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rcrisp - Automate the Delineation of Urban River Spaces

Provides tools to automate the morphological delineation of riverside urban areas based on a method introduced in Forgaci (2018) <doi:10.7480/abe.2018.31>. Delineation entails the identification of corridor boundaries, segmentation of the corridor, and delineation of the river space using two-dimensional spatial information from street network data and digital elevation data in a projected CRS. The resulting delineation can be used to characterise spatial phenomena that can be related to the river as a central element.

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8.00 score 24 stars 23 scripts 249 downloads

grumpy - Read 'NumPy' '.npy' and '.npz' Files

Lightweight way to read 'NumPy' '.npy' and '.npz' files in R. All data types supported by 'NumPy', with all sizes (converted internally to R native size), both C and 'Fortran' order, and any shape, up to an arbitrary number of dimensions, are supported.

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data-formatdata-importinteroperabilitynpy-filesnpz-filesnumpy-filesquarto

7.91 score 9 stars 10 dependents 7 scripts 888 downloads

ReliaGrowR - Reliability Growth Analysis and Repairable Systems Modeling

Modeling and plotting functions for Reliability Growth Analysis (RGA) and Non-Homogeneous Poisson Process (NHPP) models for repairable systems. RGA models include the Duane (1962) <doi:10.1109/TA.1964.4319640>, NHPP by Crow (1975) (No. AMSAATR138), Piecewise Weibull NHPP by Guo et al. (2010) <doi:10.1109/RAMS.2010.5448029>, and Piecewise Weibull NHPP with Change Point Detection based on the 'segmented' package by Muggeo (2024) <https://cran.r-project.org/package=segmented>. Repairable systems functions include the Mean Cumulative Function (MCF) using the Nelson-Aalen estimator, parametric Power Law and Log-Linear NHPP models, and forecasting.

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change-point-detectioncrow-amsaanhppreliabilityreliability-growth-testing

7.80 score 2 stars 3 dependents 56 scripts 390 downloads

RAQSAPI - A Simple Interface to the US EPA Air Quality System Data Mart API

Retrieve air monitoring data and associated metadata from the US Environmental Protection Agency's Air Quality System service using functions. See <https://aqs.epa.gov/aqsweb/documents/data_api.html> for details about the US EPA Data Mart API <doi:10.32614/CRAN.package.RAQSAPI>.

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united state environmental protection agencyenvironmental-data-retrievalair-quality-systemaqs-datamartair-monitoringenvironmental-monitoringairmonitoringaqsdatamartr03rprogrammingusepa

7.41 score 26 stars 70 scripts 546 downloads

kindling - Higher-Level Interface of 'torch' Package to Auto-Train Neural Networks

Provides a higher-level interface to the 'torch' package for defining, training, and fine-tuning neural networks through code generation. The package supports several architectures, including feedforward (multi-layer perceptron) and recurrent neural networks (RNN, LSTM, GRU), while reducing boilerplate 'torch' code. Model training methods also bridge to machine learning frameworks in R, particularly the 'tidymodels' ecosystem, including 'parsnip' model specifications, 'workflows', 'recipes', and tuning tools.

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neural-networkstidymodelstorch

7.36 score 27 stars 8 scripts 381 downloads

coevolve - Fit Bayesian Generalized Dynamic Phylogenetic Models using 'Stan' or 'JAX'

Fit Bayesian generalized dynamic phylogenetic models using 'Stan' or 'JAX'. The package allows an arbitrary number of variables with different response distributions to coevolve on a phylogenetic tree via an Ornstein-Uhlenbeck evolutionary process, allowing users to assess directionality between coevolving variables. The optional JAX backend enables high-performance sampling with NumPyro and potential GPU acceleration via 'reticulate'.

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bayesian-statisticscoevolveevolutionstanstatistical-models

6.81 score 15 stars 19 scripts

rfastlowess - High-Performance LOWESS Smoothing for R

Provides high-performance LOWESS smoothing (Locally Weighted Scatterplot Smoothing) using a 'Rust' backend. Supports various weight functions, robustness iterations, streaming/online processing, cross-validation, and uncertainty quantification. Applicable to genomic data, time series, and general-purpose smoothing tasks.

