Bayesian Meta-Analysis with Publications Bias and P-Hacking

Tools for Bayesian estimation of meta-analysis models that account for publications bias or p-hacking. For publication bias, this package implements a variant of the p-value based selection model of Hedges (1992) <doi:10.1214/ss/1177011364> with discrete selection probabilities. It also implements the mixture of truncated normals model for p-hacking described in Moss and De Bin (2019) <arXiv:1911.12445>.

Maintained by Jonas Moss. Last updated 2 years ago.

cpp

8.9 match 3 stars 3.18 score 3 scripts

ropensci

redland:RDF Library Bindings in R

Provides methods to parse, query and serialize information stored in the Resource Description Framework (RDF). RDF is described at <https://www.w3.org/TR/rdf-primer/>. This package supports RDF by implementing an R interface to the Redland RDF C library, described at <https://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph consisting of Statements composed of Subject, Predicate, and Object Nodes.

Maintained by Matthew B. Jones. Last updated 1 years ago.

redland

3.6 match 17 stars 7.85 score 98 scripts 13 dependents

r-forge

genoPlotR:Plot Publication-Grade Gene and Genome Maps

Draws gene or genome maps and comparisons between these, in a publication-grade manner. Starting from simple, common files, it will draw postscript or PDF files that can be sent as such to journals.

Maintained by Lionel Guy. Last updated 4 years ago.

5.2 match 5.33 score 106 scripts

k5cents

metro:Washington Metropolitan Area Transit Authority API

The Washington Metropolitan Area Transit Authority is a government agency operating light rail and passenger buses in the Washington D.C. area. With a free developer account, access their 'Metro Transparent Data Sets API' <https://developer.wmata.com/> to return data frames of transit data for easy analysis.

Maintained by Kiernan Nicholls. Last updated 1 years ago.

metro public-transportation transit-data washington-dc wmata wmata-api

7.5 match 4 stars 3.60 score 7 scripts

lenz99

incubate:Parametric Time-to-Event Analysis with Variable Incubation Phases

Fit parametric models for time-to-event data that show an initial 'incubation period', i.e., a variable delay phase where the hazard is zero. The delayed Weibull distribution serves as foundational data model. The specific method of 'MPSE' (maximum product of spacings estimation) and MLE-based methods are used for parameter estimation. Bootstrap confidence intervals for parameters and significance tests in a two group setting are provided.

Maintained by Matthias Kuhn. Last updated 7 months ago.

9.0 match 3.00 score

kwb-r

kwb.twitter:Simplify Access to Twitter Messages

Simplify access to Twitter messages.

Maintained by Hauke Sonnenberg. Last updated 3 years ago.

knowledge-repo project-fakin publication social-network twitter

10.0 match 2.70 score

kwb-r

kwb.pkgstatus:R package for checking KWB package status

R package for checking KWB package status (e.g. generating https://kwb-r.github.io/status).

Maintained by Michael Rustler. Last updated 12 months ago.

data-management project-fakin publication

10.0 match 2.70 score 1 scripts

rfhb

ctrdata:Retrieve and Analyze Clinical Trials Data from Public Registers

A system for querying, retrieving and analyzing protocol- and results-related information on clinical trials from four public registers, the 'European Union Clinical Trials Register' ('EUCTR', <https://www.clinicaltrialsregister.eu/>), 'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also translating queries the retired classic interface), the 'ISRCTN' (<http://www.isrctn.com/>) and the 'European Union Clinical Trials Information System' ('CTIS', <https://euclinicaltrials.eu/>). Trial information is downloaded, converted and stored in a database ('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi'). Protocols, statistical analysis plans, informed consent sheets and other documents in registers associated with trials can also be downloaded. Other functions implement trial concepts canonically across registers, identify deduplicated records, easily find and extract variables (fields) of interest even from complex nested data as used by the registers, merge variables and update queries. The package can be used for monitoring, meta- and trend-analysis of the design and conduct as well as of the results of clinical trials across registers.

