Showing 200 of total 1976 results (show query)
civisanalytics
civis:R Client for the 'Civis Platform API'
A convenient interface for making requests directly to the 'Civis Platform API' <https://www.civisanalytics.com/platform/>. Full documentation available 'here' <https://civisanalytics.github.io/civis-r/>.
Maintained by Peter Cooman. Last updated 2 months ago.
153.3 match 16 stars 7.84 score 144 scriptsrstudio
renv:Project Environments
A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.
Maintained by Kevin Ushey. Last updated 3 days ago.
46.5 match 1.0k stars 18.55 score 1.5k scripts 113 dependentskisungyou
Rdimtools:Dimension Reduction and Estimation Methods
We provide linear and nonlinear dimension reduction techniques. Intrinsic dimension estimation methods for exploratory analysis are also provided. For more details on the package, see the paper by You and Shung (2022) <doi:10.1016/j.simpa.2022.100414>.
Maintained by Kisung You. Last updated 2 years ago.
dimension-estimationdimension-reductionmanifold-learningsubspace-learningopenblascppopenmp
61.2 match 52 stars 8.37 score 186 scripts 8 dependentsreconhub
projections:Project Future Case Incidence
Provides functions and graphics for projecting daily incidence based on past incidence, and estimates of the serial interval and reproduction number. Projections are based on a branching process using a Poisson-distributed number of new cases per day, similar to the model used for estimating R in 'EpiEstim' or in 'earlyR', and described by Nouvellet et al. (2017) <doi:10.1016/j.epidem.2017.02.012>. The package provides the S3 class 'projections' which extends 'matrix', with accessors and additional helpers for handling, subsetting, merging, or adding these objects, as well as dedicated printing and plotting methods.
Maintained by Thibaut Jombart. Last updated 3 months ago.
78.8 match 14 stars 6.47 score 175 scriptsouhscbbmc
REDCapR:Interaction Between R and REDCap
Encapsulates functions to streamline calls from R to the REDCap API. REDCap (Research Electronic Data CAPture) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The Application Programming Interface (API) offers an avenue to access and modify data programmatically, improving the capacity for literate and reproducible programming.
Maintained by Will Beasley. Last updated 2 months ago.
36.6 match 118 stars 12.36 score 438 scripts 6 dependentskentonwhite
ProjectTemplate:Automates the Creation of New Statistical Analysis Projects
Provides functions to automatically build a directory structure for a new R project. Using this structure, 'ProjectTemplate' automates data loading, preprocessing, library importing and unit testing.
Maintained by Kenton White. Last updated 14 days ago.
46.4 match 626 stars 8.99 score 612 scriptspredictiveecology
SpaDES.project:Project Templates Using 'SpaDES'
Quickly setup a 'SpaDES' project directories and add modules using templates.
Maintained by Eliot J B McIntire. Last updated 2 days ago.
61.9 match 3 stars 6.66 score 21 scriptsobiba
opalr:'Opal' Data Repository Client and 'DataSHIELD' Utils
Data integration Web application for biobanks by 'OBiBa'. 'Opal' is the core database application for biobanks. Participant data, once collected from any data source, must be integrated and stored in a central data repository under a uniform model. 'Opal' is such a central repository. It can import, process, validate, query, analyze, report, and export data. 'Opal' is typically used in a research center to analyze the data acquired at assessment centres. Its ultimate purpose is to achieve seamless data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal' web services and to perform operations on the R server side. 'DataSHIELD' administration tools are also provided.
Maintained by Yannick Marcon. Last updated 2 months ago.
50.7 match 3 stars 7.76 score 179 scripts 2 dependentscjvanlissa
worcs:Workflow for Open Reproducible Code in Science
Create reproducible and transparent research projects in 'R'. This package is based on the Workflow for Open Reproducible Code in Science (WORCS), a step-by-step procedure based on best practices for Open Science. It includes an 'RStudio' project template, several convenience functions, and all dependencies required to make your project reproducible and transparent. WORCS is explained in the tutorial paper by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2021). <doi:10.3233/DS-210031>.
Maintained by Caspar J. Van Lissa. Last updated 11 days ago.
40.7 match 83 stars 9.26 score 59 scriptsstan-dev
projpred:Projection Predictive Feature Selection
Performs projection predictive feature selection for generalized linear models (Piironen, Paasiniemi, and Vehtari, 2020, <doi:10.1214/20-EJS1711>) with or without multilevel or additive terms (Catalina, Bürkner, and Vehtari, 2022, <https://proceedings.mlr.press/v151/catalina22a.html>), for some ordinal and nominal regression models (Weber, Glass, and Vehtari, 2023, <arXiv:2301.01660>), and for many other regression models (using the latent projection by Catalina, Bürkner, and Vehtari, 2021, <arXiv:2109.04702>, which can also be applied to most of the former models). The package is compatible with the 'rstanarm' and 'brms' packages, but other reference models can also be used. See the vignettes and the documentation for more information and examples.
Maintained by Frank Weber. Last updated 1 months ago.
bayesbayesianbayesian-inferencerstanarmstanstatisticsvariable-selectionopenblascpp
37.2 match 112 stars 10.08 score 241 scriptsr-lib
usethis:Automate Package and Project Setup
Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.
Maintained by Jennifer Bryan. Last updated 11 days ago.
20.9 match 869 stars 17.54 score 5.6k scripts 336 dependentsworkflowr
workflowr:A Framework for Reproducible and Collaborative Data Science
Provides a workflow for your analysis projects by combining literate programming ('knitr' and 'rmarkdown') and version control ('Git', via 'git2r') to generate a website containing time-stamped, versioned, and documented results.
Maintained by John Blischak. Last updated 4 months ago.
gitproject-managementrmarkdownwebsiteworkflow
30.8 match 845 stars 11.83 score 566 scriptsclevelandclinicqhs
projects:A Project Infrastructure for Researchers
Provides a project infrastructure with a focus on manuscript creation. Creates a project folder with a single command, containing subdirectories for specific components, templates for manuscripts, and so on.
Maintained by Nik Krieger. Last updated 4 years ago.
75.7 match 31 stars 4.70 score 32 scriptsvubiostat
redcapAPI:Interface to 'REDCap'
Access data stored in 'REDCap' databases using the Application Programming Interface (API). 'REDCap' (Research Electronic Data CAPture; <https://projectredcap.org>, Harris, et al. (2009) <doi:10.1016/j.jbi.2008.08.010>, Harris, et al. (2019) <doi:10.1016/j.jbi.2019.103208>) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The API allows users to access data and project meta data (such as the data dictionary) from the web programmatically. The 'redcapAPI' package facilitates the process of accessing data with options to prepare an analysis-ready data set consistent with the definitions in a database's data dictionary.
Maintained by Shawn Garbett. Last updated 9 days ago.
31.7 match 22 stars 10.47 score 134 scripts 2 dependentscran
datarobot:'DataRobot' Predictive Modeling API
For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Maintained by AJ Alon. Last updated 1 years ago.
92.9 match 2 stars 3.48 scorecran
popbio:Construction and Analysis of Matrix Population Models
Construct and analyze projection matrix models from a demography study of marked individuals classified by age or stage. The package covers methods described in Matrix Population Models by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak (2002).
Maintained by Chris Stubben. Last updated 12 months ago.
51.7 match 6.24 score 1.0k scripts 5 dependentsthinkr-open
lozen:Management tools for missions
Management tools for missions (internal and external). Includes weekly, GL projects, etc.
Maintained by Sébastien Rochette. Last updated 12 months ago.
57.9 match 7 stars 5.42 score 14 scriptsbioc
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.
immunooncologymicroarraysequencingmetabolomicsmetagenomicsproteomicsgenepredictionmultiplecomparisonclassificationregressionbioconductorgenomicsgenomics-datagenomics-visualizationmultivariate-analysismultivariate-statisticsomicsr-pkgr-project
22.7 match 182 stars 13.71 score 1.3k scripts 22 dependentsr-lib
here:A Simpler Way to Find Your Files
Constructs paths to your project's files. Declare the relative path of a file within your project with 'i_am()'. Use the 'here()' function as a drop-in replacement for 'file.path()', it will always locate the files relative to your project root.
Maintained by Kirill Müller. Last updated 12 hours ago.
15.8 match 417 stars 19.62 score 96k scripts 607 dependentssizespectrum
mizer:Dynamic Multi-Species Size Spectrum Modelling
A set of classes and methods to set up and run multi-species, trait based and community size spectrum ecological models, focused on the marine environment.
Maintained by Gustav Delius. Last updated 2 months ago.
ecosystem-modelfish-population-dynamicsfisheriesfisheries-managementmarine-ecosystempopulation-dynamicssimulationsize-structurespecies-interactionstransport-equationcpp
32.4 match 38 stars 9.43 score 207 scriptsreichlab
zoltr:Interface to the 'Zoltar' Forecast Repository API
'Zoltar' <https://www.zoltardata.com/> is a website that provides a repository of model forecast results in a standardized format and a central location. It supports storing, retrieving, comparing, and analyzing time series forecasts for prediction challenges of interest to the modeling community. This package provides functions for working with the 'Zoltar' API, including connecting and authenticating, getting meta information (projects, models, and forecasts, and truth), and uploading, downloading, and deleting forecast and truth data.
Maintained by Matthew Cornell. Last updated 10 days ago.
38.8 match 2 stars 7.58 score 175 scripts 3 dependentssbg
sevenbridges2:The 'Seven Bridges Platform' API Client
R client and utilities for 'Seven Bridges Platform' API, from 'Cancer Genomics Cloud' to other 'Seven Bridges' supported platforms. API documentation is hosted publicly at <https://docs.sevenbridges.com/docs/the-api>.
Maintained by Marko Trifunovic. Last updated 20 days ago.
api-clientbioinformaticscloudsevenbridges
47.8 match 2 stars 5.90 score 4 scriptsradicalcommecol
cxr:A Toolbox for Modelling Species Coexistence in R
Recent developments in modern coexistence theory have advanced our understanding on how species are able to persist and co-occur with other species at varying abundances. However, applying this mathematical framework to empirical data is still challenging, precluding a larger adoption of the theoretical tools developed by empiricists. This package provides a complete toolbox for modelling interaction effects between species, and calculate fitness and niche differences. The functions are flexible, may accept covariates, and different fitting algorithms can be used. A full description of the underlying methods is available in García-Callejas, D., Godoy, O., and Bartomeus, I. (2020) <doi:10.1111/2041-210X.13443>. Furthermore, the package provides a series of functions to calculate dynamics for stage-structured populations across sites.
Maintained by David Garcia-Callejas. Last updated 1 months ago.
42.1 match 10 stars 6.51 score 27 scriptsbioc
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.
softwaredataimportthirdpartyclientapi-clientbioconductorbioinformaticscloudcommon-workflow-languagesevenbridges
34.3 match 35 stars 7.40 score 24 scriptsropensci
rix:Reproducible Data Science Environments with 'Nix'
Simplifies the creation of reproducible data science environments using the 'Nix' package manager, as described in Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()` function generates a complete description of the environment as a `default.nix` file, which can then be built using 'Nix'. This results in project specific software environments with pinned versions of R, packages, linked system dependencies, and other tools. Additional helpers make it easy to run R code in 'Nix' software environments for testing and production.
