This package provides methods for calculating and testing the significance of pairwise monotonic association from and based on the work of Pimentel (2009) <doi:10.4135/9781412985291.n2>. Computation of association of vectors from one or multiple sets can be performed in parallel thanks to the packages foreach and doMC'.

This package provides a lightweight message system relying purely on base R. Comes with built-in and pre styled message types and provides an easy way to create custom messages. Supports individually styled and colored text as well as timing information. Designed to make console output more informative and visually organized.

This package provides a comprehensive library for colour vectors and colour palettes using a new family of colour classes (palettes_colour and palettes_palette) that always print as hex codes with colour previews. Capabilities include: formatting, casting and coercion, extraction and updating of components, plotting, colour mixing arithmetic, and colour interpolation.

Estimate networks and causal relationships in complex systems through Structural Equation Modeling. This package also includes functions for importing, weight, manipulate, and fit biological network models within the Structural Equation Modeling framework as outlined in the Supplementary Material of Grassi M, Palluzzi F, Tarantino B (2022) <doi:10.1093/bioinformatics/btac567>.

Reflection is a native GTK4 and libadwaita note-taking application that supports local-first collaboration built on the p2panda peer-to-peer protocol. Several people can edit the same note together, with or without an Internet connection, and their changes are merged automatically once the peers can reach one another again.

This package provides clean, tidy access to climate and weather data from the National Oceanic and Atmospheric Administration ('NOAA') via the National Centers for Environmental Information ('NCEI') Data Service API <https://www.ncei.noaa.gov/support/access-data-service-api-user-documentation>. Covers daily weather observations, monthly and annual summaries, and 30-year climate normals from over 100,000 stations across 180 countries. No API key is required. Dedicated functions handle the most common datasets, while a generic fetcher provides access to all NCEI datasets. Station discovery functions help users find stations by location or name. Data is downloaded on first use and cached locally for subsequent calls. This package is not endorsed or certified by NOAA'.

Partitions the phenotypic variance of a plastic trait, studied through its reaction norm. The variance partition distinguishes between the variance arising from the average shape of the reaction norms (V_Plas) and the (additive) genetic variance . The latter is itself separated into an environment-blind component (V_G/V_A) and the component arising from plasticity (V_GxE/V_AxE). The package also provides a way to further partition V_Plas into aspects (slope/curvature) of the shape of the average reaction norm (pi-decomposition) and partition V_Add (gamma-decomposition) and V_AxE (iota-decomposition) into the impact of genetic variation in the reaction norm parameters. Reference: de Villemereuil & Chevin (2025) <doi:10.32942/X2NC8B>.

This package provides classes and methods for handling genetic data. It includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...

This package contains a collection of functions (written as shiny modules) for the visualisation and the statistical analysis of omics data. These plots can be displayed individually or embedded in a global Shiny module. Additionaly, it is possible to integrate third party modules to the main interface of the package omXplore.

Estimates possible 3D orientations of an object from the 2D image coordinates of two landmarks and an approximate camera-object elevation angle. Because a projected 2D angle can be compatible with multiple 3D pitch, yaw, and view-elevation angles, the package returns compatible sets of orientations rather than a single unconstrained estimate.

Interface to the Python package BERTopic <https://maartengr.github.io/BERTopic/index.html> for transformer-based topic modeling. Provides R wrappers to fit BERTopic models, transform new documents, update and reduce topics, extract topic- and document-level information, and generate interactive visualizations. Python backends and dependencies are managed via the reticulate package.

Models time-to-event data from interval-censored screening studies. It accounts for latent prevalence at baseline and incorporates misclassification due to imperfect test sensitivity. For usage details, see the package vignette "BayesPIM_intro". Further details can be found in Klausch, Lissenberg-Witte and Coupé (2026) <doi:10.1002/sim.70433>.

Interface with the Brickset API <https://brickset.com/article/52664/api-version-3-documentation> for getting data about LEGO sets. Data sets that can be used for teaching and learning without the need of a Brickset account and API key are also included. Includes all LEGO since through the end of 2025.

Geometric circle fitting with Levenberg-Marquardt (a, b, R), Levenberg-Marquardt reduced (a, b), Landau, Spath and Chernov-Lesort. Algebraic circle fitting with Taubin, Kasa, Pratt and Fitzgibbon-Pilu-Fisher. Geometric ellipse fitting with ellipse LMG (geometric parameters) and conic LMA (algebraic parameters). Algebraic ellipse fitting with Fitzgibbon-Pilu-Fisher and Taubin.

Data screening is an important first step of any statistical analysis. dataMaid auto generates a customizable data report with a thorough summary of the checks and the results that a human can use to identify possible errors. It provides an extendable suite of test for common potential errors in a dataset.

Authenticate users in Shiny applications using Google Firebase with any of the many methods provided; email and password, email link, or using a third-party provider such as Github', Twitter', or Google'. Use Firebase Storage to store files securely, and leverage Firebase Analytics to easily log events and better understand your audience.

Interactive forest plot for clinical trial safety analysis using metalite', reactable', plotly', and Analysis Data Model (ADaM) datasets. Includes functionality for adverse event filtering, incidence-based group filtering, hover-over reveals, and search and sort operations. The workflow allows for metadata construction, data preparation, output formatting, and interactive plot generation.

Automatically process Fluorescence Recovery After Photobleaching (FRAP) data and generate consistent, publishable figures. Note: this package does not replace ImageJ (or its equivalence) in raw image quantification. Some references about the methods: Sprague, Brian L. (2004) <doi:10.1529/biophysj.103.026765>; Day, Charles A. (2012) <doi:10.1002/0471142956.cy0219s62>.

Estimation and display of various types of population attributable fraction and impact fractions. As well as the usual calculations of attributable fractions and impact fractions, functions are provided for attributable fraction nomograms and fan plots, continuous exposures, for pathway specific population attributable fractions, and for joint, average and sequential population attributable fractions.

This package provides extension types and conversions to between R-native object types and Arrow columnar types. This includes integration among the arrow', nanoarrow', sf', and wk packages such that spatial metadata is preserved wherever possible. Extension type implementations ensure first-class geometry data type support in the arrow and nanoarrow packages.

Extend ggplot2 facets to panel layouts arranged in a grid with ragged edges. facet_ragged_rows() groups panels into rows that can vary in length, facet_ragged_cols() does the same but for columns. These can be useful, for example, to represent nested or partially crossed relationships between faceting variables.

S3 functions implementing both statistical and graphical goodness-of-fit measures between observed and simulated values, mainly oriented to be used during the calibration, validation, and application of hydrological models. Missing values in observed and/or simulated values can be removed before computations. Comments / questions / collaboration of any kind are very welcomed.

This package provides methods (standard and advanced) for analysis of agreement between measurement methods. These cover Bland-Altman plots, Deming regression, Lin's Total deviation index, and difference-on-average regression. See Carstensen B. (2010) "Comparing Clinical Measurement Methods: A Practical Guide (Statistics in Practice)" <doi:10.1002/9780470683019> for more information.

Plotting functions for mutational signatures and mutational spectra, including single base substitutions (SBS), doublet base substitutions (DBS), and small insertions and deletions (indels). Generates plots similar to those used previously in Alexandrov et al. (2020)<doi:10.1038/s41586-020-1943-3> and Rozen et al. (2026)<doi:10.5281/zenodo.18451842>.