Maintained by Ralf Herold. Last updated 12 hours ago.

clinical-data clinical-research clinical-studies clinical-trials ctgov database duckdb mongodb nodbi postgresql register sqlite studies trial

3.4 match 45 stars 7.92 score 32 scripts

nickreich

coarseDataTools:Analysis of Coarsely Observed Data

Functions to analyze coarse data. Specifically, it contains functions to (1) fit parametric accelerated failure time models to interval-censored survival time data, and (2) estimate the case-fatality ratio in scenarios with under-reporting. This package's development was motivated by applications to infectious disease: in particular, problems with estimating the incubation period and the case fatality ratio of a given disease. Sample data files are included in the package. See Reich et al. (2009) <doi:10.1002/sim.3659>, Reich et al. (2012) <doi:10.1111/j.1541-0420.2011.01709.x>, and Lessler et al. (2009) <doi:10.1016/S1473-3099(09)70069-6>.

Maintained by Nicholas G. Reich. Last updated 2 years ago.

3.3 match 9 stars 8.07 score 37 scripts 8 dependents

edwbaker

sonicscrewdriver:Bioacoustic Analysis and Publication Tools

Provides tools for manipulating sound files for bioacoustic analysis, and preparing analyses these for publication. The package validates that values are physically possible wherever feasible.

Maintained by Ed Baker. Last updated 1 months ago.

bioacoustics ecoacoustics

3.7 match 6 stars 7.12 score 26 scripts

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 1 days ago.

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

2.7 match 152 stars 9.73 score 235 scripts

bioc

GenomicSuperSignature:Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

This package provides a novel method for interpreting new transcriptomic datasets through near-instantaneous comparison to public archives without high-performance computing requirements. Through the pre-computed index, users can identify public resources associated with their dataset such as gene sets, MeSH term, and publication. Functions to identify interpretable annotations and intuitive visualization options are implemented in this package.

Maintained by Sehyun Oh. Last updated 5 months ago.

transcriptomics systemsbiology principalcomponent rnaseq sequencing pathways clustering bioconductor-package exploratory-data-analysis gsea mesh principal-component-analysis rna-sequencing-profiles transferlearning

3.7 match 16 stars 6.97 score 59 scripts

ropensci

rb3:Download and Parse Public Data Released by B3 Exchange

Download and parse public files released by B3 and convert them into useful formats and data structures common to data analysis practitioners.

Maintained by Wilson Freitas. Last updated 16 days ago.

brazil exchange-data finance financial-data financial-services market-data

3.4 match 74 stars 7.63 score 48 scripts

svmiller

stevemisc:Steve's Miscellaneous Functions

These are miscellaneous functions that I find useful for my research and teaching. The contents include themes for plots, functions for simulating quantities of interest from regression models, functions for simulating various forms of fake data for instructional/research purposes, and many more. All told, the functions provided here are broadly useful for data organization, data presentation, data recoding, and data simulation.

Maintained by Steve Miller. Last updated 6 days ago.

dplyr mixed-effects-models multivariate-normal-distribution tidyverse

3.8 match 10 stars 6.85 score 392 scripts 2 dependents

bioc

AnnotationHubData:Transform public data resources into Bioconductor Data Structures

These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.

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

dataimport

5.1 match 5.02 score 22 scripts 4 dependents

gaborcsardi

secret:Share Sensitive Information in R Packages

Allow sharing sensitive information, for example passwords, 'API' keys, etc., in R packages, using public key cryptography.

Maintained by Gábor Csárdi. Last updated 5 years ago.

4.0 match 103 stars 6.31 score 50 scripts

bioc

cardelino:Clone Identification from Single Cell Data

Methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stochastic dropout events as well as systematic allelic imbalance is used.

Maintained by Davis McCarthy. Last updated 5 months ago.

singlecell rnaseq visualization transcriptomics geneexpression sequencing software exomeseq clonal-clustering gibbs-sampling scrna-seq single-cell somatic-mutations

3.6 match 61 stars 7.05 score 62 scripts

ropengov

federalregister:Client Package for the U.S. Federal Register API

Access data from the Federal Register API <https://www.federalregister.gov/developers/api/v1>.

Maintained by Thomas J. Leeper. Last updated 4 days ago.

5.6 match 16 stars 4.51 score

tidyverts

tsibble:Tidy Temporal Data Frames and Tools

Provides a 'tbl_ts' class (the 'tsibble') for temporal data in an data- and model-oriented format. The 'tsibble' provides tools to easily manipulate and analyse temporal data, such as filling in time gaps and aggregating over calendar periods.