Maintained by Bruno Rodrigues. Last updated 5 days ago.
nixpeer-reviewedreproducibilityreproducible-research
23.4 match 235 stars 10.54 score 67 scriptsthinkr-open
gitlabr:Access to the 'GitLab' API
Provides R functions to access the API of the project and repository management web application 'GitLab'. For many common tasks (repository file access, issue assignment and status, commenting) convenience wrappers are provided, and in addition the full API can be used by specifying request locations. 'GitLab' is open-source software and can be self-hosted or used on <https://about.gitlab.com>.
Maintained by Sébastien Rochette. Last updated 10 months ago.
27.6 match 40 stars 8.40 score 69 scripts 1 dependentsmalaria-atlas-project
malariaAtlas:An R Interface to Open-Access Malaria Data, Hosted by the 'Malaria Atlas Project'
A suite of tools to allow you to download all publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from the 'Malaria Atlas Project' <https://malariaatlas.org/> servers as well as utility functions for plotting the downloaded data.
Maintained by Mauricio van den Berg. Last updated 8 months ago.
24.8 match 44 stars 9.10 score 118 scripts 3 dependentsbioc
TCGAbiolinks:TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.
Maintained by Tiago Chedraoui Silva. Last updated 27 days ago.
dnamethylationdifferentialmethylationgeneregulationgeneexpressionmethylationarraydifferentialexpressionpathwaysnetworksequencingsurvivalsoftwarebiocbioconductorgdcintegrative-analysistcgatcga-datatcgabiolinks
15.2 match 305 stars 14.45 score 1.6k scripts 6 dependentscloudyr
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.
apicloud-computingcloudyrgoogle-cloudgoogleauthrlaunching-virtual-machines
22.2 match 152 stars 9.73 score 235 scriptsropensci
gutenbergr:Download and Process Public Domain Works from Project Gutenberg
Download and process public domain works in the Project Gutenberg collection <https://www.gutenberg.org/>. Includes metadata for all Project Gutenberg works, so that they can be searched and retrieved.
Maintained by Jon Harmon. Last updated 2 months ago.
20.6 match 105 stars 10.50 score 1.1k scripts 1 dependentskylegrealis
froggeR:Enhance 'Quarto' Project Workflows and Standards
Streamlines 'Quarto' workflows by providing tools for consistent project setup and documentation. Enables portability through reusable metadata, automated project structure creation, and standardized templates. Features include enhanced project initialization, pre-formatted 'Quarto' documents, comprehensive data protection settings, custom styling, and structured documentation generation. Designed to improve efficiency and collaboration in R data science projects by reducing repetitive setup tasks while maintaining consistent formatting across multiple documents. There are many valuable resources providing in-depth explanations of customizing 'Quarto' templates and theme styling by the Posit team: <https://quarto.org/docs/output-formats/html-themes.html#customizing-themes> & <https://quarto.org/docs/output-formats/html-themes-more.html>, and at the Bootstrap community's GitHub at <https://github.com/twbs/bootstrap/blob/main/scss/_variables.scss>.
Maintained by Kyle Grealis. Last updated 5 hours ago.
data-scienceproject-managementquarto
32.0 match 26 stars 6.67 score 6 scriptsggobi
tourr:Tour Methods for Multivariate Data Visualisation
Implements geodesic interpolation and basis generation functions that allow you to create new tour methods from R.
Maintained by Dianne Cook. Last updated 17 days ago.
18.9 match 65 stars 11.17 score 426 scripts 9 dependentsbioc
recount:Explore and download data from the recount project
Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.
Maintained by Leonardo Collado-Torres. Last updated 3 months ago.
coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportimmunooncologyannotation-agnosticbioconductorcountderfinderdeseq2exongenehumanilluminajunctionrecount
22.1 match 41 stars 9.57 score 498 scripts 3 dependentslindbrook
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.
choleradata-visualizationdatasetsepidemiologyjohn-snowpublic-healthtriangulation-delaunayvoronoivoronoi-polygons
22.5 match 136 stars 9.33 score 95 scriptsr-lib
rprojroot:Finding Files in Project Subdirectories
Robust, reliable and flexible paths to files below a project root. The 'root' of a project is defined as a directory that matches a certain criterion, e.g., it contains a certain regular file.
Maintained by Kirill Müller. Last updated 1 months ago.
12.4 match 150 stars 16.70 score 1.4k scripts 1.4k dependentsdexter-psychometrics
dexter:Data Management and Analysis of Tests
A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Maintained by Jesse Koops. Last updated 6 days ago.
22.2 match 8 stars 8.97 score 135 scripts 2 dependentsmolgenis
MolgenisArmadillo:Armadillo Client for the Armadillo Service
A set of functions to manage data shared on a 'MOLGENIS Armadillo' server.
Maintained by Mariska Slofstra. Last updated 16 days ago.
25.9 match 3 stars 7.51 score 28 scriptsopenair-project
openair:Tools for the Analysis of Air Pollution Data
Tools to analyse, interpret and understand air pollution data. Data are typically regular time series and air quality measurement, meteorological data and dispersion model output can be analysed. The package is described in Carslaw and Ropkins (2012, <doi:10.1016/j.envsoft.2011.09.008>) and subsequent papers.
Maintained by David Carslaw. Last updated 25 days ago.
air-qualityair-quality-datameteorologyopenaircpp
15.0 match 311 stars 12.91 score 1.2k scripts 12 dependentscenterforassessment
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-projectionsquantile-regressionsgpsgp-analysesstudent-growth-percentilesstudent-growth-projections
19.7 match 20 stars 9.69 score 88 scriptsjfrench
autoimage:Multiple Heat Maps for Projected Coordinates
Functions for displaying multiple images or scatterplots with a color scale, i.e., heat maps, possibly with projected coordinates. The package relies on the base graphics system, so graphics are rendered rapidly.
Maintained by Joshua French. Last updated 4 years ago.
28.0 match 7 stars 6.73 score 57 scripts 3 dependentsigraph
igraph:Network Analysis and Visualization
Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Maintained by Kirill Müller. Last updated 13 hours ago.
complex-networksgraph-algorithmsgraph-theorymathematicsnetwork-analysisnetwork-graphfortranlibxml2glpkopenblascpp
8.5 match 582 stars 21.11 score 31k scripts 1.9k dependentsrstudio
packrat:A Dependency Management System for Projects and their R Package Dependencies
Manage the R packages your project depends on in an isolated, portable, and reproducible way.
Maintained by Aron Atkins. Last updated 1 months ago.
14.7 match 406 stars 12.15 score 256 scripts 9 dependentsrspatial
raster:Geographic Data Analysis and Modeling
Reading, writing, manipulating, analyzing and modeling of spatial data. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.
Maintained by Robert J. Hijmans. Last updated 2 months ago.
10.3 match 164 stars 17.05 score 58k scripts 555 dependentsprojectmosaic
mosaic:Project MOSAIC Statistics and Mathematics Teaching Utilities
Data sets and utilities from Project MOSAIC (<http://www.mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.
Maintained by Randall Pruim. Last updated 1 years ago.
13.1 match 93 stars 13.32 score 7.2k scripts 7 dependentsrstudio
rstudioapi:Safely Access the RStudio API
Access the RStudio API (if available) and provide informative error messages when it's not.
Maintained by Kevin Ushey. Last updated 4 months ago.
9.1 match 172 stars 18.81 score 3.6k scripts 2.1k dependentsbiomodhub
biomod2:Ensemble Platform for Species Distribution Modeling
Functions for species distribution modeling, calibration and evaluation, ensemble of models, ensemble forecasting and visualization. The package permits to run consistently up to 10 single models on a presence/absences (resp presences/pseudo-absences) dataset and to combine them in ensemble models and ensemble projections. Some bench of other evaluation and visualisation tools are also available within the package.
Maintained by Maya Gueguen. Last updated 5 days ago.
12.2 match 95 stars 13.88 score 536 scripts 7 dependentstkonopka
umap:Uniform Manifold Approximation and Projection
Uniform manifold approximation and projection is a technique for dimension reduction. The algorithm was described by McInnes and Healy (2018) in <arXiv:1802.03426>. This package provides an interface for two implementations. One is written from scratch, including components for nearest-neighbor search and for embedding. The second implementation is a wrapper for 'python' package 'umap-learn' (requires separate installation, see vignette for more details).
Maintained by Tomasz Konopka. Last updated 11 months ago.
dimensionality-reductionumapcpp
13.1 match 132 stars 12.74 score 3.6k scripts 43 dependentssatijalab
Seurat:Tools for Single Cell Genomics
A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Maintained by Paul Hoffman. Last updated 1 years ago.
human-cell-atlassingle-cell-genomicssingle-cell-rna-seqcpp
9.9 match 2.4k stars 16.86 score 50k scripts 73 dependentsinbo
checklist:A Thorough and Strict Set of Checks for R Packages and Source Code
An opinionated set of rules for R packages and R source code projects.
Maintained by Thierry Onkelinx. Last updated 27 days ago.
checklistcontinuous-integrationcontinuous-testingquality-assurance
22.7 match 19 stars 7.24 score 21 scripts 2 dependentssyncrosim
rsyncrosim:The R Interface to 'SyncroSim'
'SyncroSim' is a generalized framework for managing scenario-based datasets (<https://syncrosim.com/>). 'rsyncrosim' provides an interface to 'SyncroSim'. Simulation models can be added to 'SyncroSim' in order to transform these datasets, taking advantage of general features such as defining scenarios of model inputs, running Monte Carlo simulations, and summarizing model outputs. 'rsyncrosim' requires 'SyncroSim' 2.3.5 or higher (API documentation: <https://docs.syncrosim.com/>).
Maintained by Katie Birchard. Last updated 9 days ago.
22.9 match 9 stars 7.09 score 189 scriptsropensci
ruODK:An R Client for the ODK Central API
Access and tidy up data from the 'ODK Central' API. 'ODK Central' is a clearinghouse for digitally captured data using ODK <https://docs.getodk.org/central-intro/>. It manages user accounts and permissions, stores form definitions, and allows data collection clients like 'ODK Collect' to connect to it for form download and submission upload. The 'ODK Central' API is documented at <https://docs.getodk.org/central-api/>.
Maintained by Florian W. Mayer. Last updated 4 months ago.
databaseopen-dataodkapidatadatasetodataodata-clientodk-centralopendatakit
20.9 match 42 stars 7.73 score 57 scripts 1 dependentscrunch-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.
15.3 match 9 stars 10.53 score 200 scripts 2 dependentsdormancy1
lefko3:Historical and Ahistorical Population Projection Matrix Analysis
Complete analytical environment for the construction and analysis of matrix population models and integral projection models. Includes the ability to construct historical matrices, which are 2d matrices comprising 3 consecutive times of demographic information. Estimates both raw and function-based forms of historical and standard ahistorical matrices. It also estimates function-based age-by-stage matrices and raw and function-based Leslie matrices.
Maintained by Richard P. Shefferson. Last updated 4 days ago.
48.7 match 3.30 score 11 scriptsblue-matter
MSEtool:Management Strategy Evaluation Toolkit
Development, simulation testing, and implementation of management procedures for fisheries (see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Maintained by Adrian Hordyk. Last updated 26 days ago.
20.7 match 8 stars 7.69 score 163 scripts 3 dependentsdewittpe
REDCapExporter:Automated Construction of R Data Packages from REDCap Projects
Export all data, including metadata, from a REDCap (Research Electronic Data Capture) Project via the REDCap API <https://projectredcap.org/wp-content/resources/REDCapTechnicalOverview.pdf>. The exported (meta)data will be processed and formatted into a stand alone R data package which can be installed and shared between researchers. Several default reports are generated as vignettes in the resulting package.
