Constrained clustering, transfer functions, and other methods for analysing Quaternary science data.

This package provides a high-performance interface for calculating string similarities and distances, leveraging the efficient library RapidFuzz <https://github.com/rapidfuzz/rapidfuzz-cpp>. This package integrates the C++ implementation, allowing R users to access cutting-edge algorithms for fuzzy matching and text analysis. Supported metrics include Levenshtein, Damerau-Levenshtein, Hamming, Jaro, Jaro-Winkler, Longest Common Subsequence (LCS), Optimal String Alignment (OSA), Indel, Prefix, and Postfix distances and similarities, as well as multiple fuzzy matching ratios.

Useful tools for determining whether two samples are from the same distribution. Utilizes a robust method to address the problematic structure of the similarity graph constructed from high-dimensional data. The method is provided in Yichuan Bai and Lynna Chu (2023) <arXiv:2307.12325>.

Graphics for statistics on a sphere, as applied to geological fault data, crystallography, earthquake focal mechanisms, radiation patterns, ternary plots and geographical/geological maps. Non-double couple plotting of focal spheres and source type maps are included for statistical analysis of moment tensors.

An implementation of robust bent line regression. It can fit the bent line regression and test the existence of change point, for the paper, "Feipeng Zhang and Qunhua Li (2016). Robust bent line regression, submitted.".

HydroBudget is a spatially distributed groundwater recharge model that computes a superficial water budget on grid cells with outputs aggregated into monthly time steps. It was developed as an accessible and computationally affordable model to simulate groundwater recharge over large areas (thousands of km2, regional-scale watersheds) and for long time periods (decades), in cold and humid climates. Model algorithms are based on the research of Dubois, E. et al. (2021a) <doi:10.5683/SP3/EUDV3H> and Dubois, E. et al. (2021b) <doi:10.5194/hess-25-6567-2021>.

We implement linear regression when the outcome of interest and some of the covariates are observed in two different datasets that cannot be linked, based on D'Haultfoeuille, Gaillac, Maurel (2022) <doi:10.3386/w29953>. The package allows for common regressors observed in both datasets, and for various shape constraints on the effect of covariates on the outcome of interest. It also provides the tools to perform a test of point identification. See the associated vignette <https://github.com/cgaillac/RegCombin/blob/master/RegCombin_vignette.pdf> for theory and code examples.

Represents high-dimensional data as tables of features, samples and measurements, and a design list for tracking the meaning of individual variables. Using this format, filtering, normalization, and other transformations of a dataset can be carried out in a flexible manner. romic takes advantage of these transformations to create interactive shiny apps for exploratory data analysis such as an interactive heatmap.

Various tools for handling fuzzy measures, calculating Shapley value and interaction index, Choquet and Sugeno integrals, as well as fitting fuzzy measures to empirical data are provided. Construction of fuzzy measures from empirical data is done by solving a linear programming problem by using lpsolve package, whose source in C adapted to the R environment is included. The description of the basic theory of fuzzy measures is in the manual in the Doc folder in this package. Please refer to the following: [1] <https://personal-sites.deakin.edu.au/~gleb/fmtools.html> [2] G. Beliakov, H. Bustince, T. Calvo, A Practical Guide to Averaging', Springer, (2016, ISBN: 978-3-319-24753-3). [3] G. Beliakov, S. James, J-Z. Wu, Discrete Fuzzy Measures', Springer, (2020, ISBN: 978-3-030-15305-2).

Reversion mutations are secondary mutations that reverse the deleterious effects of an original pathogenic mutation, partially or fully restoring the gene's function. The revert package detects reversion mutations for a specific pathogenic mutation from DNA-seq bam files.

An implementation of functionalities to transform directed graphs that are bound to a set of known forbidden paths. There are several transformations, following the rules provided by Villeneuve and Desaulniers (2005) <doi: 10.1016/j.ejor.2004.01.032>, and Hsu et al. (2009) <doi: 10.1007/978-3-642-03095-6_60>. The resulting graph is generated in a data-frame format. See rsppfp website for more information, documentation an examples.

This package provides R-squared values and standardized regression coefficients for linear models applied to multiply imputed datasets as obtained by mice'. Confidence intervals, zero-order correlations, and alternative adjusted R-squared estimates are also available. The methods are described in Van Ginkel and Karch (2024) <doi:10.1111/bmsp.12344> and in Van Ginkel (2020) <doi:10.1007/s11336-020-09696-4>.

Perform the complete processing of a set of proton nuclear magnetic resonance spectra from the free induction decay (raw data) and based on a processing sequence (macro-command file). An additional file specifies all the spectra to be considered by associating their sample code as well as the levels of experimental factors to which they belong. More detail can be found in Jacob et al. (2017) <doi:10.1007/s11306-017-1178-y>.

Facilitates making a connection to the Revenera API and executing various queries. You can use it to get event data and metadata. The Revenera documentation is available at <https://rui-api.redoc.ly/>. This package is not supported by Flexera (owner of the software).

This package provides a flexible framework for implementing hierarchical access control in shiny applications. Features include user permission management through a two-tier system of access panels and units, pluggable shiny module for administrative interfaces, and support for multiple storage backends (local, AWS S3', Posit Connect'). The system enables fine-grained control over application features, with built-in audit trails and user management capabilities. Integrates seamlessly with Posit Connect's authentication system.

Use rmarkdown partials, also know as child documents in knitr', so you can make components for HTML, PDF, and Word documents. The package provides various helper functions to make certain functions easier. You may want to use this package, if you want to flexibly summarise objects using a combination of figures, tables, text, and HTML widgets. Unlike HTML widgets, the output is Markdown and can hence be turn into other output formats than HTML. Currently does not play well with rmarkdown notebooks, not tested with Quarto.

This package provides access to the Ravelry API <https://www.ravelry.com/groups/ravelry-api>. An R wrapper for pulling data from Ravelry.com', an organizational tool for crocheters, knitters, spinners, and weavers. You can retrieve pattern, yarn, author, and shop information by search or by a given id.

This package provides random number generating functions that are much more context aware than the built-in functions. The functions are also much safer, as they check for incompatible values, and more reproducible.

Perform a supervised data analysis on a database through a shiny graphical interface. It includes methods such as linear regression, penalized regression, k-nearest neighbors, decision trees, ada boosting, extreme gradient boosting, random forest, neural networks, deep learning and support vector machines.

Create presentations and display them inside the R REPL (Read-Eval-Print loop), aka the R console. Presentations can be written in RMarkdown or any other text format. A set of convenient navigation options as well as code evaluation during a presentation is provided. It is great for tech talks with live coding examples and tutorials. While this is not a replacement for standard presentation formats, it's old-school looks might just be what sets it apart. This project has been inspired by the REPLesent project for presentations in the Scala REPL'.

This package provides a series of functions that allow users to access the LinkedIn API to get information about connections, search for people and jobs, share updates with their network, and create group discussions. For more information about using the API please visit <https://developer.linkedin.com/>.

This package contains function rkt which computes the Mann-Kendall test (MK) and the Seasonal and the Regional Kendall Tests for trend (SKT and RKT) and Theil-Sen's slope estimator.

Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2025) <doi:10.1007/978-3-031-89669-9>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.

Build regular expressions piece by piece using human readable code. This package contains Unicode functionality, and is primarily intended to be used by package developers.