Maintained by Earo Wang. Last updated 2 months ago.

1.8 match 538 stars 14.47 score 4.4k scripts 42 dependents

gesistsa

adaR:A Fast 'WHATWG' Compliant URL Parser

A wrapper for 'ada-url', a 'WHATWG' compliant and fast URL parser written in modern 'C++'. Also contains auxiliary functions such as a public suffix extractor.

Maintained by David Schoch. Last updated 25 days ago.

url-parser cpp

3.6 match 27 stars 6.95 score 11 scripts 2 dependents

uribo

zipangu:Japanese Utility Functions and Data

Some data treated by the Japanese R user require unique operations and processing. These are caused by address, Kanji, and traditional year representations. 'zipangu' transforms specific to Japan into something more general one.

Maintained by Shinya Uryu. Last updated 4 months ago.

3.9 match 56 stars 6.38 score 41 scripts 1 dependents

project-gen3sis

gen3sis:General Engine for Eco-Evolutionary Simulations

Contains an engine for spatially-explicit eco-evolutionary mechanistic models with a modular implementation and several support functions. It allows exploring the consequences of ecological and macroevolutionary processes across realistic or theoretical spatio-temporal landscapes on biodiversity patterns as a general term. Reference: Oskar Hagen, Benjamin Flueck, Fabian Fopp, Juliano S. Cabral, Florian Hartig, Mikael Pontarp, Thiago F. Rangel, Loic Pellissier (2021) "gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth's biodiversity" <doi:10.1371/journal.pbio.3001340>.

Maintained by Oskar Hagen. Last updated 1 years ago.

biodiversity ecology evolution mechanistic model modeling simulation cpp

3.3 match 29 stars 7.56 score 69 scripts

mathurlabstanford

multibiasmeta:Sensitivity Analysis for Multiple Biases in Meta-Analyses

Meta-analyses can be compromised by studies' internal biases (e.g., confounding in nonrandomized studies) as well as by publication bias. This package conducts sensitivity analyses for the joint effects of these biases (per Mathur (2022) <doi:10.31219/osf.io/u7vcb>). These sensitivity analyses address two questions: (1) For a given severity of internal bias across studies and of publication bias, how much could the results change?; and (2) For a given severity of publication bias, how severe would internal bias have to be, hypothetically, to attenuate the results to the null or by a given amount?

Maintained by Peter Solymos. Last updated 2 years ago.

6.1 match 4.00 score 6 scripts

crew102

slowraker:A Slow Version of the Rapid Automatic Keyword Extraction (RAKE) Algorithm

A mostly pure-R implementation of the RAKE algorithm (Rose, S., Engel, D., Cramer, N. and Cowley, W. (2010) <doi:10.1002/9780470689646.ch1>), which can be used to extract keywords from documents without any training data.

Maintained by Christopher Baker. Last updated 7 months ago.

openjdk

4.5 match 6 stars 5.37 score 13 scripts 1 dependents

parklab

Nozzle.R1:Nozzle Reports

The Nozzle package provides an API to generate HTML reports with dynamic user interface elements based on JavaScript and CSS (Cascading Style Sheets). Nozzle was designed to facilitate summarization and rapid browsing of complex results in data analysis pipelines where multiple analyses are performed frequently on big data sets. The package can be applied to any project where user-friendly reports need to be created.

Maintained by Nils Gehlenborg. Last updated 10 years ago.

gehlenborglab html-report reproducible-research

4.5 match 68 stars 5.31 score 10 scripts 2 dependents

frankkramer-lab

mully:Create, Modify and Visualize Multi-Layered Networks

Allows the user to create graphs with multiple layers. The user can also modify the layers, the nodes, and the edges. The graph can also be visualized. Zaynab Hammoud and Frank Kramer (2018) <doi:10.3390/genes9110519>. More about multilayered graphs and their usage can be found in our review paper: Zaynab Hammoud and Frank Kramer (2020) <doi:10.1186/s41044-020-00046-0>.

Maintained by Zaynab Hammoud. Last updated 2 years ago.

big-networks data-visualization graph-theory graphs igraph multilayer-networks node-colored-graphs

4.0 match 45 stars 5.95 score 6 scripts

rstudio

keras3:R Interface to 'Keras'

Interface to 'Keras' <https://keras.io>, a high-level neural networks API. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both CPU and GPU devices.