Maintained by Peter DeWitt. Last updated 4 months ago.
apidata-exportredcapredcap-api
29.9 match 2 stars 5.28 score 21 scriptspachadotdev
analogsea:Interface to 'DigitalOcean'
Provides a set of functions for interacting with the 'DigitalOcean' API <https://www.digitalocean.com/>, including creating images, destroying them, rebooting, getting details on regions, and available images.
Maintained by Mauricio Vargas. Last updated 2 years ago.
20.7 match 159 stars 7.56 score 100 scripts 1 dependentsbioc
projectR:Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering
Functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering.
Maintained by Genevieve Stein-OBrien. Last updated 5 months ago.
functionalpredictiongeneregulationbiologicalquestionsoftware
19.0 match 62 stars 8.11 score 70 scriptsyannabraham
Radviz:Project Multidimensional Data in 2D Space
An implementation of the radviz projection in R. It enables the visualization of multidimensional data while maintaining the relation to the original dimensions. This package provides functions to create and plot radviz projections, and a number of summary plots that enable comparison and analysis. For reference see Ankerst *et al.* (1996) (<https://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.68.1811>) for original implementation, see Di Caro *et al* (2012) (<https://link.springer.com/chapter/10.1007/978-3-642-13672-6_13>) for the original method for dimensional anchor arrangements, see Demsar *et al.* (2007) (<doi:10.1016/j.jbi.2007.03.010>) for the original Freeviz implementation.
Maintained by Yann Abraham. Last updated 3 years ago.
high-dimensional-dataradvizsciencevisualizationcpp
24.8 match 10 stars 6.19 score 52 scriptsalfrzlp
sae.projection:Small Area Estimation Using Model-Assisted Projection Method
Combines information from two independent surveys using a model-assisted projection method. Designed for survey sampling scenarios where a large sample collects only auxiliary information (Survey 1) and a smaller sample provides data on both variables of interest and auxiliary variables (Survey 2). Implements a working model to generate synthetic values of the variable of interest by fitting the model to Survey 2 data and predicting values for Survey 1 based on its auxiliary variables (Kim & Rao, 2012) <doi:10.1093/biomet/asr063>.
Maintained by Ridson Al Farizal P. Last updated 30 days ago.
46.1 match 3.30 score 7 scriptsropensci
drake:A Pipeline Toolkit for Reproducible Computation at Scale
A general-purpose computational engine for data analysis, drake rebuilds intermediate data objects when their dependencies change, and it skips work when the results are already up to date. Not every execution starts from scratch, there is native support for parallel and distributed computing, and completed projects have tangible evidence that they are reproducible. Extensive documentation, from beginner-friendly tutorials to practical examples and more, is available at the reference website <https://docs.ropensci.org/drake/> and the online manual <https://books.ropensci.org/drake/>.
Maintained by William Michael Landau. Last updated 3 months ago.
data-sciencedrakehigh-performance-computingmakefilepeer-reviewedpipelinereproducibilityreproducible-researchropensciworkflow
12.8 match 1.3k stars 11.49 score 1.7k scripts 1 dependentsbioc
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.
immunooncologysinglecellsoftwareclassificationsupportvectormachinernaseqvisualizationtranscriptomicsdatarepresentationtranscriptionsequencingpreprocessinggeneexpressiondataimportbioconductor-packagehuman-cell-atlasprojection-mappingsingle-cell-rna-seqopenblascpp
16.3 match 95 stars 8.82 score 172 scriptsiainmstott
popdemo:Demographic Modelling Using Projection Matrices
Tools for modelling populations and demography using matrix projection models, with deterministic and stochastic model implementations. Includes population projection, indices of short- and long-term population size and growth, perturbation analysis, convergence to stability or stationarity, and diagnostic and manipulation tools.
Maintained by Iain Stott. Last updated 3 years ago.
27.6 match 5.16 score 172 scripts 7 dependentsoscarkjell
text:Analyses of Text using Transformers Models from HuggingFace, Natural Language Processing and Machine Learning
Link R with Transformers from Hugging Face to transform text variables to word embeddings; where the word embeddings are used to statistically test the mean difference between set of texts, compute semantic similarity scores between texts, predict numerical variables, and visual statistically significant words according to various dimensions etc. For more information see <https://www.r-text.org>.
Maintained by Oscar Kjell. Last updated 4 days ago.
deep-learningmachine-learningnlptransformersopenjdk
10.8 match 146 stars 13.16 score 436 scripts 1 dependentsraymondbalise
rUM:R Templates from the University of Miami
This holds some r markdown and quarto templates and a template to create a research project in "R Studio".
Maintained by Raymond Balise. Last updated 10 days ago.
20.5 match 9 stars 6.84 score 16 scriptsbioc
gypsum:Interface to the gypsum REST API
Client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various adminstrative and management tasks. Check out the documentation at https://github.com/ArtifactDB/gypsum-worker for more details.
Maintained by Aaron Lun. Last updated 5 months ago.
22.1 match 1 stars 6.32 score 20 scripts 2 dependentsolink-proteomics
OlinkAnalyze:Facilitate Analysis of Proteomic Data from Olink
A collection of functions to facilitate analysis of proteomic data from Olink, primarily NPX data that has been exported from Olink Software. The functions also work on QUANT data from Olink by log- transforming the QUANT data. The functions are focused on reading data, facilitating data wrangling and quality control analysis, performing statistical analysis and generating figures to visualize the results of the statistical analysis. The goal of this package is to help users extract biological insights from proteomic data run on the Olink platform.
Maintained by Kathleen Nevola. Last updated 20 days ago.
olinkproteomicsproteomics-data-analysis
14.3 match 104 stars 9.72 score 61 scriptsadeverse
ade4:Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Maintained by Aurélie Siberchicot. Last updated 13 days ago.
9.2 match 39 stars 14.96 score 2.2k scripts 256 dependentsnatverse
nat:NeuroAnatomy Toolbox for Analysis of 3D Image Data
NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).
Maintained by Gregory Jefferis. Last updated 5 months ago.
3dconnectomicsimage-analysisneuroanatomyneuroanatomy-toolboxneuronneuron-morphologyneurosciencevisualisation
13.4 match 67 stars 9.94 score 436 scripts 2 dependentsr-a-dobson
dynamicSDM:Species Distribution and Abundance Modelling at High Spatio-Temporal Resolution
A collection of novel tools for generating species distribution and abundance models (SDM) that are dynamic through both space and time. These highly flexible functions incorporate spatial and temporal aspects across key SDM stages; including when cleaning and filtering species occurrence data, generating pseudo-absence records, assessing and correcting sampling biases and autocorrelation, extracting explanatory variables and projecting distribution patterns. Throughout, functions utilise Google Earth Engine and Google Drive to minimise the computing power and storage demands associated with species distribution modelling at high spatio-temporal resolution.
Maintained by Rachel Dobson. Last updated 27 days ago.
dynamicsdmgoogle-earth-enginegoogledrivesdmspatiotemporalspatiotemporal-data-analysisspatiotemporal-forecastingspecies-distribution-modellingspecies-distributions
21.3 match 6 stars 6.16 score 20 scriptskwb-r
kwb.abimo:R Package with Functions for Working with Water Balance Model ABIMO
R Package with functions for working with water balance bodel ABIMO https://www.stadtentwicklung.berlin.de/umwelt/umweltatlas/download/goedecke_et_al_abimo2019_doku.pdf).
Maintained by Andreas Matzinger. Last updated 1 years ago.
abimoproject-amarexproject-basarproject-flusshygieneproject-keysproject-kurasproject-ogreproject-spurwater-balance-model
52.5 match 2.48 score 1 dependentspik-piam
mrremind:MadRat REMIND Input Data Package
The mrremind packages contains data preprocessing for the REMIND model.
Maintained by Lavinia Baumstark. Last updated 3 days ago.
20.4 match 4 stars 6.25 score 15 scripts 1 dependentsadamlilith
fasterRaster:Faster Raster and Spatial Vector Processing Using 'GRASS GIS'
Processing of large-in-memory/large-on disk rasters and spatial vectors using 'GRASS GIS' <https://grass.osgeo.org/>. Most functions in the 'terra' package are recreated. Processing of medium-sized and smaller spatial objects will nearly always be faster using 'terra' or 'sf', but for large-in-memory/large-on-disk objects, 'fasterRaster' may be faster. To use most of the functions, you must have the stand-alone version (not the 'OSGeoW4' installer version) of 'GRASS GIS' 8.0 or higher.
Maintained by Adam B. Smith. Last updated 19 days ago.
aspectdistancefragmentationfragmentation-indicesgisgrassgrass-gisrasterraster-projectionrasterizeslopetopographyvectorization
16.5 match 58 stars 7.69 score 8 scriptshusson
FactoMineR:Multivariate Exploratory Data Analysis and Data Mining
Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).
Maintained by Francois Husson. Last updated 3 months ago.
8.6 match 47 stars 14.71 score 5.6k scripts 112 dependentsrostools
prodigenr:Research Project Directory Generator
Create a project directory structure, along with typical files for that project. This allows projects to be quickly and easily created, as well as for them to be standardized. Designed specifically with scientists in mind (mainly bio-medical researchers, but likely applies to other fields).
Maintained by Luke Johnston. Last updated 3 months ago.
devtoolsopen-scienceopen-sourceproject-managementreproducibilityreproducible-researchreproducible-sciencerstudiousethis
19.8 match 43 stars 6.33 score 25 scriptshanase
wpp2019:World Population Prospects 2019
Provides data from the United Nation's World Population Prospects 2019.
Maintained by Hana Sevcikova. Last updated 5 years ago.
39.4 match 1 stars 3.17 score 99 scripts 5 dependentsedzer
sp:Classes and Methods for Spatial Data
Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc. From this version, 'rgdal', 'maptools', and 'rgeos' are no longer used at all, see <https://r-spatial.org/r/2023/05/15/evolution4.html> for details.
Maintained by Edzer Pebesma. Last updated 2 months ago.
6.5 match 127 stars 18.63 score 35k scripts 1.3k dependentsepicentre-msf
redcap:R Utilities For REDCap
R utilities for interacting with the REDCap API.
Maintained by Patrick Barks. Last updated 3 months ago.
35.0 match 7 stars 3.45 score 5 scriptskwb-r
kwb.pilot:Importing, Aggregating and Visualising Data From KWB Pilot Plants
Collects, aggregates and visualises operational and analytical data from water suppliers (including a standardised reporting document).
Maintained by Michael Rustler. Last updated 2 years ago.
data-aggregationdata-importdata-visualisationproject-aquanesproject-mbr40project-sulemanproject-ultimate
30.0 match 1 stars 4.01 score 17 scriptsdavidcsterratt
retistruct:Retinal Reconstruction Program
Reconstructs retinae by morphing a flat surface with cuts (a dissected flat-mount retina) onto a curvilinear surface (the standard retinal shape). It can estimate the position of a point on the intact adult retina to within 8 degrees of arc (3.6% of nasotemporal axis). The coordinates in reconstructed retinae can be transformed to visuotopic coordinates. For more details see Sterratt, D. C., Lyngholm, D., Willshaw, D. J. and Thompson, I. D. (2013) <doi:10.1371/journal.pcbi.1002921>.