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rustcargo

6.61 score 7 stars 31 scripts

logolink - An Interface for Running 'NetLogo' Simulations

An interface for 'NetLogo' <https://www.netlogo.org> that enables programmatic setup and execution of simulations. Designed to facilitate integrating 'NetLogo' models into reproducible workflows by creating and running 'BehaviorSpace' experiments and retrieving their results.

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agent-based-modelingapisbehaviorspacecomplexity-sciencecomputational-sciencecomputational-social-sciencedata-scienceecological-modelingenvironmental-modelingheadless-executionindividual-based-modelingmulti-agent-systemsnetlogosimulationssystem-dynamicstidyversequarto

6.55 score 18 stars 14 scripts 317 downloads

nert - Curated Access to TERN Environmental Raster Data

Provides curated access to gridded environmental data published by Australia's Terrestrial Ecosystem Research Network (TERN; <https://www.tern.org.au/>), spanning national soil attribute, soil classification, soil biodiversity, soil moisture, actual evapotranspiration, vegetation canopy height and phenology products. The package reads Cloud-Optimised GeoTIFF and virtual raster files directly from the TERN data server via GDAL /vsicurl range requests, streaming only the requested spatial and temporal subset for efficient data transfer. The environmental raster data are returned as terra::SpatRaster objects. A convenient helper function is also provided that provides a batch-download capability given specific locations and dates, returning the extracted data values in an analysis-ready data.table. Access to the TERN datasets using this package requires a TERN API key.

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ternsoil-dataaustraliaearth-sciencedata-access

6.51 score 4 stars 1 dependents 14 scripts

pladdrr - Direct Access to the Core Algorithms of Praat

Provides direct access to Praat C implemented functionality from R. This package allows R users to leverage Praat's powerful phonetic analysis capabilities directly from R. The package exposes 39 Praat modules with 500+ methods for sound manipulation, robust formant tracking (FormantPath, FormantModeler), speech synthesis (KlattGrid), pitch analysis, intensity measurements, spectral analysis (ComplexSpectrogram), cepstral coefficients (MFCC, LFCC), statistical analysis (PCA, Discriminant), auditory modeling (Cochleagram, Excitation), TextGrid annotation, voice quality assessment, geometric operations (Polygon), and a persistent Praat script interpreter with bidirectional R-Praat object transfer.

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gslopenblascpp

6.30 score 74 scripts

tarpolyglot - Run 'Python', 'Julia', 'Rust', and 'C++' Inside 'targets' Pipeline Steps

Adds target constructors that make it easy to use 'Python', 'Julia', 'Rust', and 'C++' inside a 'targets' pipeline using 'reticulate', 'JuliaCall', 'rextendr', and 'Rcpp'. Provides tar_target_py(), tar_target_jl(), tar_target_rs(), and tar_target_cpp() (with matching _raw() variants), each mirroring 'targets' tar_target() and tar_target_raw() functions. 'Python' and 'Julia' steps run a script via a live interpreter with optional R pre- and post-scripts; 'Rust' and 'C++' steps compile functions and call them from an R post-script. Results are then returned either as converted R objects or as files written to disk (format = "file"). Dynamic branching, environment/version selection, a 'crew' controller for isolation, and the full set of tar_target_raw() arguments are supported.

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6.22 score 11 stars 301 downloads

bridgr - Bridging Data Frequencies for Timely Economic Forecasts

Implements bridge and MIDAS-style mixed-frequency models for nowcasting and forecasting macroeconomic variables by linking higher-frequency indicator variables to a lower-frequency target series. The package standardizes input data, infers regular frequencies, forecasts missing indicator observations, and aggregates indicators to the target frequency before fitting a regression with autoregressive target dynamics. Frequency alignment can be customized through user-supplied conversion rules. For more on bridge and MIDAS models, see Baffigi, A., Golinelli, R., & Parigi, G. (2004) <doi:10.1016/S0169-2070(03)00067-0>, Ghysels, Sinko, & Valkanov (2007) <doi:10.1080/07474930600972467>, Andreou, Ghysels, & Kourtellos (2010) <doi:10.1016/j.jeconom.2010.01.004>, Schumacher (2016) <doi:10.1016/j.ijforecast.2015.07.004>, and Burri (2026) <doi:10.1111/obes.70073>.