Maintained by Tomasz Kalinowski. Last updated 4 days ago.

1.8 match 845 stars 13.57 score 264 scripts 2 dependents

walkerke

tidycensus:Load US Census Boundary and Attribute Data as 'tidyverse' and 'sf'-Ready Data Frames

An integrated R interface to several United States Census Bureau APIs (<https://www.census.gov/data/developers/data-sets.html>) and the US Census Bureau's geographic boundary files. Allows R users to return Census and ACS data as tidyverse-ready data frames, and optionally returns a list-column with feature geometry for mapping and spatial analysis.

Maintained by Kyle Walker. Last updated 2 months ago.

1.7 match 647 stars 14.27 score 7.5k scripts 10 dependents

massimoaria

bibliometrix:Comprehensive Science Mapping Analysis

Tool for quantitative research in scientometrics and bibliometrics. It implements the comprehensive workflow for science mapping analysis proposed in Aria M. and Cuccurullo C. (2017) <doi:10.1016/j.joi.2017.08.007>. 'bibliometrix' provides various routines for importing bibliographic data from 'SCOPUS', 'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions' (<https://www.dimensions.ai/>), 'OpenAlex' (<https://openalex.org/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>), and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis and building networks for co-citation, coupling, scientific collaboration and co-word analysis.

Maintained by Massimo Aria. Last updated 8 days ago.

bibliometric-analysis bibliometrics citation citation-network citations co-authors co-occurence co-word-analysis correspondence-analysis coupling isi-web journal manuscript quantitative-analysis scholars science science-mapping scientific scientometrics scopus

1.9 match 545 stars 12.54 score 518 scripts 2 dependents

nlsy-links

NlsyLinks:Utilities and Kinship Information for Research with the NLSY

Utilities and kinship information for behavior genetics and developmental research using the National Longitudinal Survey of Youth (NLSY; <https://www.nlsinfo.org/>).

Maintained by S. Mason Garrison. Last updated 8 days ago.

behavior-genetics kinship-information national-longitudinal-survey nlsy

3.1 match 7 stars 7.49 score 185 scripts

ropensci

deposits:A universal client for depositing and accessing research data anywhere

A universal client for depositing and accessing research data anywhere. Currently supported services are zenodo and figshare.

Maintained by Mark Padgham. Last updated 6 months ago.

3.8 match 39 stars 6.21 score 8 scripts 2 dependents

bioc

genefu:Computation of Gene Expression-Based Signatures in Breast Cancer

This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.

Maintained by Benjamin Haibe-Kains. Last updated 4 months ago.

differentialexpression geneexpression visualization clustering classification

3.1 match 7.42 score 193 scripts 3 dependents

ropensci

ritis:Integrated Taxonomic Information System Client

An interface to the Integrated Taxonomic Information System ('ITIS') (<https://www.itis.gov>). Includes functions to work with the 'ITIS' REST API methods (<https://www.itis.gov/ws_description.html>), as well as the 'Solr' web service (<https://www.itis.gov/solr_documentation.html>).

Maintained by Julia Blum. Last updated 1 months ago.

taxonomy biology nomenclature json api web api-client identifiers species names api-wrapper itis taxize

3.0 match 16 stars 7.72 score 64 scripts 24 dependents

best-practice-and-impact

aftables:Create Spreadsheet Publications Following Best Practice

Generate spreadsheet publications that follow best practice guidance from the UK government's Analysis Function, available at <https://analysisfunction.civilservice.gov.uk/policy-store/releasing-statistics-in-spreadsheets/>, with a focus on accessibility. See also the 'Python' package 'gptables'.