Maintained by David C. Sterratt. Last updated 9 days ago.
25.7 match 8 stars 4.60 scorevpnagraj
rrefine:r Client for OpenRefine API
'OpenRefine' (formerly 'Google Refine') is a popular, open source data cleaning software. This package enables users to programmatically trigger data transfer between R and 'OpenRefine'. Available functionality includes project import, export and deletion.
Maintained by VP Nagraj. Last updated 2 years ago.
20.3 match 22 stars 5.77 score 27 scriptsjonlinca
galvanizer:Interface to Galvanize 'Highbond' Internal Audit Software
An R interface to the Galvanize 'Highbond' API <https://docs-apis.highbond.com>.
Maintained by Jonathan Lin. Last updated 4 years ago.
38.8 match 2 stars 3.00 score 2 scriptspepkit
pepr:Reading Portable Encapsulated Projects
A PEP, or Portable Encapsulated Project, is a dataset that subscribes to the PEP structure for organizing metadata. It is written using a simple YAML + CSV format, it is your one-stop solution to metadata management across data analysis environments. This package reads this standardized project configuration structure into R. Described in Sheffield et al. (2021) <doi:10.1093/gigascience/giab077>.
Maintained by Nathan Sheffield. Last updated 1 years ago.
20.5 match 3 stars 5.62 score 20 scriptshuizezhang-sherry
ferrn:Facilitate Exploration of touRR optimisatioN
Diagnostic plots for optimisation, with a focus on projection pursuit. These show paths the optimiser takes in the high-dimensional space in multiple ways: by reducing the dimension using principal component analysis, and also using the tour to show the path on the high-dimensional space. Several botanical colour palettes are included, reflecting the name of the package. A paper describing the methodology can be found at <https://journal.r-project.org/archive/2021/RJ-2021-105/index.html>.
Maintained by H. Sherry Zhang. Last updated 11 days ago.
22.4 match 6 stars 5.16 score 20 scriptsdatawookie
clockify:A Wrapper for the 'Clockify' API
A wrapper for the Clockify API <https://docs.clockify.me/>, making it possible to query, insert and update time keeping data.
Maintained by Andrew B. Collier. Last updated 10 months ago.
28.7 match 2 stars 3.95 score 6 scriptsproject-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.
biodiversityecologyevolutionmechanisticmodelmodelingsimulationcpp
15.0 match 29 stars 7.56 score 69 scriptsr-lidar
lidR:Airborne LiDAR Data Manipulation and Visualization for Forestry Applications
Airborne LiDAR (Light Detection and Ranging) interface for data manipulation and visualization. Read/write 'las' and 'laz' files, computation of metrics in area based approach, point filtering, artificial point reduction, classification from geographic data, normalization, individual tree segmentation and other manipulations.
Maintained by Jean-Romain Roussel. Last updated 1 months ago.
alsforestrylaslazlidarpoint-cloudremote-sensingopenblascppopenmp
7.8 match 623 stars 14.47 score 844 scripts 8 dependentsflr
FLasher:Projection and Forecasting of Fish Populations, Stocks and Fleets
Projection of future population and fishery dynamics is carried out for a given set of management targets. A system of equations is solved, using Automatic Differentation (AD), for the levels of effort by fishery (fleet) that will result in the required abundances, catches or fishing mortalities.
Maintained by Iago Mosqueira. Last updated 10 days ago.
16.4 match 2 stars 6.86 score 254 scripts 6 dependentsr-spatial
link2GI:Linking Geographic Information Systems, Remote Sensing and Other Command Line Tools
Functions and tools for using open GIS and remote sensing command-line interfaces in a reproducible environment.
Maintained by Chris Reudenbach. Last updated 4 months ago.
12.3 match 26 stars 9.05 score 78 scripts 1 dependentsisglobal-brge
SNPassoc:SNPs-Based Whole Genome Association Studies
Functions to perform most of the common analysis in genome association studies are implemented. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented. Max-statistic and genetic risk-allele score exact distributions are also possible to be estimated. The methods are described in Gonzalez JR et al., 2007 <doi: 10.1093/bioinformatics/btm025>.
Maintained by Dolors Pelegri. Last updated 5 months ago.
12.0 match 16 stars 9.14 score 89 scripts 6 dependentsr-spatial
sf:Simple Features for R
Support for simple feature access, a standardized way to encode and analyze spatial vector data. Binds to 'GDAL' <doi: 10.5281/zenodo.5884351> for reading and writing data, to 'GEOS' <doi: 10.5281/zenodo.11396894> for geometrical operations, and to 'PROJ' <doi: 10.5281/zenodo.5884394> for projection conversions and datum transformations. Uses by default the 's2' package for geometry operations on geodetic (long/lat degree) coordinates.
Maintained by Edzer Pebesma. Last updated 16 days ago.
4.8 match 1.4k stars 22.42 score 117k scripts 1.2k dependentse-kotov
rJavaEnv:'Java' Environments for R Projects
Quickly install 'Java Development Kit (JDK)' without administrative privileges and set environment variables in current R session or project to solve common issues with 'Java' environment management in 'R'. Recommended to users of 'Java'/'rJava'-dependent 'R' packages such as 'r5r', 'opentripplanner', 'xlsx', 'openNLP', 'rWeka', 'RJDBC', 'tabulapdf', and many more. 'rJavaEnv' prevents common problems like 'Java' not found, 'Java' version conflicts, missing 'Java' installations, and the inability to install 'Java' due to lack of administrative privileges. 'rJavaEnv' automates the download, installation, and setup of the 'Java' on a per-project basis by setting the relevant 'JAVA_HOME' in the current 'R' session or the current working directory (via '.Rprofile', with the user's consent). Similar to what 'renv' does for 'R' packages, 'rJavaEnv' allows different 'Java' versions to be used across different projects, but can also be configured to allow multiple versions within the same project (e.g. with the help of 'targets' package). Note: there are a few extra steps for 'Linux' users, who don't have any 'Java' previously installed in their system, and who prefer package installation from source, rather then installing binaries from 'Posit Package Manager'. See documentation for details.
Maintained by Egor Kotov. Last updated 10 days ago.
environmentsjavareproducibilityreproducible-research
16.0 match 13 stars 6.74 score 7 scriptsopenair-project
worldmet:Import Surface Meteorological Data from NOAA Integrated Surface Database (ISD)
Functions to import data from more than 30,000 surface meteorological sites around the world managed by the National Oceanic and Atmospheric Administration (NOAA) Integrated Surface Database (ISD, see <https://www.ncei.noaa.gov/products/land-based-station/integrated-surface-database>).
Maintained by David Carslaw. Last updated 2 months ago.
15.0 match 55 stars 7.06 score 77 scriptstguillerme
dispRity:Measuring Disparity
A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics. The package also provides functions for looking at disparity in a serial way (e.g. disparity through time) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.
Maintained by Thomas Guillerme. Last updated 2 days ago.
disparityecologymultidimensionalitypalaeobiology
12.1 match 26 stars 8.69 score 220 scripts 1 dependentsivanwilli
DemoKin:Estimate Population Kin Distribution
Estimate population kin counts and its distribution by type, age and sex. The package implements one-sex and two-sex framework for studying living-death availability, with time varying rates or not, and multi-stage model.
Maintained by Iván Williams. Last updated 18 days ago.
19.0 match 23 stars 5.51 score 20 scriptsnguyennico
planr:Tools for Supply Chain Management, Demand and Supply Planning
Perform flexible and quick calculations for Demand and Supply Planning, such as projected inventories and coverages, as well as replenishment plan. For any time bucket, daily, weekly or monthly, and any granularity level, product or group of products.
Maintained by Nicolas Nguyen. Last updated 20 days ago.
14.8 match 43 stars 7.01 score 12 scriptszarquon42b
Morpho:Calculations and Visualisations Related to Geometric Morphometrics
A toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.
Maintained by Stefan Schlager. Last updated 5 months ago.
10.3 match 51 stars 10.00 score 218 scripts 13 dependentsclugen
clugenr:Multidimensional Cluster Generation Using Support Lines
An implementation of the clugen algorithm for generating multidimensional clusters with arbitrary distributions. Each cluster is supported by a line segment, the position, orientation and length of which guide where the respective points are placed. This package is described in Fachada & de Andrade (2023) <doi:10.1016/j.knosys.2023.110836>.
Maintained by Nuno Fachada. Last updated 7 months ago.
multidimensional-clustersmultidimensional-datasynthetic-clusterssynthetic-data-generatorsynthetic-dataset-generation
19.1 match 5 stars 5.39 score 14 scriptsropensci
targets:Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
Pipeline tools coordinate the pieces of computationally demanding analysis projects. The 'targets' package is a 'Make'-like pipeline tool for statistics and data science in R. The package skips costly runtime for tasks that are already up to date, orchestrates the necessary computation with implicit parallel computing, and abstracts files as R objects. If all the current output matches the current upstream code and data, then the whole pipeline is up to date, and the results are more trustworthy than otherwise. The methodology in this package borrows from GNU 'Make' (2015, ISBN:978-9881443519) and 'drake' (2018, <doi:10.21105/joss.00550>).
Maintained by William Michael Landau. Last updated 2 days ago.
data-sciencehigh-performance-computingmakepeer-reviewedpipeliner-targetopiareproducibilityreproducible-researchtargetsworkflow
6.8 match 973 stars 15.20 score 4.6k scripts 22 dependentsstatistikat
VIM:Visualization and Imputation of Missing Values
New tools for the visualization of missing and/or imputed values are introduced, which can be used for exploring the data and the structure of the missing and/or imputed values. Depending on this structure of the missing values, the corresponding methods may help to identify the mechanism generating the missing values and allows to explore the data including missing values. In addition, the quality of imputation can be visually explored using various univariate, bivariate, multiple and multivariate plot methods. A graphical user interface available in the separate package VIMGUI allows an easy handling of the implemented plot methods.
Maintained by Matthias Templ. Last updated 7 months ago.
hotdeckimputation-methodsmodel-predictionsvisualizationcpp
7.1 match 85 stars 14.44 score 2.6k scripts 19 dependentss-u
proj4:A simple interface to the PROJ.4 cartographic projections library
A simple interface to lat/long projection and datum transformation of the PROJ.4 cartographic projections library. It allows transformation of geographic coordinates from one projection and/or datum to another.
Maintained by Simon Urbanek. Last updated 1 years ago.
12.9 match 3 stars 7.94 score 408 scripts 39 dependentskwb-r
kwb.qmra:QMRA (quantitative microbial risk assessment)
QMRA for water supply systems.
Maintained by Michael Rustler. Last updated 4 years ago.
project-aquanesproject-demowareproject-smartcontrolqmraqmra-webapp-backend-engine
22.5 match 4 stars 4.53 score 21 scriptsdmurdoch
rgl:3D Visualization Using OpenGL
Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Maintained by Duncan Murdoch. Last updated 2 months ago.
graphicsopenglrglwebgllibglulibglvndlibpnglibx11freetypecpp
5.8 match 91 stars 17.49 score 7.3k scripts 300 dependentshanase
wpp2017:World Population Prospects 2017
Provides data from the United Nation's World Population Prospects 2017.
Maintained by Hana Sevcikova. Last updated 5 years ago.