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bridge-regressionforecastingmidas-regressionmixed-frequency-datanowcastingtime-seriestime-series-models

6.10 score 5 stars 9 scripts 361 downloads

GeoPressureR - Global Positioning by Atmospheric Pressure

R package to determine the position and trajectory of a bird based on light-weight data-logger measuring at lease atmospheric pressure.

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birddataloggerera5geolocatormigrationpressure-sensorwindspeed

5.58 score 9 stars 217 scripts

ocean3d - Three-Dimensional Marine Spatial Analysis

Facilitates the analysis of marine habitat in 3D, enabling descriptions of habitat by depth and area. Provides tools for volume calculation, environmental extraction, and spatial overlap analysis between species ranges, fisheries, and depth-stratified environmental data.

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5.57 score 11 stars 10 scripts

OptSurvCutR - Optimal Survival Cut-Point Discovery for Time-to-Event Analysis with 'OptSurvCutR'

Provides a robust workflow for optimal cut-point analysis in time-to-event ('survival') data. Functions determine the optimal number of cut-points via find_cutpoint_number(), find their precise locations via find_cutpoint() using systematic or genetic algorithms (via the 'rgenoud' package), and validate stability via bootstrapping using validate_cutpoint(). Features include covariate adjustment, parallel processing, and an extensible S3 plotting engine for clinical dashboards and diagnostics.

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bioinformatics-pipelinecut-pointssurvival-analysisvalidationcpp

5.56 score 2 stars 8 scripts 219 downloads

cowfootR - Dairy Farm Carbon Footprint Assessment

Calculates the carbon footprint of dairy farms based on methodologies of the International Dairy Federation and the Intergovernmental Panel on Climate Change. Includes tools for single-farm and batch analysis, report generation, and visualization. Methods follow International Dairy Federation (2022) "The IDF global Carbon Footprint standard for the dairy sector" (Bulletin of the IDF n° 520/2022) <doi:10.56169/FKRK7166> and IPCC (2019) "2019 Refinement to the 2006 IPCC Guidelines for National Greenhouse Gas Inventories, Chapter 10: Emissions from Livestock and Manure Management" <https://www.ipcc-nggip.iges.or.jp/public/2019rf/pdf/4_Volume4/19R_V4_Ch10_Livestock.pdf> guidelines.

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5.53 score 1 stars 14 scripts 340 downloads

dyadicMarkov - Pattern Estimation and Identification for Dyadic Sequences Using Transition Matrices in R

Provides methods for analyzing categorical dyadic sequences using transition matrices within the Longitudinal Actor-Partner Interdependence Model and Markov-chain framework. The package supports empirical transition counts, maximum likelihood estimation of transition probabilities, and identification of univariate and bivariate patterns of interaction in dyadic sequences.

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apimcategorical-datadyadic-datalongitudinal-datatransition-matrices

5.30 score 321 downloads

HydraR - Stateful Agentic Orchestration for Scientific Reproducibility

A high-performance framework for orchestrating complex agentic workflows in R, specifically designed for scientific reproducibility and auditability. HydraR provides a robust, state-managed engine for Directed Acyclic Graphs (DAGs) and iterative state machines, prioritizing CLI-native LLM interactions (e.g., Gemini, Claude, Copilot) and hardened state persistence (DuckDB/SQLite). It features isolated execution via Git Worktrees for parallel file-modifying tasks, autonomous quality control through integrated auditors, and human-readable visualization using Mermaid.js. Ideal for creating auditable, resumable research assistants and complex bioinformatics pipelines.

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5.21 score 1 stars 109 scripts

seasight - Tools for Seasonal Adjustment Diagnostics and Reporting

Provides tools for automated diagnostics, model selection and reporting for seasonal adjustment based on X-13ARIMA-SEATS. Wraps the 'seasonal' package to run and compare alternative specifications, extract quality indicators and residual diagnostics, and generate reproducible R Markdown reports for official statistics and other production workflows.