Maintained by Olivia Box Power. Last updated 25 days ago.

accessibility openxlsx reproducible-analytical-pipeline spreadsheet uk-gov-data-science

3.4 match 44 stars 6.72 score 4 scripts

m-jahn

WeightedTreemaps:Generate and Plot Voronoi or Sunburst Treemaps from Hierarchical Data

Treemaps are a visually appealing graphical representation of numerical data using a space-filling approach. A plane or 'map' is subdivided into smaller areas called cells. The cells in the map are scaled according to an underlying metric which allows to grasp the hierarchical organization and relative importance of many objects at once. This package contains two different implementations of treemaps, Voronoi treemaps and Sunburst treemaps. The Voronoi treemap function subdivides the plot area in polygonal cells according to the highest hierarchical level, then continues to subdivide those parental cells on the next lower hierarchical level, and so on. The Sunburst treemap is a computationally less demanding treemap that does not require iterative refinement, but simply generates circle sectors that are sized according to predefined weights. The Voronoi tesselation is based on functions from Paul Murrell (2012) <https://www.stat.auckland.ac.nz/~paul/Reports/VoronoiTreemap/voronoiTreeMap.html>.

Maintained by Michael Jahn. Last updated 3 months ago.

r-programming rcpp sunburst-treemap voronoi-diagram voronoi-treemap cpp

3.4 match 50 stars 6.73 score 18 scripts

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 7 days ago.

1.5 match 100 stars 15.36 score 1.4k scripts 36 dependents

martigso

stortingscrape:Access Data from the Norwegian Parliament API

Functions for retrieving general and specific data from the Norwegian Parliament, through the Norwegian Parliament API at <https://data.stortinget.no>.

Maintained by Martin Søyland. Last updated 9 days ago.

scraping stortinget

3.8 match 11 stars 6.02 score 24 scripts

sakk-statistics

survSAKK:Create Publication Ready Kaplan-Meier Plots

Incorporate various statistics and layout customization options to enhance the efficiency and adaptability of the Kaplan-Meier plots.

Maintained by Katrin Gysel. Last updated 2 months ago.

4.7 match 1 stars 4.81 score 10 scripts

schochastics

networkdata:Repository of Network Datasets

The package contains a large collection of network dataset with different context. This includes social networks, animal networks and movie networks. All datasets are in 'igraph' format.

Maintained by David Schoch. Last updated 12 months ago.

dataset network-analysis

4.5 match 143 stars 5.01 score 143 scripts

josie-athens

pubh:A Toolbox for Public Health and Epidemiology

A toolbox for making R functions and capabilities more accessible to students and professionals from Epidemiology and Public Health related disciplines. Includes a function to report coefficients and confidence intervals from models using robust standard errors (when available), functions that expand 'ggplot2' plots and functions relevant for introductory papers in Epidemiology or Public Health. Please note that use of the provided data sets is for educational purposes only.

Maintained by Josie Athens. Last updated 5 months ago.

3.9 match 5 stars 5.73 score 72 scripts

jamesdalg

CNVScope:A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization

Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps.

Maintained by James Dalgleish. Last updated 3 years ago.

4.0 match 8 stars 5.58 score 24 scripts

trevorhastie

ISLR2:Introduction to Statistical Learning, Second Edition

We provide the collection of data-sets used in the book 'An Introduction to Statistical Learning with Applications in R, Second Edition'. These include many data-sets that we used in the first edition (some with minor changes), and some new datasets.

Maintained by Trevor Hastie. Last updated 2 years ago.

4.0 match 2 stars 5.49 score 2.2k scripts

tarakc02

rmapzen:Client for 'Mapzen' and Related Map APIs

Provides an interface to 'Mapzen'-based APIs (including geocode.earth, Nextzen, and NYC GeoSearch) for geographic search and geocoding, isochrone calculation, and vector data to draw map tiles. See <https://www.mapzen.com/documentation/> for more information. The original Mapzen has gone out of business, but 'rmapzen' can be set up to work with any provider who implements the Mapzen API.

Maintained by Tarak Shah. Last updated 1 years ago.

3.4 match 34 stars 6.39 score 72 scripts

eu-ecdc

epitweetr:Early Detection of Public Health Threats from 'Twitter' Data

It allows you to automatically monitor trends of tweets by time, place and topic aiming at detecting public health threats early through the detection of signals (e.g. an unusual increase in the number of tweets). It was designed to focus on infectious diseases, and it can be extended to all hazards or other fields of study by modifying the topics and keywords. More information is available in the 'epitweetr' peer-review publication (doi:10.2807/1560-7917.ES.2022.27.39.2200177).