39.4 match 1 stars 2.56 score 30 scripts 4 dependentsrichardli
SUMMER:Small-Area-Estimation Unit/Area Models and Methods for Estimation in R
Provides methods for spatial and spatio-temporal smoothing of demographic and health indicators using survey data, with particular focus on estimating and projecting under-five mortality rates, described in Mercer et al. (2015) <doi:10.1214/15-AOAS872>, Li et al. (2019) <doi:10.1371/journal.pone.0210645>, Wu et al. (DHS Spatial Analysis Reports No. 21, 2021), and Li et al. (2023) <doi:10.48550/arXiv.2007.05117>.
Maintained by Zehang R Li. Last updated 2 months ago.
bayesian-inferencesmall-area-estimationspace-time
9.7 match 23 stars 10.28 score 134 scripts 2 dependentsericmarcon
entropart:Entropy Partitioning to Measure Diversity
Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>. 'entropart' provides functions to calculate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity. Estimation-bias corrections are available.
Maintained by Eric Marcon. Last updated 2 months ago.
biodiversitydiversityentropy-partitioningestimatormeasurespecies
12.8 match 9 stars 7.81 score 115 scripts 1 dependentsusaid-oha-si
glamr:SI Utilities Package
Provides a series of base functions useful to the GH OHA SI team. This includes project setup, pulling from DATIM, and key functions for working with the MSD.
Maintained by Aaron Chafetz. Last updated 6 months ago.
13.4 match 2 stars 7.28 score 1.3k scripts 1 dependentsbioc
genArise:Microarray Analysis tool
genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.
Maintained by IFC Development Team. Last updated 5 months ago.
microarraytwochannelpreprocessing
22.6 match 4.30 score 1 scriptsbioc
CytoMDS:Low Dimensions projection of cytometry samples
This package implements a low dimensional visualization of a set of cytometry samples, in order to visually assess the 'distances' between them. This, in turn, can greatly help the user to identify quality issues like batch effects or outlier samples, and/or check the presence of potential sample clusters that might align with the exeprimental design. The CytoMDS algorithm combines, on the one hand, the concept of Earth Mover's Distance (EMD), a.k.a. Wasserstein metric and, on the other hand, the Multi Dimensional Scaling (MDS) algorithm for the low dimensional projection. Also, the package provides some diagnostic tools for both checking the quality of the MDS projection, as well as tools to help with the interpretation of the axes of the projection.
Maintained by Philippe Hauchamps. Last updated 2 months ago.
flowcytometryqualitycontroldimensionreductionmultidimensionalscalingsoftwarevisualization
18.2 match 1 stars 5.32 score 2 scriptskzst
mfpp:'Matrix-Based Flexible Project Planning'
Matrix-Based Flexible Project Planning. This package models, plans, and schedules flexible, such as agile, extreme, and hybrid project plans. The package contains project planning, scheduling, and risk assessment functions. Kosztyan (2022) <doi:10.1016/j.softx.2022.100973>.
Maintained by Zsolt T. Kosztyan. Last updated 3 months ago.
32.3 match 3.00 score 1 scriptsecospat
ecospat:Spatial Ecology Miscellaneous Methods
Collection of R functions and data sets for the support of spatial ecology analyses with a focus on pre, core and post modelling analyses of species distribution, niche quantification and community assembly. Written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) and Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland. Read Di Cola et al. (2016) <doi:10.1111/ecog.02671> for details.
Maintained by Olivier Broennimann. Last updated 1 months ago.
10.3 match 32 stars 9.35 score 418 scripts 1 dependentsthinkr-open
rtodoist:Create and Manage Todolist using 'Todoist.com' API
Allows you to interact with the API of the "Todoist" platform. 'Todoist' <https://todoist.com/> provides an online task manager service for teams.
Maintained by Cervan Girard. Last updated 2 years ago.
20.1 match 12 stars 4.78 score 7 scriptssatijalab
SeuratObject:Data Structures for Single Cell Data
Defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. Provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.
Maintained by Paul Hoffman. Last updated 1 years ago.
8.2 match 25 stars 11.69 score 1.2k scripts 88 dependentspvanlaake
CFtime:Using CF-Compliant Calendars with Climate Projection Data
Support for all calendars as specified in the Climate and Forecast (CF) Metadata Conventions for climate and forecasting data. The CF Metadata Conventions is widely used for distributing files with climate observations or projections, including the Coupled Model Intercomparison Project (CMIP) data used by climate change scientists and the Intergovernmental Panel on Climate Change (IPCC). This package specifically allows the user to work with any of the CF-compliant calendars (many of which are not compliant with POSIXt). The CF time coordinate is formally defined in the CF Metadata Conventions document available at <https://cfconventions.org/Data/cf-conventions/cf-conventions-1.12/cf-conventions.html#time-coordinate>.
Maintained by Patrick Van Laake. Last updated 10 days ago.
10.4 match 5 stars 9.20 score 48 scripts 15 dependentsthinkr-open
golem:A Framework for Robust Shiny Applications
An opinionated framework for building a production-ready 'Shiny' application. This package contains a series of tools for building a robust 'Shiny' application from start to finish.
Maintained by Colin Fay. Last updated 7 months ago.
golemversehacktoberfestshinyshiny-appsshiny-rshinyapps
6.7 match 921 stars 14.23 score 167 scripts 62 dependentsdankelley
oce:Analysis of Oceanographic Data
Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature. This package is discussed extensively by Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.
Maintained by Dan Kelley. Last updated 1 days ago.
5.9 match 146 stars 15.42 score 4.2k scripts 18 dependentsbioc
chevreulShiny:Tools for managing SingleCellExperiment objects as projects
Tools for managing SingleCellExperiment objects as projects. Includes functions for analysis and visualization of single-cell data. Also included is a shiny app for visualization of pre-processed scRNA data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.
Maintained by Kevin Stachelek. Last updated 13 days ago.
coveragernaseqsequencingvisualizationgeneexpressiontranscriptionsinglecelltranscriptomicsnormalizationpreprocessingqualitycontroldimensionreductiondataimport
17.9 match 5.08 scorer-lib
lintr:A 'Linter' for R Code
Checks adherence to a given style, syntax errors and possible semantic issues. Supports on the fly checking of R code edited with 'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text', 'Atom' and 'Visual Studio Code'.
Maintained by Michael Chirico. Last updated 9 days ago.
5.3 match 1.2k stars 17.00 score 916 scripts 33 dependentsopenair-project
openairmaps:Create Maps of Air Pollution Data
Combine the air quality data analysis methods of 'openair' with the JavaScript 'Leaflet' (<https://leafletjs.com/>) library. Functionality includes plotting site maps, "directional analysis" figures such as polar plots, and air mass trajectories.
Maintained by Jack Davison. Last updated 1 days ago.
15.0 match 21 stars 6.04 score 47 scriptssantoroma
CircSpaceTime:Spatial and Spatio-Temporal Bayesian Model for Circular Data
Implementation of Bayesian models for spatial and spatio-temporal interpolation of circular data using Gaussian Wrapped and Gaussian Projected distributions. We developed the methods described in Jona Lasinio G. et al. (2012) <doi: 10.1214/12-aoas576>, Wang F. et al. (2014) <doi: 10.1080/01621459.2014.934454> and Mastrantonio G. et al. (2016) <doi: 10.1007/s11749-015-0458-y>.
Maintained by Mario Santoro. Last updated 6 years ago.
bayesian-statisticscircular-statisticsprojected-gaussianprojected-normalspatial-data-analysisspatio-temporalwrapped-gaussianwrapped-normalopenblascppopenmp
22.5 match 7 stars 3.98 score 27 scriptsadeckmyn
mapproj:Map Projections
Converts latitude/longitude into projected coordinates.
Maintained by Alex Deckmyn. Last updated 2 years ago.
10.3 match 3 stars 8.63 score 2.6k scripts 56 dependentsddsjoberg
starter:Starter Kit for New Projects
Get started with new projects by dropping a skeleton of a new project into a new or existing directory, initialise git repositories, and create reproducible environments with the 'renv' package. The package allows for dynamically named files, folders, file content, as well as the functionality to drop individual template files into existing projects.
Maintained by Daniel D. Sjoberg. Last updated 5 months ago.
14.3 match 27 stars 6.18 score 28 scriptsstrengejacke
ggeffects:Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs
Compute marginal effects and adjusted predictions from statistical models and returns the result as tidy data frames. These data frames are ready to use with the 'ggplot2'-package. Effects and predictions can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The main functions are ggpredict(), ggemmeans() and ggeffect(). There is a generic plot()-method to plot the results using 'ggplot2'.
Maintained by Daniel Lüdecke. Last updated 5 days ago.
estimated-marginal-meanshacktoberfestmarginal-effectsprediction
5.6 match 588 stars 15.55 score 3.6k scripts 7 dependentsropensci
osfr:Interface to the 'Open Science Framework' ('OSF')
An interface for interacting with 'OSF' (<https://osf.io>). 'osfr' enables you to access open research materials and data, or create and manage your own private or public projects.
Maintained by Aaron Wolen. Last updated 8 months ago.
open-scienceosfreproducible-research
8.5 match 145 stars 10.18 score 588 scripts 3 dependentspik-piam
piamInterfaces:Project specific interfaces to REMIND / MAgPIE
Project specific interfaces to REMIND / MAgPIE.
Maintained by Falk Benke. Last updated 2 days ago.
13.0 match 6.63 score 38 scripts 7 dependentsnatydasilva
PPforest:Projection Pursuit Classification Forest
Implements projection pursuit forest algorithm for supervised classification.
Maintained by Natalia da Silva. Last updated 8 months ago.
15.4 match 18 stars 5.53 score 19 scriptstlverse
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-scienceensemble-learningensemble-modelmachine-learningmodel-selectionregressionstackingstatistics
8.6 match 100 stars 9.94 score 748 scripts 7 dependentsropensci
stplanr:Sustainable Transport Planning
Tools for transport planning with an emphasis on spatial transport data and non-motorized modes. The package was originally developed to support the 'Propensity to Cycle Tool', a publicly available strategic cycle network planning tool (Lovelace et al. 2017) <doi:10.5198/jtlu.2016.862>, but has since been extended to support public transport routing and accessibility analysis (Moreno-Monroy et al. 2017) <doi:10.1016/j.jtrangeo.2017.08.012> and routing with locally hosted routing engines such as 'OSRM' (Lowans et al. 2023) <doi:10.1016/j.enconman.2023.117337>. The main functions are for creating and manipulating geographic "desire lines" from origin-destination (OD) data (building on the 'od' package); calculating routes on the transport network locally and via interfaces to routing services such as <https://cyclestreets.net/> (Desjardins et al. 2021) <doi:10.1007/s11116-021-10197-1>; and calculating route segment attributes such as bearing. The package implements the 'travel flow aggregration' method described in Morgan and Lovelace (2020) <doi:10.1177/2399808320942779> and the 'OD jittering' method described in Lovelace et al. (2022) <doi:10.32866/001c.33873>. Further information on the package's aim and scope can be found in the vignettes and in a paper in the R Journal (Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053>, and in a paper outlining the landscape of open source software for geographic methods in transport planning (Lovelace, 2021) <doi:10.1007/s10109-020-00342-2>.
