Estimates marginal likelihood from a posterior sample using the method described in Wang et al. (2023) <doi:10.1093/sysbio/syad007>, which does not require evaluation of any additional points and requires only the log of the unnormalized posterior density for each sampled parameter vector.

Conducts various numerical analyses and simulations in population genetics and evolutionary theory, primarily for the purpose of teaching (and learning about) key concepts in population & quantitative genetics, and evolutionary theory.

This package provides a fast generalized edit distance and string alignment computation mainly for linguistic aims. As a generalization to the classic edit distance algorithms, the package allows users to define custom cost for every symbol's insertion, deletion, and substitution. The package also allows character combinations in any length to be seen as a single symbol which is very useful for International Phonetic Alphabet (IPA) transcriptions with diacritics. In addition to edit distance result, users can get detailed alignment information such as all possible alignment scenarios between two strings which is useful for testing, illustration or any further usage. Either the distance matrix or its long table form can be obtained and tools to do such conversions are provided. All functions in the package are implemented in C++ and the distance matrix computation is parallelized leveraging the RcppThread package.

Extends the functionality of the tourr package by an interactive graphical user interface. The interactivity allows users to effortlessly refine their tourr results by manual intervention, which allows for integration of expert knowledge and aids the interpretation of results. For more information on tourr see Wickham et. al (2011) <doi:10.18637/jss.v040.i02> or <https://github.com/ggobi/tourr>.

This package provides tools for creating and using lenses to simplify data manipulation. Lenses are composable getter/setter pairs for working with data in a purely functional way. Inspired by the Haskell library lens (Kmett, 2012) <https://hackage.haskell.org/package/lens>. For a fairly comprehensive (and highly technical) history of lenses please see the lens wiki <https://github.com/ekmett/lens/wiki/History-of-Lenses>.

Fits semi-confirmatory structural equation modeling (SEM) via penalized likelihood (PL) or penalized least squares (PLS). For details, please see Huang (2020) <doi:10.18637/jss.v093.i07>.

This package provides a comprehensive framework for linear regression modeling and associated statistical analysis. The package implements methods for correlation analysis, including computation of correlation matrices with corresponding significance levels and visualization via correlation heatmaps. It supports estimation of multiple linear regression models, along with automated model selection through backward elimination procedures based on statistical significance criteria. In addition, the package offers a suite of diagnostic tools to assess key assumptions of linear regression, including multicollinearity using variance inflation factors, heteroscedasticity using the Goldfeld-Quandt test, and normality of residuals using the Shapiro-Wilk test. These functionalities, as described in Draper and Smith (1998) <doi:10.1002/9781118625590>, are designed to facilitate robust model building, evaluation, and interpretation in applied statistical and data analytical contexts.

This package provides a minimal-dependency client for Large Language Model chat APIs. Supports OpenAI <https://openai.com/>, Anthropic Claude <https://claude.com/>, Moonshot Kimi <https://www.moonshot.ai/>, OpenAI Codex subscription endpoints, Ollama <https://ollama.com/>, and other OpenAI'-compatible endpoints. Includes an agent loop with tool use and a Model Context Protocol client <https://modelcontextprotocol.io/>. API design is derived from the ellmer package, reimplemented with only base R, curl', jsonlite', and tinyoauth'.

This package provides flexible but lightweight logging facilities for R scripts. Supports priority levels for logs and messages, flagging messages, capturing script output, switching logs, and logging to files or connections.

Computing statistical hypothesis testing for loading in principal component analysis (PCA) (Yamamoto, H. et al. (2014) <doi:10.1186/1471-2105-15-51>), orthogonal smoothed PCA (OS-PCA) (Yamamoto, H. et al. (2021) <doi:10.3390/metabo11030149>), one-sided kernel PCA (Yamamoto, H. (2023) <doi:10.51094/jxiv.262>), partial least squares (PLS) and PLS discriminant analysis (PLS-DA) (Yamamoto, H. et al. (2009) <doi:10.1016/j.chemolab.2009.05.006>), PLS with rank order of groups (PLS-ROG) (Yamamoto, H. (2017) <doi:10.1002/cem.2883>), regularized canonical correlation analysis discriminant analysis (RCCA-DA) (Yamamoto, H. et al. (2008) <doi:10.1016/j.bej.2007.12.009>), multiset PLS and PLS-ROG (Yamamoto, H. (2022) <doi:10.1101/2022.08.30.505949>).