Maintained by Laura Espinosa. Last updated 1 years ago.

early-warning-systems epidemic-surveillance lucene machine-learning signal-detection spark twitter

3.6 match 56 stars 5.98 score 86 scripts

bioc

HubPub:Utilities to create and use Bioconductor Hubs

HubPub provides users with functionality to help with the Bioconductor Hub structures. The package provides the ability to create a skeleton of a Hub style package that the user can then populate with the necessary information. There are also functions to help add resources to the Hub package metadata files as well as publish data to the Bioconductor S3 bucket.

Maintained by Kayla Interdonato. Last updated 2 days ago.

dataimport infrastructure software thirdpartyclient bioconductor-package

4.2 match 3 stars 5.18 score 4 scripts

walkerke

tigris:Load Census TIGER/Line Shapefiles

Download TIGER/Line shapefiles from the United States Census Bureau (<https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html>) and load into R as 'sf' objects.

Maintained by Kyle Walker. Last updated 4 months ago.

1.7 match 331 stars 12.87 score 5.3k scripts 16 dependents

massimoaria

pubmedR:Gathering Metadata About Publications, Grants, Clinical Trials from 'PubMed' Database

A set of tools to extract bibliographic content from 'PubMed' database using 'NCBI' REST API <https://www.ncbi.nlm.nih.gov/home/develop/api/>.

Maintained by Massimo Aria. Last updated 12 months ago.

2.8 match 38 stars 7.70 score 39 scripts 3 dependents

josesamos

sigugr:Workflow for Geographic Data

Streamlines geographic data transformation, storage and publication, simplifying data preparation and enhancing interoperability across formats and platforms.

Maintained by Jose Samos. Last updated 3 months ago.

4.9 match 1 stars 4.40 score 4 scripts

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 2 months ago.

infrastructure dataimport hdf5 rhdf5 openssl curl zlib cpp

1.3 match 62 stars 15.93 score 4.2k scripts 232 dependents

ropengov

hansard:Provides Easy Downloading Capabilities for the UK Parliament API

Provides functions to download data from the <https://explore.data.parliament.uk/> APIs. Because of the structure of the API, there is a named function for each type of available data for ease of use, as well as some functions designed to retrieve specific pieces of commonly used data. Functions for each new API will be added as and when they become available.

Maintained by Evan Odell. Last updated 2 years ago.

ropengov

7.8 match 1 stars 2.70 score

njlyon0

supportR:Support Functions for Wrangling and Visualization

Suite of helper functions for data wrangling and visualization. The only theme for these functions is that they tend towards simple, short, and narrowly-scoped. These functions are built for tasks that often recur but are not large enough in scope to warrant an ecosystem of interdependent functions.

Maintained by Nicholas J Lyon. Last updated 4 months ago.

data-science

3.4 match 5 stars 6.22 score 15 scripts

mikelydeamore

condensr:Academic Group Website Generator

Helps automate 'Quarto' website creation for small academic groups. Builds a database-like structure of people, projects and publications, linking them together with a string-based ID system. Then, provides functions to automate production of clean markdown for these structures, and in-built CSS formatting using CSS flexbox.

Maintained by Michael Lydeamore. Last updated 2 years ago.

7.8 match 1 stars 2.70 score 6 scripts

bioc

recountmethylation:Access and analyze public DNA methylation array data compilations

Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina's Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info.

Maintained by Sean K Maden. Last updated 5 months ago.

dnamethylation epigenetics microarray methylationarray experimenthub

3.3 match 9 stars 6.28 score 9 scripts

omniacsdao

Rnumerai:Interface to the Numerai Machine Learning Tournament API

Routines to interact with the Numerai Machine Learning Tournament API <https://numer.ai>. The functionality includes the ability to automatically download the current tournament data, submit predictions, and to get information for your user.

Maintained by Eric Hare. Last updated 3 years ago.

3.8 match 35 stars 5.53 score 39 scripts

baptiste

egg:Extensions for 'ggplot2': Custom Geom, Custom Themes, Plot Alignment, Labelled Panels, Symmetric Scales, and Fixed Panel Size

Miscellaneous functions to help customise 'ggplot2' objects. High-level functions are provided to post-process 'ggplot2' layouts and allow alignment between plot panels, as well as setting panel sizes to fixed values. Other functions include a custom 'geom', and helper functions to enforce symmetric scales or add tags to facetted plots.

Maintained by Baptiste Auguie. Last updated 4 years ago.