Maintained by Robin Lovelace. Last updated 7 months ago.
cyclecyclingdesire-linesorigin-destinationpeer-reviewedpubic-transportroute-networkroutesroutingspatialtransporttransport-planningtransportationwalking
6.9 match 427 stars 12.31 score 684 scripts 3 dependentstdhock
directlabels:Direct Labels for Multicolor Plots
An extensible framework for automatically placing direct labels onto multicolor 'lattice' or 'ggplot2' plots. Label positions are described using Positioning Methods which can be re-used across several different plots. There are heuristics for examining "trellis" and "ggplot" objects and inferring an appropriate Positioning Method.
Maintained by Toby Dylan Hocking. Last updated 11 months ago.
8.0 match 83 stars 10.62 score 1.8k scripts 16 dependentsamices
mice:Multivariate Imputation by Chained Equations
Multiple imputation using Fully Conditional Specification (FCS) implemented by the MICE algorithm as described in Van Buuren and Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has its own imputation model. Built-in imputation models are provided for continuous data (predictive mean matching, normal), binary data (logistic regression), unordered categorical data (polytomous logistic regression) and ordered categorical data (proportional odds). MICE can also impute continuous two-level data (normal model, pan, second-level variables). Passive imputation can be used to maintain consistency between variables. Various diagnostic plots are available to inspect the quality of the imputations.
Maintained by Stef van Buuren. Last updated 6 days ago.
chained-equationsfcsimputationmicemissing-datamissing-valuesmultiple-imputationmultivariate-datacpp
5.1 match 462 stars 16.50 score 10k scripts 154 dependentsg6t
cloudfs:Streamlined Interface to Interact with Cloud Storage Platforms
A unified interface for simplifying cloud storage interactions, including uploading, downloading, reading, and writing files, with functions for both 'Google Drive' (<https://www.google.com/drive/>) and 'Amazon S3' (<https://aws.amazon.com/s3/>).
Maintained by Iaroslav Domin. Last updated 10 months ago.
19.5 match 2 stars 4.30 score 3 scriptsjonathanlees
GEOmap:Topographic and Geologic Mapping
Set of routines for making map projections (forward and inverse), topographic maps, perspective plots, geological maps, geological map symbols, geological databases, interactive plotting and selection of focus regions.
Maintained by Jonathan M. Lees. Last updated 8 months ago.
24.8 match 3.38 score 162 scripts 3 dependentsyihui
xfun:Supporting Functions for Packages Maintained by 'Yihui Xie'
Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Maintained by Yihui Xie. Last updated 3 days ago.
4.6 match 145 stars 18.18 score 916 scripts 4.4k dependentstherneau
survival:Survival Analysis
Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
Maintained by Terry M Therneau. Last updated 3 months ago.
4.0 match 400 stars 20.43 score 29k scripts 3.9k dependentsbioc
recount3:Explore and download data from the recount3 project
The recount3 package enables access to a large amount of uniformly processed RNA-seq data from human and mouse. You can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level with sample metadata and QC statistics. In addition we provide access to sample coverage BigWig files.
Maintained by Leonardo Collado-Torres. Last updated 3 months ago.
coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportannotation-agnosticbioconductorcountderfinderexongenehumanilluminajunctionmouserecountrecount3
9.9 match 33 stars 8.03 score 216 scriptsnspyrison
spinifex:Manual Tours, Manual Control of Dynamic Projections of Numeric Multivariate Data
Data visualization tours animates linear projection of multivariate data as its basis (ie. orientation) changes. The 'spinifex' packages generates paths for manual tours by manipulating the contribution of a single variable at a time Cook & Buja (1997) <doi:10.1080/10618600.1997.10474754>. Other types of tours, such as grand (random walk) and guided (optimizing some objective function) are available in the 'tourr' package Wickham et al. <doi:10.18637/jss.v040.i02>. 'spinifex' builds on 'tourr' and can render tours with 'gganimate' and 'plotly' graphics, and allows for exporting as an .html widget and as an .gif, respectively. This work is fully discussed in Spyrison & Cook (2020) <doi:10.32614/RJ-2020-027>.
Maintained by Nicholas Spyrison. Last updated 2 months ago.
dimensionreductiontoursvisualization
12.6 match 3 stars 6.28 score 105 scripts 1 dependentsbioc
GenomicDataCommons:NIH / NCI Genomic Data Commons Access
Programmatically access the NIH / NCI Genomic Data Commons RESTful service.
Maintained by Sean Davis. Last updated 1 months ago.
dataimportsequencingapi-clientbioconductorbioinformaticscancercore-servicesdata-sciencegenomicsncitcgavignette
6.5 match 87 stars 11.94 score 238 scripts 12 dependentsemilyriederer
projmgr:Task Tracking and Project Management with GitHub
Provides programmatic access to 'GitHub' API with a focus on project management. Key functionality includes setting up issues and milestones from R objects or 'YAML' configurations, querying outstanding or completed tasks, and generating progress updates in tables, charts, and RMarkdown reports. Useful for those using 'GitHub' in personal, professional, or academic settings with an emphasis on streamlining the workflow of data analysis projects.
Maintained by Emily Riederer. Last updated 1 years ago.
11.3 match 124 stars 6.84 score 34 scripts 5 dependentscsids
org:Organising Projects
A framework to help you organize projects. Most analyses have three (or more) main sections: code, results, and data, each with different requirements (version control/sharing/encryption). You provide folder locations and 'org' helps you take care of the details.
Maintained by Richard Aubrey White. Last updated 6 days ago.
13.1 match 1 stars 5.78 score 60 scriptspadrinodb
ipmr:Integral Projection Models
Flexibly implements Integral Projection Models using a mathematical(ish) syntax. This package will not help with the vital rate modeling process, but will help convert those regression models into an IPM. 'ipmr' handles density dependence and environmental stochasticity, with a couple of options for implementing the latter. In addition, provides functions to avoid unintentional eviction of individuals from models. Additionally, provides model diagnostic tools, plotting functionality, stochastic/deterministic simulations, and analysis tools. Integral projection models are described in depth by Easterling et al. (2000) <doi:10.1890/0012-9658(2000)081[0694:SSSAAN]2.0.CO;2>, Merow et al. (2013) <doi:10.1111/2041-210X.12146>, Rees et al. (2014) <doi:10.1111/1365-2656.12178>, and Metcalf et al. (2015) <doi:10.1111/2041-210X.12405>. Williams et al. (2012) <doi:10.1890/11-2147.1> discuss the problem of unintentional eviction.
Maintained by Sam Levin. Last updated 5 months ago.
demographyintegral-projection-modelscpp
10.8 match 7 stars 6.92 score 66 scripts 1 dependentsbradleyjeck
epanet2toolkit:Call 'EPANET' Functions to Simulate Pipe Networks
Enables simulation of water piping networks using 'EPANET'. The package provides functions from the 'EPANET' programmer's toolkit as R functions so that basic or customized simulations can be carried out from R. The package uses 'EPANET' version 2.2 from Open Water Analytics <https://github.com/OpenWaterAnalytics/EPANET/releases/tag/v2.2>.
Maintained by Bradley Eck. Last updated 3 months ago.
epanetepanet-apisimulationwaterwater-distribution-networks
14.3 match 15 stars 5.17 score 66 scriptstylerjpike
sovereign:State-Dependent Empirical Analysis
A set of tools for state-dependent empirical analysis through both VAR- and local projection-based state-dependent forecasts, impulse response functions, historical decompositions, and forecast error variance decompositions.
Maintained by Tyler J. Pike. Last updated 2 years ago.
econometricsforecastingimpulse-responselocal-projectionmacroeconomicsstate-dependenttime-seriesvector-autoregression
15.4 match 11 stars 4.74 score 8 scriptsscholaempirica
reschola:The Schola Empirica Package
A collection of utilies, themes and templates for data analysis at Schola Empirica.
Maintained by Jan Netík. Last updated 5 months ago.
14.8 match 4 stars 4.83 score 14 scriptscvxgrp
CVXR:Disciplined Convex Optimization
An object-oriented modeling language for disciplined convex programming (DCP) as described in Fu, Narasimhan, and Boyd (2020, <doi:10.18637/jss.v094.i14>). It allows the user to formulate convex optimization problems in a natural way following mathematical convention and DCP rules. The system analyzes the problem, verifies its convexity, converts it into a canonical form, and hands it off to an appropriate solver to obtain the solution. Interfaces to solvers on CRAN and elsewhere are provided, both commercial and open source.
Maintained by Anqi Fu. Last updated 4 months ago.
5.6 match 207 stars 12.89 score 768 scripts 51 dependentsbbuchsbaum
multivarious:Extensible Data Structures for Multivariate Analysis
Provides a set of basic and extensible data structures and functions for multivariate analysis, including dimensionality reduction techniques, projection methods, and preprocessing functions. The aim of this package is to offer a flexible and user-friendly framework for multivariate analysis that can be easily extended for custom requirements and specific data analysis tasks.
Maintained by Bradley Buchsbaum. Last updated 3 months ago.
20.2 match 3.53 score 17 scriptsvalentint
rrcov:Scalable Robust Estimators with High Breakdown Point
Robust Location and Scatter Estimation and Robust Multivariate Analysis with High Breakdown Point: principal component analysis (Filzmoser and Todorov (2013), <doi:10.1016/j.ins.2012.10.017>), linear and quadratic discriminant analysis (Todorov and Pires (2007)), multivariate tests (Todorov and Filzmoser (2010) <doi:10.1016/j.csda.2009.08.015>), outlier detection (Todorov et al. (2010) <doi:10.1007/s11634-010-0075-2>). See also Todorov and Filzmoser (2009) <urn:isbn:978-3838108148>, Todorov and Filzmoser (2010) <doi:10.18637/jss.v032.i03> and Boudt et al. (2019) <doi:10.1007/s11222-019-09869-x>.
Maintained by Valentin Todorov. Last updated 7 months ago.
6.7 match 2 stars 10.57 score 484 scripts 96 dependentsjulianfaraway
faraway:Datasets and Functions for Books by Julian Faraway
Books are "Linear Models with R" published 1st Ed. August 2004, 2nd Ed. July 2014, 3rd Ed. February 2025 by CRC press, ISBN 9781439887332, and "Extending the Linear Model with R" published by CRC press in 1st Ed. December 2005 and 2nd Ed. March 2016, ISBN 9781584884248 and "Practical Regression and ANOVA in R" contributed documentation on CRAN (now very dated).
Maintained by Julian Faraway. Last updated 1 months ago.
7.5 match 29 stars 9.43 score 1.7k scripts 1 dependentsolivroy
reuseme:Collections of Utility Functions to Work Across Projects
Allows you to browse current projects, rename files safely, add screenshots to project on Windows. It is also my personal library and contains wrapper around common functions, from dplyr and readxl. It takes advantage of cli hyperlinks. Finally, it provides a custom print method for tibbles, inspired by janitor, and readr.
Maintained by Olivier Roy. Last updated 26 days ago.
18.4 match 5 stars 3.83 score 3 scriptsresourcecode-project
resourcecode:Access to the 'RESOURCECODE' Hindcast Database
Utility functions to download data from the 'RESOURCECODE' hindcast database of sea-states, time series of sea-state parameters and time series of 1D and 2D wave spectra. See <https://resourcecode.ifremer.fr> for more details about the available data. Also provides facilities to plot and analyse downloaded data, such as computing the sea-state parameters from both the 1D and 2D surface elevation variance spectral density.
Maintained by Nicolas Raillard. Last updated 3 months ago.