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5.10 score 5 stars 8 scripts

emodnet.wcs - Access EMODnet Web Coverage Service data through R

Access and interrogate EMODnet Web Coverage Service data through R.

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biologydataproductsemodnetgeospatialmarine-dataraster-datawcs

5.10 score 8 stars 13 scripts

pkgaudit - Static Analysis Security Testing (SAST) for R Packages

A static analysis tool that flags security-relevant files and code in R source packages for human review without executing anything it scans. Models package lifecycle execution semantics -- it reports not just what a package does, but when it runs, so code that executes on install or load is distinguishable from code that runs only when called. Reads every surface a package can execute, including 'configure' scripts, help-file macros, and vignettes, and states what it could not read, so a clean result can be checked rather than trusted. Detection rules are data, shipped in a versioned and hash-verified 'SQLite' database.

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cybersecurityr-securitysecuritysoftware-supply-chain-securitystatic-code-analysisstatic-code-analyzersupply-chain-security

5.08 score 5 stars

nonabsdid - Visualize Heterogeneity-Robust Event Studies for Non-Absorbing Treatments

Runs several heterogeneity-robust difference-in-differences (DID) event-study estimators for non-absorbing (i.e., treatment can switch on and off over time, allowing treatment reversal) binary treatments through their respective packages, harmonizes their output onto a common time axis and tidy data structure, and overlays them in a single 'ggplot2' panel for visual comparison. Supported estimators include those provided by 'DIDmultiplegtDYN', 'PanelMatch', and 'fect', with an optional naive two-way fixed-effects reference series via 'fixest'. The underlying methods are respectively described in Clement de Chaisemartin and Xavier D'Haultfoeuille. "Difference-in-Differences Estimators of Intertemporal Treatment Effects." The Review of Economics and Statistics (2026) <doi:10.1162/rest_a_01414>, Kosuke Imai, In Song Kim, and Erik H. Wang. "Matching methods for causal inference with time‐series cross‐sectional data." American Journal of Political Science 67.3 (2023) <doi:10.1111/ajps.12685>, Licheng Liu, Ye Wang, and Yiqing Xu. "A practical guide to counterfactual estimators for causal inference with time‐series cross‐sectional data." American Journal of Political Science 68.1 (2024) <doi:10.1111/ajps.12723>, and Laurent R. Bergé, Kyle Butts, and Grant McDermott. "Fast and user-friendly econometrics estimations: The R package 'fixest'." arXiv preprint (2026) <doi:10.48550/arXiv.2601.21749>. A single nabs_event_study() wrapper runs any supported estimator with a common interface; nabs_event_study_simple() provides a one-line front door for quick exploratory runs; the S3 generic as_nabs_event_study() coerces estimator output into a tidy stable schema; and nabs_event_plot() overlays multiple methods on a single 'ggplot2' panel, with optional naive two-way fixed effects drawn in a neutral color as a reference.

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5.02 score 7 scripts 323 downloads

ActiGlobe - Wearable Recording Processor for Time Shift Adjustment and Data Analysis

Cross-continental travel and local practices of daylight saving time can induce time shift. When left unadjusted, it can lead to biases in interpreting wearable measures. This research tool streamlines data processing and analysis (e.g., cosinor analysis, circularized kernel density estimation) for longitudinal recordings. Together with additional features such as exporting daily wearable measures and creating visual reports, it aims to facilitate research on longitudinal wearable measurements. To learn its application, please refer to the provided vignettes for a brief tutorial. This tool is developed based on the methodology detailed in: Varesco, G. Yao, C. W., Dubé, E., Simonelli, G., Bieuzen, F., (2024) <doi:10.1113/ep092195>.