1.8 match 13 stars 11.84 score 2.4k scripts 67 dependents

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

2.9 match 65 stars 7.25 score 69 scripts

bfast2

strucchangeRcpp:Testing, Monitoring, and Dating Structural Changes: C++ Version

A fast implementation with additional experimental features for testing, monitoring and dating structural changes in (linear) regression models. 'strucchangeRcpp' features tests/methods from the generalized fluctuation test framework as well as from the F test (Chow test) framework. This includes methods to fit, plot and test fluctuation processes (e.g. cumulative/moving sum, recursive/moving estimates) and F statistics, respectively. These methods are described in Zeileis et al. (2002) <doi:10.18637/jss.v007.i02>. Finally, the breakpoints in regression models with structural changes can be estimated together with confidence intervals, and their magnitude as well as the model fit can be evaluated using a variety of statistical measures.

Maintained by Dainius Masiliunas. Last updated 5 months ago.

openblas cpp

4.0 match 5 stars 5.18 score 4 scripts 2 dependents

atsa-es

MARSS:Multivariate Autoregressive State-Space Modeling

The MARSS package provides maximum-likelihood parameter estimation for constrained and unconstrained linear multivariate autoregressive state-space (MARSS) models, including partially deterministic models. MARSS models are a class of dynamic linear model (DLM) and vector autoregressive model (VAR) model. Fitting available via Expectation-Maximization (EM), BFGS (using optim), and 'TMB' (using the 'marssTMB' companion package). Functions are provided for parametric and innovations bootstrapping, Kalman filtering and smoothing, model selection criteria including bootstrap AICb, confidences intervals via the Hessian approximation or bootstrapping, and all conditional residual types. See the user guide for examples of dynamic factor analysis, dynamic linear models, outlier and shock detection, and multivariate AR-p models. Online workshops (lectures, eBook, and computer labs) at <https://atsa-es.github.io/>.

Maintained by Elizabeth Eli Holmes. Last updated 1 years ago.

multivariate-timeseries state-space-models statistics time-series

2.0 match 52 stars 10.34 score 596 scripts 3 dependents

smin95

smplot2:Create Standalone and Composite Plots in 'ggplot2' for Publications

Provides functions for creating and annotating a composite plot in 'ggplot2'. Offers background themes and shortcut plotting functions that produce figures that are appropriate for the format of scientific journals. Some methods are described in Min and Zhou (2021) <doi:10.3389/fgene.2021.802894>.

Maintained by Seung Hyun Min. Last updated 1 months ago.

easy-to-use ggplot2 scientific-visualization visualization

2.9 match 24 stars 7.08 score 288 scripts 1 dependents

jchrom

trelloR:Access the Trello API

An R client for the Trello API. Supports free-tier features such as access to private boards, creating and updating cards and other resources, and downloading data in a structured way.

Maintained by Jakub Chromec. Last updated 2 years ago.

api trello

3.3 match 42 stars 6.18 score 24 scripts

bioc

mixOmics:Omics Data Integration Project

Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.

Maintained by Eva Hamrud. Last updated 4 days ago.

immunooncology microarray sequencing metabolomics metagenomics proteomics geneprediction multiplecomparison classification regression bioconductor genomics genomics-data genomics-visualization multivariate-analysis multivariate-statistics omics r-pkg r-project

1.5 match 182 stars 13.71 score 1.3k scripts 22 dependents

bioc

SimBu:Simulate Bulk RNA-seq Datasets from Single-Cell Datasets

SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions. You can either use your own single-cell study for the simulation or the sfaira database. Different pre-defined simulation scenarios exist, as are options to run custom simulations. Additionally, expression values can be adapted by adding an mRNA bias, which produces more biologically relevant simulations.

Maintained by Alexander Dietrich. Last updated 5 months ago.

software rnaseq singlecell

3.0 match 14 stars 6.81 score 29 scripts

equitable-equations

fqar:Floristic Quality Assessment Tools for R

Tools for downloading and analyzing floristic quality assessment data. See Freyman et al. (2015) <doi:10.1111/2041-210X.12491> for more information about floristic quality assessment and the associated database.

Maintained by Andrew Gard. Last updated 2 months ago.

3.5 match 5 stars 5.88 score 5 scripts