15.0 match 1 stars 4.65 score 4 scriptspbs-assess
sdmTMB:Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
Implements spatial and spatiotemporal GLMMs (Generalized Linear Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial Differential Equation) Gaussian Markov random field approximation to Gaussian random fields. One common application is for spatially explicit species distribution models (SDMs). See Anderson et al. (2024) <doi:10.1101/2022.03.24.485545>.
Maintained by Sean C. Anderson. Last updated 2 days ago.
ecologyglmmspatial-analysisspecies-distribution-modellingtmbcpp
6.4 match 203 stars 10.71 score 848 scripts 1 dependentsbioc
chevreulProcess:Tools for managing SingleCellExperiment objects as projects
Tools analyzing SingleCellExperiment objects as projects. for input into the Chevreul app downstream. Includes functions for analysis of single cell RNA sequencing data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.
Maintained by Kevin Stachelek. Last updated 1 months ago.
coveragernaseqsequencingvisualizationgeneexpressiontranscriptionsinglecelltranscriptomicsnormalizationpreprocessingqualitycontroldimensionreductiondataimport
12.8 match 5.38 score 2 scripts 2 dependentsblue-matter
SAMtool:Stock Assessment Methods Toolkit
Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform data-rich fisheries. 'SAMtool' provides a conditioning model, assessment models of varying complexity with standardized reporting, model-based management procedures, and diagnostic tools for evaluating assessments inside closed-loop simulation.
Maintained by Quang Huynh. Last updated 20 days ago.
10.6 match 3 stars 6.49 score 36 scripts 1 dependentscran
BoundaryStats:Boundary Overlap Statistics
Analysis workflow for finding geographic boundaries of ecological or landscape traits and comparing the placement of geographic boundaries of two traits. If data are trait values, trait data are transformed to boundary intensities based on approximate first derivatives across latitude and longitude. The package includes functions to create custom null models based on the input data. The boundary statistics are described in: Fortin, Drapeau, and Jacquez (1996) <doi:10.2307/3545584>.
Maintained by Amy Luo. Last updated 5 months ago.
25.4 match 2.70 score 3 scriptsicarda-git
QBMS:Query the Breeding Management System(s)
This R package assists breeders in linking data systems with their analytic pipelines, a crucial step in digitizing breeding processes. It supports querying and retrieving phenotypic and genotypic data from systems like 'EBS' <https://ebs.excellenceinbreeding.org/>, 'BMS' <https://bmspro.io>, 'BreedBase' <https://breedbase.org>, and 'GIGWA' <https://github.com/SouthGreenPlatform/Gigwa2> (using 'BrAPI' <https://brapi.org> calls). Extra helper functions support environmental data sources, including 'TerraClimate' <https://www.climatologylab.org/terraclimate.html> and 'FAO' 'HWSDv2' <https://gaez.fao.org/pages/hwsd> soil database.
Maintained by Khaled Al-Shamaa. Last updated 6 months ago.
8.7 match 8 stars 7.85 score 33 scripts 1 dependentsmthrun
GeneralizedUmatrix:Credible Visualization for Two-Dimensional Projections of Data
Projections are common dimensionality reduction methods, which represent high-dimensional data in a two-dimensional space. However, when restricting the output space to two dimensions, which results in a two dimensional scatter plot (projection) of the data, low dimensional similarities do not represent high dimensional distances coercively [Thrun, 2018] <DOI: 10.1007/978-3-658-20540-9>. This could lead to a misleading interpretation of the underlying structures [Thrun, 2018]. By means of the 3D topographic map the generalized Umatrix is able to depict errors of these two-dimensional scatter plots. The package is derived from the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9> and the main algorithm called simplified self-organizing map for dimensionality reduction methods is published in <DOI: 10.1016/j.mex.2020.101093>.
Maintained by Michael Thrun. Last updated 2 months ago.
11.2 match 1 stars 5.97 score 52 scripts 6 dependentskwb-r
kwb.nextcloud:R Package for Accessing Nextcloud Using WebDAV API
R package to access file infos or download data from an Nextcloud instance using the WebDav API (https://docs.nextcloud.com/server/17/developer_manual/client_apis/WebDAV/).
Maintained by Michael Rustler. Last updated 5 months ago.
apinextcloudproject-dwcproject-ultimate
15.0 match 6 stars 4.43 score 2 scripts 3 dependentsswarm-lab
trackdf:Data Frame Class for Tracking Data
Data frame class for storing collective movement data (e.g. fish schools, ungulate herds, baboon troops) collected from GPS trackers or computer vision tracking software.
Maintained by Simon Garnier. Last updated 2 years ago.
animal-behavioranimal-behaviourgpsgps-data
12.2 match 4 stars 5.42 score 11 scripts 1 dependentsgenie-bpc
genieBPC:Project GENIE BioPharma Collaborative Data Processing Pipeline
The American Association Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE) BioPharma Collaborative represents a multi-year, multi-institution effort to build a pan-cancer repository of linked clinico-genomic data. The genomic and clinical data are provided in multiple releases (separate releases for each cancer cohort with updates following data corrections), which are stored on the data sharing platform 'Synapse' <https://www.synapse.org/>. The 'genieBPC' package provides a seamless way to obtain the data corresponding to each release from 'Synapse' and to prepare datasets for analysis.
Maintained by Jessica A. Lavery. Last updated 8 months ago.
8.8 match 9 stars 7.57 score 26 scriptsashbaldry
vstsr:Access to 'Azure DevOps' API via R
Implementation of 'Azure DevOps' <https://azure.microsoft.com/> API calls. It enables the extraction of information about repositories, build and release definitions and individual releases. It also helps create repositories and work items within a project without logging into 'Azure DevOps'. There is the ability to use any API service with a shell for any non-predefined call.
Maintained by Ashley Baldry. Last updated 2 years ago.
18.6 match 5 stars 3.54 score 14 scriptsluca-scr
mclust:Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation
Gaussian finite mixture models fitted via EM algorithm for model-based clustering, classification, and density estimation, including Bayesian regularization, dimension reduction for visualisation, and resampling-based inference.
Maintained by Luca Scrucca. Last updated 11 months ago.
5.3 match 21 stars 12.23 score 6.6k scripts 587 dependentsegenn
rtemis:Machine Learning and Visualization
Advanced Machine Learning and Visualization. Unsupervised Learning (Clustering, Decomposition), Supervised Learning (Classification, Regression), Cross-Decomposition, Bagging, Boosting, Meta-models. Static and interactive graphics.
Maintained by E.D. Gennatas. Last updated 1 months ago.
data-sciencedata-visualizationmachine-learningmachine-learning-libraryvisualization
9.1 match 145 stars 7.09 score 50 scripts 2 dependentswinvector
rquery:Relational Query Generator for Data Manipulation at Scale
A piped query generator based on Edgar F. Codd's relational algebra, and on production experience using 'SQL' and 'dplyr' at big data scale. The design represents an attempt to make 'SQL' more teachable by denoting composition by a sequential pipeline notation instead of nested queries or functions. The implementation delivers reliable high performance data processing on large data systems such as 'Spark', databases, and 'data.table'. Package features include: data processing trees or pipelines as observable objects (able to report both columns produced and columns used), optimized 'SQL' generation as an explicit user visible table modeling step, plus explicit query reasoning and checking.
Maintained by John Mount. Last updated 2 years ago.
6.8 match 110 stars 9.53 score 126 scripts 3 dependentsface-it-project
FjordLight:Available Light Within the Water Column and on the Seafloor of Arctic Fjords
Satellite data collected between 2003 and 2022, in conjunction with gridded bathymetric data (50-150 m resolution), are used to estimate the irradiance reaching the bottom of a series of representative EU Arctic fjords. An Earth System Science Data (ESSD) manuscript, Schlegel et al. (2024), provides a detailed explanation of the methodology.
Maintained by Robert W. Schlegel. Last updated 7 months ago.
15.0 match 4.30 score 6 scriptsmhpob
otndo:Understand your OTN data
This package provides functions to summarize the various type of OTN-style data.
Maintained by Michael OBrien. Last updated 9 days ago.
animal-trackingbiotelemetryfishfisheriesvisualization
13.1 match 4 stars 4.92 score 6 scripts 1 dependentsropensci
babelquarto:Renders a Multilingual Quarto Book
Automate rendering and cross-linking of Quarto books following a prescribed structure.
Maintained by Maëlle Salmon. Last updated 1 months ago.
8.5 match 43 stars 7.52 score 23 scripts 1 dependentsweiliang
clusterGeneration:Random Cluster Generation (with Specified Degree of Separation)
We developed the clusterGeneration package to provide functions for generating random clusters, generating random covariance/correlation matrices, calculating a separation index (data and population version) for pairs of clusters or cluster distributions, and 1-D and 2-D projection plots to visualize clusters. The package also contains a function to generate random clusters based on factorial designs with factors such as degree of separation, number of clusters, number of variables, number of noisy variables.
Maintained by Weiliang Qiu. Last updated 2 years ago.
9.9 match 1 stars 6.45 score 225 scripts 94 dependentsnifu-no
saros.base:Base Tools for Semi-Automatic Reporting of Ordinary Surveys
Scaffold an entire web-based report using template chunks, based on a small chapter overview and a dataset. Highly adaptable with prefixes, suffixes, translations, etc. Also contains tools for password-protecting, e.g. for each organization's report on a website. Developed for the common case of a survey across multiple organizations/sites where each organization wants to obtain results for their organization compared with everyone else. See 'saros' (<https://CRAN.R-project.org/package=saros>) for tools used for authors in the drafted reports.
Maintained by Stephan Daus. Last updated 1 months ago.
10.4 match 1 stars 5.98 score 7 scriptsifellows
OpenStreetMap:Access to Open Street Map Raster Images
Accesses high resolution raster maps using the OpenStreetMap protocol. Dozens of road, satellite, and topographic map servers are directly supported, including Apple, Mapnik, Bing, and stamen. Additionally raster maps may be constructed using custom tile servers. Maps can be plotted using either base graphics, or ggplot2. This package is not affiliated with the OpenStreetMap.org mapping project.
Maintained by Ian Fellows. Last updated 1 years ago.
7.6 match 11 stars 8.09 score 498 scripts 4 dependentslearnitr
learnitgrid:Manage Rubrics or Assessment Grids for GitHub Repositories
Create and manage semi-automatically rubrics to assess GitHub projects (R scripts, R Markdown or Quarto files). Create directed projects where students have to complete documents and submit them to GitHub (classroom) so that they are evaluated using the rubric (or assessment grid).
Maintained by Philippe Grosjean. Last updated 9 months ago.
20.4 match 1 stars 3.00 score 7 scriptsglobeandmail
upstartr:Utilities Powering the Globe and Mail's Data Journalism Template
Core functions necessary for using The Globe and Mail's R data journalism template, 'startr', along with utilities for day-to-day data journalism tasks, such as reading and writing files, producing graphics and cleaning up datasets.
Maintained by Tom Cardoso. Last updated 1 years ago.
datadata-analysisdata-journalismdata-visualizationjournalismnews
14.5 match 6 stars 4.14 score 46 scriptsjlmelville
rnndescent:Nearest Neighbor Descent Method for Approximate Nearest Neighbors
The Nearest Neighbor Descent method for finding approximate nearest neighbors by Dong and co-workers (2010) <doi:10.1145/1963405.1963487>. Based on the 'Python' package 'PyNNDescent' <https://github.com/lmcinnes/pynndescent>.