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accelerometeractigraphycircadian-rhythmpipelinereproducibilitysleep-research

4.95 score 5 stars 4 scripts

camtrapReport - Camera-Trap Report Generator

Provides an extensible workflow for processing camera-trap data in the 'Camtrap DP' format and automatically generating reproducible data-status and ecological reports in HTML or PDF format. The package supports data-quality checks, ecological summaries, visualisations, maps, tables and modular report sections for wildlife-monitoring applications. Optional taxonomic enrichment queries the Global Biodiversity Information Facility Species API <https://techdocs.gbif.org/en/openapi/v1/species> through 'taxize'.

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automating-camera-trap-data-reportingcamera-trapsecological-reportingmodular-r-packagereproducible-workflowwildlife-monitoring

4.92 score 6 stars 5 scripts

metasurvey.core - Local Engine for Reproducible Survey Data Processing

The processing engine of the 'metasurvey' ecosystem. Provides a step-based pipeline for reproducible processing of microdata from complex surveys, building on the 'survey' package for design-based estimation. Supports rotating panels with bootstrap replicate weights and a recipe system for reproducing data transformation workflows across editions of the same study.

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4.89 score 1 dependents

taxastand - Taxonomic Name Standardization

Standardizes taxonomic names by matching species names to entries in a user-supplied reference taxonomy, then resolving synonyms to their accepted names. Fuzzy matching on parsed name components (genus, epithet, author, infraspecific rank, etc.) allows for orthographic differences between the query and reference names. This facilitates reproducible joining of datasets that use different taxonomic synonyms for the same species.

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databasetaxonomy

4.81 score 23 stars 14 scripts

DeCovarT - Covariance-Aware Deconvolution of Bulk Transcriptomic Samples

Estimates cell-type proportions in bulk transcriptomic samples with a probabilistic convolution model that integrates the gene-gene covariance structure of purified reference profiles. Cellular ratios are recovered by maximum likelihood under a multivariate Gaussian convolution, using analytic gradients and Hessians, an isometric log-ratio reparametrisation (Helmert basis) that enforces the simplex constraint, and Marquardt-Levenberg or Newton-type optimisers. The methodology is described in Chassagnol, Nuel and Becht (2023) <doi:10.48550/arXiv.2309.09557>.

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quarto

4.56 score 1 stars

corila - Sparse modelling with grouped and correlated features allowing for privileged information

Implements lasso regression (Gaussian, binomial, Poisson, and Cox) for features in heterogeneous groups (e.g., where some groups contain subgroups of correlated features), overlapping groups (i.e., where some features belong to two or more groups), and misspecified groups (i.e., where some group labels are incorrect or missing). Involves an initial ridge regression followed by a final adaptive lasso regression. Exchanges information between features according to their assumed adjacencies or their observed correlations to improve selection and predictive performance. Allows for features that can provide information on other features but must not themselves be selected (i.e., privileged information).

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correlated-featuresgroup-lassoinformation-exchangeprivileged-informationsparsity

4.20 score 4 scripts

expoquimR - Qualitative and Quantitative Assessment of Occupational Chemical Exposure Risk

Provides a unified toolkit for occupational chemical exposure risk assessment, implementing three internationally recognised methods end to end: the qualitative control-banding methods COSHH Essentials (UK Health and Safety Executive) and the method of the French National Research and Safety Institute (INRS), together with the quantitative statistical procedure of the UNE-EN 689 standard for comparing measured exposure levels against occupational exposure limits. Every step of each method, from hazard banding and exposure scoring to lognormal or normal distribution fitting, one-sided tolerance limits, and monitoring-interval recommendations, is implemented as a small, independently callable, and unit-tested function, so assessments are reproducible and auditable without depending on any graphical interface. Optional 'shiny' applications provide a guided, interactive workflow for occupational hygienists and health and safety practitioners who prefer not to write code. References: UK Health and Safety Executive (2003) <https://www.hse.gov.uk/coshh/essentials/index.htm>; Mallet, Pilorget and Berne (2013, ISBN:978-2-7389-2166-2) "Méthodologie d'évaluation simplifiée du risque chimique: un outil d'aide à la décision" INRS ND 2233; European Committee for Standardisation (2018) <https://www.en-standard.eu/bs-en-689-2018-workplace-exposure-measurement-of-exposure-by-inhalation-to-chemical-agents-strategy-for-testing-compliance-with-occupational-exposure-limit-values/>.

