This package computes model II simple linear regression using ordinary least squares (OLS), major axis (MA), standard major axis (SMA), and ranged major axis (RMA).

Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization Algorithm; it is used for optimizing smooth nonlinear objective functions with constraints. Linear or nonlinear equality and inequality constraints are allowed.

This package provides tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.

This package fits generalized linear models efficiently using RcppEigen'. The iteratively reweighted least squares implementation utilizes the step-halving approach of Marschner to help safeguard against convergence issues.

This lightweight package that adds progress bar to vectorized R functions apply. The implementation can easily be added to functions where showing the progress is useful e.g. bootstrap.

This package implements the R version of the log4j package. It offers hierarchic loggers, multiple handlers per logger, level based filtering, space handling in messages and custom formatting.

cl-random is a library for generating random draws from various commonly used distributions, and for calculating statistical functions, such as density, distribution and quantiles for these distributions.

This package provides a utility library intended at providing configurable reader macros for common tasks such as accessors, hash-tables, sets, uiop:run-program, arrays and a few others.

a Bayesian normalization procedure derived from first principles. Sanity estimates expression values and associated error bars directly from raw unique molecular identifier (UMI) counts without any tunable parameters.

Feature-based variance-sensitive clustering of omics data. Optimizes cluster assignment by taking into account individual feature variance. Includes several modules for statistical testing, clustering and enrichment analysis.

Binford's hunter-gatherer data includes more than 200 variables coding aspects of hunter-gatherer subsistence, mobility, and social organization for 339 ethnographically documented groups of hunter-gatherers.

Using numeric or raster data, this package contains functions to calculate: complete water balance, bioclimatic balance, bioclimatic intensities, reports for individual locations, multi-layered rasters for spatial analysis.

Estimation of latent variable models using Bayesian methods. Currently estimates the loglinear cognitive diagnosis model of Henson, Templin, and Willse (2009) <doi:10.1007/s11336-008-9089-5>.

Sample size estimation in cluster (group) randomized trials. Contains traditional power-based methods, empirical smoothing (Rotondi and Donner, 2009), and updated meta-analysis techniques (Rotondi and Donner, 2012).

Datasets for the book entitled "Modelling Survival Data in Medical Research" by Collett (2023) <doi:10.1201/9781003282525>. The datasets provide extensive examples of time-to-event data.

Git hook scripts are useful for identifying simple issues before submission to code review. captain (hook) is an R package to manage and run git pre-commit hooks.

Automated method for doublet detection in flow or mass cytometry data, based on simulating doublets and finding events whose protein expression patterns are similar to the simulated doublets.

Computer algebra via the SymPy library (<https://www.sympy.org/>). This makes it possible to solve equations symbolically, find symbolic integrals, symbolic sums and other important quantities.

Calculate multiple or pairwise dissimilarity for orders q = 0-N (CqN; Chao et al. 2008 <doi:10/fcvn63>) for a set of species assemblages or interaction networks.

An efficient algorithm to fit and tune kernel quantile regression models based on the majorization-minimization (MM) method. It can also fit multiple quantile curves simultaneously without crossing.

Routines for exploratory and descriptive analysis of functional data such as depth measurements, atypical curves detection, regression models, supervised classification, unsupervised classification and functional analysis of variance.

Adds standardized regression coefficients to objects created by lm'. Also extends the S3 methods print', summary and coef with additional boolean argument standardized and provides xtable'-support.

Implementations of Hurst exponent estimators based on the relationship between wavelet lifting scales and wavelet energy of Knight et al (2017) <doi:10.1007/s11222-016-9698-2>.

Defines classes and methods to learn models and use them to predict binary outcomes. These are generic tools, but we also include specific examples for many common classifiers.