Maintained by James Melville. Last updated 8 months ago.
approximate-nearest-neighbor-searchcpp
8.2 match 11 stars 7.31 score 75 scriptsphippsy
brandwatchR:'Brandwatch' API to R
Interact with the 'Brandwatch' API <https://developers.brandwatch.com/docs>. Allows you to authenticate to the API and obtain data for projects, queries, query groups tags and categories. Also allows you to directly obtain mentions and aggregate data for a specified query or query group.
Maintained by Donal Phipps. Last updated 7 years ago.
14.4 match 11 stars 4.16 score 26 scriptswa-department-of-agriculture
soils:Visualize and Report Soil Health Data
Collection of soil health data visualization and reporting tools, including a RStudio project template with everything you need to generate custom HTML and Microsoft Word reports for each participant in your soil health sampling project.
Maintained by Jadey N Ryan. Last updated 1 months ago.
10.4 match 11 stars 5.74 score 9 scriptspakillo
template:Generic template for data analysis projects structured as R packages
This package works as a template for new research or data analysis projects, under the idea of having everything (data, R scripts, functions and manuscript/reports) contained in the same package (a 'research compendium') to facilitate collaboration and promote reproducibility.
Maintained by Francisco Rodriguez-Sanchez. Last updated 4 years ago.
project-templateresearch-compendiumworkflow
12.7 match 175 stars 4.70 score 57 scriptsdfriend21
quadtree:Region Quadtrees for Spatial Data
Provides functionality for working with raster-like quadtrees (also called “region quadtrees”), which allow for variable-sized cells. The package allows for flexibility in the quadtree creation process. Several functions defining how to split and aggregate cells are provided, and custom functions can be written for both of these processes. In addition, quadtrees can be created using other quadtrees as “templates”, so that the new quadtree's structure is identical to the template quadtree. The package also includes functionality for modifying quadtrees, querying values, saving quadtrees to a file, and calculating least-cost paths using the quadtree as a resistance surface.
Maintained by Derek Friend. Last updated 2 years ago.
9.3 match 19 stars 6.34 score 58 scriptsgabriellajg
equaltestMI:Examine Measurement Invariance via Equivalence Testing and Projection Method
Functions for examining measurement invariance via equivalence testing are included in this package. The traditionally used RMSEA (Root Mean Square Error of Approximation) cutoff values are adjusted based on simulation results. In addition, a projection-based method is implemented to test the equality of latent factor means across groups without assuming the equality of intercepts. For more information, see Yuan, K. H., & Chan, W. (2016) <doi:10.1037/met0000080>, Deng, L., & Yuan, K. H. (2016) <doi:10.1007/s11336-015-9491-8>, and Jiang, G., Mai, Y., & Yuan, K. H. (2017) <doi:10.3389/fpsyg.2017.01823>.
Maintained by Ge Jiang. Last updated 4 years ago.
12.9 match 1 stars 4.58 score 19 scriptschrhennig
fpc:Flexible Procedures for Clustering
Various methods for clustering and cluster validation. Fixed point clustering. Linear regression clustering. Clustering by merging Gaussian mixture components. Symmetric and asymmetric discriminant projections for visualisation of the separation of groupings. Cluster validation statistics for distance based clustering including corrected Rand index. Standardisation of cluster validation statistics by random clusterings and comparison between many clustering methods and numbers of clusters based on this. Cluster-wise cluster stability assessment. Methods for estimation of the number of clusters: Calinski-Harabasz, Tibshirani and Walther's prediction strength, Fang and Wang's bootstrap stability. Gaussian/multinomial mixture fitting for mixed continuous/categorical variables. Variable-wise statistics for cluster interpretation. DBSCAN clustering. Interface functions for many clustering methods implemented in R, including estimating the number of clusters with kmeans, pam and clara. Modality diagnosis for Gaussian mixtures. For an overview see package?fpc.
Maintained by Christian Hennig. Last updated 6 months ago.
6.4 match 11 stars 9.25 score 2.6k scripts 70 dependentsjuliasilge
tidytext:Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools
Using tidy data principles can make many text mining tasks easier, more effective, and consistent with tools already in wide use. Much of the infrastructure needed for text mining with tidy data frames already exists in packages like 'dplyr', 'broom', 'tidyr', and 'ggplot2'. In this package, we provide functions and supporting data sets to allow conversion of text to and from tidy formats, and to switch seamlessly between tidy tools and existing text mining packages.
Maintained by Julia Silge. Last updated 11 months ago.
natural-language-processingtext-miningtidy-datatidyverse
3.5 match 1.2k stars 16.86 score 17k scripts 61 dependentsbioc
TrajectoryGeometry:This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns
Given a time series or pseudo-times series of gene expression data, we might wish to know: Do the changes in gene expression in these data exhibit directionality? Are there turning points in this directionality. Do different subsets of the data move in different directions? This package uses spherical geometry to probe these sorts of questions. In particular, if we are looking at (say) the first n dimensions of the PCA of gene expression, directionality can be detected as the clustering of points on the (n-1)-dimensional sphere.
Maintained by Michael Shapiro. Last updated 5 months ago.
biologicalquestionstatisticalmethodgeneexpressionsinglecell
12.8 match 4.60 score 7 scriptsocean-tracking-network
glatos:A package for the Great Lakes Acoustic Telemetry Observation System
Functions useful to members of the Great Lakes Acoustic Telemetry Observation System https://glatos.glos.us; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.
Maintained by Christopher Holbrook. Last updated 6 months ago.
9.1 match 10 stars 6.38 score 112 scriptsrspatial
terra:Spatial Data Analysis
Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).
Maintained by Robert J. Hijmans. Last updated 1 days ago.
geospatialrasterspatialvectoronetbbprojgdalgeoscpp
3.3 match 559 stars 17.64 score 17k scripts 851 dependentsjonathan-g
kayadata:Kaya Identity Data for Nations and Regions
Provides data for Kaya identity variables (population, gross domestic product, primary energy consumption, and energy-related CO2 emissions) for the world and for individual nations, and utility functions for looking up data, plotting trends of Kaya variables, and plotting the fuel mix for a given country or region. The Kaya identity (Yoichi Kaya and Keiichi Yokobori, "Environment, Energy, and Economy: Strategies for Sustainability" (United Nations University Press, 1998) and <https://en.wikipedia.org/wiki/Kaya_identity>) expresses a nation's or region's greenhouse gas emissions in terms of its population, per-capita Gross Domestic Product, the energy intensity of its economy, and the carbon-intensity of its energy supply.
Maintained by Jonathan Gilligan. Last updated 8 months ago.
11.7 match 4.98 score 32 scriptsbhklab
mRMRe:Parallelized Minimum Redundancy, Maximum Relevance (mRMR)
Computes mutual information matrices from continuous, categorical and survival variables, as well as feature selection with minimum redundancy, maximum relevance (mRMR) and a new ensemble mRMR technique. Published in De Jay et al. (2013) <doi:10.1093/bioinformatics/btt383>.
Maintained by Benjamin Haibe-Kains. Last updated 4 years ago.
6.5 match 19 stars 8.95 score 105 scripts 2 dependentspredictiveecology
Require:Installing and Loading R Packages for Reproducible Workflows
A single key function, 'Require' that makes rerun-tolerant versions of 'install.packages' and `require` for CRAN packages, packages no longer on CRAN (i.e., archived), specific versions of packages, and GitHub packages. This approach is developed to create reproducible workflows that are flexible and fast enough to use while in development stages, while able to build snapshots once a stable package collection is found. As with other functions in a reproducible workflow, this package emphasizes functions that return the same result whether it is the first or subsequent times running the function, with subsequent times being sufficiently fast that they can be run every time without undue waiting burden on the user or developer.
Maintained by Eliot J B McIntire. Last updated 15 days ago.
6.1 match 22 stars 9.42 score 144 scripts 13 dependentsbxc147
Epi:Statistical Analysis in Epidemiology
Functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data. In particular representation, manipulation, rate estimation and simulation for multistate data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. Contains functions for Age-Period-Cohort and Lee-Carter modeling and a function for interval censored data and some useful functions for tabulation and plotting, as well as a number of epidemiological data sets.
Maintained by Bendix Carstensen. Last updated 2 months ago.
6.0 match 4 stars 9.65 score 708 scripts 11 dependentsssa-statistical-team-projects
povmap:Extension to the 'emdi' Package
The R package 'povmap' supports small area estimation of means and poverty headcount rates. It adds several new features to the 'emdi' package (see "The R Package emdi for Estimating and Mapping Regionally Disaggregated Indicators" by Kreutzmann et al. (2019) <doi:10.18637/jss.v091.i07>). These include new options for incorporating survey weights, ex-post benchmarking of estimates, two additional transformations, several new convenient functions to assist with reporting results, and a wrapper function to facilitate access from 'Stata'.
Maintained by Ifeanyi Edochie. Last updated 5 months ago.
12.5 match 1 stars 4.60 score 10 scriptsbblonder
hypervolume:High Dimensional Geometry, Set Operations, Projection, and Inference Using Kernel Density Estimation, Support Vector Machines, and Convex Hulls
Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation, support vector machine delineation, and convex hull generation. Applications include modeling trait and niche hypervolumes and species distribution modeling.
Maintained by Benjamin Blonder. Last updated 2 months ago.
5.9 match 23 stars 9.75 score 211 scripts 7 dependentsexpersso
maddison:Maddison Project Database
Contains the Maddison Project 2018 database, which provides estimates of GDP per capita for all countries in the world between AD 1 and 2016. See http://www.ggdc.net/maddison for more information.
Maintained by Eric Persson. Last updated 6 years ago.
11.2 match 10 stars 5.11 score 26 scriptsbarnhilldave
TML:Tropical Geometry Tools for Machine Learning
Suite of tropical geometric tools for use in machine learning applications. These methods may be summarized in the following references: Yoshida, et al. (2022) <arxiv:2209.15045>, Barnhill et al. (2023) <arxiv:2303.02539>, Barnhill and Yoshida (2023) <doi:10.3390/math11153433>, Aliatimis et al. (2023) <arXiv:2306.08796>, Yoshida et al. (2022) <arXiv:2206.04206>, and Yoshida et al. (2019) <doi:10.1007/s11538-018-0493-4>.
Maintained by David Barnhill. Last updated 8 months ago.
15.6 match 3 stars 3.65 score 1 scriptsquarto-dev
quarto:R Interface to 'Quarto' Markdown Publishing System
Convert R Markdown documents and 'Jupyter' notebooks to a variety of output formats using 'Quarto'.
Maintained by Christophe Dervieux. Last updated 1 months ago.
3.8 match 147 stars 14.96 score 1.3k scripts 36 dependentsthierryo
qrcode:Generate QRcodes with R
Create static QR codes in R. The content of the QR code is exactly what the user defines. We don't add a redirect URL, making it impossible for us to track the usage of the QR code. This allows to generate fast, free to use and privacy friendly QR codes.
Maintained by Thierry Onkelinx. Last updated 6 months ago.
qrcodeqrcode-generatorr-project
7.5 match 44 stars 7.56 score 456 scripts 7 dependentstidyverse
ggplot2:Create Elegant Data Visualisations Using the Grammar of Graphics
A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.
Maintained by Thomas Lin Pedersen. Last updated 9 days ago.
data-visualisationvisualisation
2.3 match 6.6k stars 25.10 score 645k scripts 7.5k dependents