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4.18 score 259 downloads

fcmconfr - Fuzzy Cognitive Map Analysis in R

fcmconfr streamlines the process of conducting dynamic simulations using Fuzzy Cognitive Maps (FCMs). The package supports multiple FCM types (conventional, Interval-Value Fuzzy Number (IVFN) and Triangular Fuzzy Number (TFN)) and provides tools for model aggregation and the propagation of uncertainty from individual FCMs through to the aggregate.

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4.08 score 3 stars 3 scripts

qualtdict - Generate Variable Dictionaries and Labelled Survey Data for 'Qualtrics' Surveys

Generates Variable Dictionaries from 'Qualtrics' <https://www.qualtrics.com/about/> survey metadata and applies those dictionaries to create Labelled Survey Data. This package is a metadata and labelled-export companion to 'qualtRics', which provides access to 'Qualtrics' survey data and metadata via the 'Qualtrics' API <https://api.qualtrics.com/>.

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qualtricsqualtrics-apiqualtrics-survey

3.95 score 2 stars 4 scripts

tezr - Access Thesis Metadata from Turkiye's National Thesis Center

Retrieve, parse, cache, and analyze thesis metadata from the Council of Higher Education's National Thesis Center (Ulusal Tez Merkezi) at <https://tez.yok.gov.tr>. Supports basic, advanced, and detailed search. Also supports thesis detail retrieval, lookup tables, adaptive pagination for capped search results, and aggregate statistics for retrieval checks.

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3.70 score 1 stars 6 scripts

tantale - Mining and Analysis of Transcription Activator-Like Effectors

A toolkit for the study of transcription activator-like effectors (TALEs) of Xanthomonas. tell_tales() finds TALE genes in genome assemblies and can correct the frameshifts that make them hard to annotate in error-prone long-read assemblies. TALEs are held in S3 classes that record each one as a series of parts (N-terminus, repeats with their repeat-variable diresidues (RVDs), C-terminus), with methods to validate, subset, combine and plot them. TALEs are aligned repeat by repeat, compared with R implementations of the 'DisTAL' and 'FuncTAL' distances <doi:10.3389/fpls.2015.00545>, and grouped into families by hierarchical clustering or k-medoids. Wrappers for 'AnnoTALE' <doi:10.1038/srep21077>, 'TALEcorrection' <doi:10.1186/s12864-023-09228-1>, 'TALVEZ' <doi:10.1371/journal.pone.0068464> and 'PrediTALE' <doi:10.1371/journal.pcbi.1007206> read their results into the same objects; the last two predict target sites in host genomes.

Last updated

softwarequarto

3.61 score 27 scripts

rosettaR - Turn Plain Language Statements Into RDF, CSV, or Anything

Core functions to work with Rosetta Statements, which use templates to convert plain language strings into RDF, CSV or other representations. This package is designed to make the creation of knowledge graphs easier.

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3.60 score 6 scripts

bddkR - What the Package Does (Title Case)

The package fetches monthly financial tables and banking sector data published on the official website of the Banking Regulation and Supervision Agency (BRSA, BDDK) of Turkey and also enables you to save it as an Excel file. It is a R implementation of the Python package of [bddkdata](https://pypi.org/project/bddkdata/).

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3.54 score 7 stars 4 scripts 335 downloads

HazardMaps - Spatial Dependence Modeling and Pseudoscenario Generation for Natural Hazards

An R package for reproducible analysis of spatial dependence in environmental and climate-related variables. The package provides a unified workflow to ingest spatial datasets, estimate and visualize spatial correlation structures, fit multiple dependence models including vine copulas (C-vine and D-vine), Gaussian models, and stochastic fields, and compare them using quantitative indicators to support model selection. Based on the selected model, the package enables the generation of spatially dependent pseudoscenarios for uncertainty analysis and simulation studies. The design emphasizes numerical robustness, modularity, and reproducibility across heterogeneous spatial data sources.

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3.40 score