This package provides functions to automatically retrieve and deduplicate reference metadata based on saved search strings. Access to Web of Science and Scopus requires personal API keys, while PubMed can be queried without one. The optional deduplication functionality requires the package ASySD available from <https://github.com/camaradesuk/ASySD>.

This is an extension package to logrx', which is a log creation program focused on Clinical Reporting within the Pharma Industry. This package enables a simple shiny-based Add-in that provides a point and click interface to produce a log for a single program.

Download and read data on lobbying in the United States Congress. Data is queried from the Senate's Application Programming Interface (<https://lda.senate.gov/api/>). This supports filings since 2008. Functions exist for all primary data endpoints, including queries by filings, contributions, registrations, clients, and lobbyists.

This package provides an interactive shiny application to construct stage-structured life tables from tabular input data. The application includes input validation, demographic calculations, visualization tools, and export of tables and figures to support reproducible workflows in ecological and entomological studies. Methods for life table construction follow classical demographic approaches described in Martinez (2015) <doi:10.13140/RG.2.2.21333.65760>.

Calculate and extract remote sensing metrics for spatial analysis in the field of health. The package offers R users a quick and straightforward way to obtain areal or zonal statistics of key environmental indicators, covariates, and vector-borne disease data ideal for modeling infectious diseases within the framework of spatial epidemiology.

An emulator designed for rapid sequential emulation (e.g., Markov chain Monte Carlo applications). Works via extension of the laGP approach by Gramacy and Apley (2015 <doi:10.1080/10618600.2014.914442>). Details are given in Rumsey et al. (2023 <doi:10.1002/sta4.576>).

Interactive shiny application for working with different kinds of latent variable analysis, with the lavaan package. Graphical output for models are provided and different estimators are supported.

This package provides bindings to the Leaflet.glify JavaScript library which extends the leaflet JavaScript library to render large data in the browser using WebGl'.

This package provides an extension to factors called lfactor that are similar to factors but allows users to refer to lfactor levels by either the level or the label.

The first stand-alone R package for computation of latent correlation that takes into account all variable types (continuous/binary/ordinal/zero-inflated), comes with an optimized memory footprint, and is computationally efficient, essentially making latent correlation estimation almost as fast as rank-based correlation estimation. The estimation is based on latent copula Gaussian models. For continuous/binary types, see Fan, J., Liu, H., Ning, Y., and Zou, H. (2017). For ternary type, see Quan X., Booth J.G. and Wells M.T. (2018) <doi:10.48550/arXiv.1809.06255>. For truncated type or zero-inflated type, see Yoon G., Carroll R.J. and Gaynanova I. (2020) <doi:10.1093/biomet/asaa007>. For approximation method of computation, see Yoon G., Müller C.L. and Gaynanova I. (2021) <doi:10.1080/10618600.2021.1882468>. The latter method uses multi-linear interpolation originally implemented in the R package <https://cran.r-project.org/package=chebpol>.

This package provides tools to authenticate with LOBSTER (Limit Order Book System - The Efficient Reconstruction, <https://app.lobsterdata.com/>), request, download, and process high-frequency limit order book data. Streamlines the end-to-end workflow from data request to analysis-ready datasets. For advanced high-frequency econometric analysis, see the highfrequency package.

This package produces Labour Market Areas from commuting flows available at elementary territorial units. It provides tools for automatic tuning based on spatial contiguity. It also allows for statistical analyses and visualisation of the new functional geography.

This package contains some functions to learn and teach basic plane Geometry at undergraduate level with the aim of being helpful to young students with little programming skills.

This package provides functions for normalizing standard laboratory measurements (e.g. hemoglobin, cholesterol levels) according to age and sex, based on the algorithms described in "Personalized lab test models to quantify disease potentials in healthy individuals" (Netta Mendelson Cohen, Omer Schwartzman, Ram Jaschek, Aviezer Lifshitz, Michael Hoichman, Ran Balicer, Liran I. Shlush, Gabi Barbash & Amos Tanay, <doi:10.1038/s41591-021-01468-6>). Allows users to easily obtain normalized values for standard lab results, and to visualize their distributions. See more at <https://tanaylab.weizmann.ac.il/labs/>.