This package provides a spatio-dynamic modelling package that focuses on three characteristic wetland plant communities in a semiarid Mediterranean wetland in response to hydrological pressures from the catchment. The package includes the data on watershed hydrological pressure and the initial raster maps of plant communities but also allows for random initial distribution of plant communities. For more detailed info see: Martinez-Lopez et al. (2015) <doi:10.1016/j.ecolmodel.2014.11.024>.

This package provides an R and shiny interface to the Web Awesome component library. The package is generator-driven, exposing Web Awesome web components as R functions that produce HTML tags and integrate with the reactive model that shiny uses.

Simple Component Analysis (SCA) often provides much more interpretable components than Principal Components (PCA) while still representing much of the variability in the data.

Explore continuous, date and categorical variables with summary statistics, visualisations, and frequency tables. Brings the ease and simplicity of the sum and tab commands from Stata to R', including support for two-way cross-tabulations, hypothesis tests, duplicate and missing data exploration, and automated HTML or PDF exploratory reports.

Applies re-sampled kernel density method to detect vote fraud. It estimates the proportion of coarse vote-shares in the observed data relative to the null hypothesis of no fraud.

This package implements the "Residual (Sur)Realism" algorithm described by Stefanski (2007) <doi:10.1198/000313007X190079> to generate datasets that reveal hidden images or messages in their residual plots. It offers both predefined datasets and tools to embed custom text or images into residual structures. Allowing users to create intriguing visual demonstrations for teaching model diagnostics.

Generalised additive P-spline regression models estimation using the separation of overlapping precision matrices (SOP) method. Estimation is based on the equivalence between P-splines and linear mixed models, and variance/smoothing parameters are estimated based on restricted maximum likelihood (REML). The package enables users to estimate P-spline models with overlapping penalties. Based on the work described in Rodriguez-Alvarez et al. (2015) <doi:10.1007/s11222-014-9464-2>; Rodriguez-Alvarez et al. (2019) <doi:10.1007/s11222-018-9818-2>, and Eilers and Marx (1996) <doi:10.1214/ss/1038425655>.

Identification of sets of objects with shared features is a common operation in all disciplines. Analysis of intersections among multiple sets is fundamental for in-depth understanding of their complex relationships. This package implements a theoretical framework for efficient computation of statistical distributions of multi-set intersections based upon combinatorial theory, and provides multiple scalable techniques for visualizing the intersection statistics. The statistical algorithm behind this package was published in Wang et al. (2015) <doi:10.1038/srep16923>.

Provide estimation and data generation tools for the skew-unit family discussed based on Mukhopadhyay and Brani (1995) <doi:10.2307/2348710>. The family contains extensions for popular distributions such as the ArcSin discussed in Arnold and Groeneveld (1980) <doi:10.1080/01621459.1980.10477449>, triangular, U-quadratic and Johnson-SB proposed in Cortina-Borja (2006) <doi:10.1111/j.1467-985X.2006.00446_12.x> distributions, among others.

Gives design points from a sequential full factorial-based Latin hypercube design, as described in Duan, Ankenman, Sanchez, and Sanchez (2015, Technometrics, <doi:10.1080/00401706.2015.1108233>).

The goal of siteymlgen is to make it easy to organise the building of your R Markdown website. The init() function placed within the first code chunk of the index.Rmd file of an R project directory will initiate the generation of an automatically written _site.yml file. siteymlgen recommends a specific naming convention for your R Markdown files. This naming will ensure that your navbar layout is ordered according to a hierarchy.

Statistical tools for analyzing time-to-event data using machine learning. Implements survival stacking for conditional survival estimation, standardized survival function estimation for current status data, and methods for algorithm-agnostic variable importance. See Wolock CJ, Gilbert PB, Simon N, and Carone M (2024) <doi:10.1080/10618600.2024.2304070>.

Estimates sparse regression models (i.e., with few non-zero coefficients) in high-dimensional multi-task learning and transfer learning settings, as proposed by Rauschenberger et al. (2025) <https://orbilu.uni.lu/handle/10993/63425>.

This package provides a consistently well behaved method of interpolation based on piecewise rational functions using Stineman's algorithm.

This package provides functionality to fit a zero-inflated estimator for small area estimation. This estimator is a combines a linear mixed effects regression model and a logistic mixed effects regression model via a two-stage modeling approach. The estimator's mean squared error is estimated via a parametric bootstrap method. Chandra and others (2012, <doi:10.1080/03610918.2011.598991>) introduce and describe this estimator and mean squared error estimator. White and others (2024+, <doi:10.48550/arXiv.2402.03263>) describe the applicability of this estimator to estimation of forest attributes and further assess the estimator's properties.

Produce small area population estimates by fitting census data to survey data.

This software is useful for loading .fasta or .gbk files, and for retrieving sequences from GenBank dataset <https://www.ncbi.nlm.nih.gov/genbank/>. This package allows to detect differences or asymmetries based on nucleotide composition by using local linear kernel smoothers. Also, it is possible to draw inference about critical points (i. e. maximum or minimum points) related with the derivative curves. Additionally, bootstrap methods have been used for estimating confidence intervals and speed computational techniques (binning techniques) have been implemented in seq2R'.

Simulate genotypes in SNP (single nucleotide polymorphisms) Matrix as random numbers from an uniform distribution, for diploid organisms (coded by 0, 1, 2), Sikorska et al., (2013) <doi:10.1186/1471-2105-14-166>, or half-sib/full-sib SNP matrix from real or simulated parents SNP data, assuming mendelian segregation. Simulate phenotypic traits for real or simulated SNP data, controlled by a specific number of quantitative trait loci and their effects, sampled from a Normal or an Uniform distributions, assuming a pure additive model. This is useful for testing association and genomic prediction models or for educational purposes.

Simple result caching in R based on R.cache. The global environment is not considered when caching results simplifying moving files between multiple instances of R. Relies on more base functions than R.cache (e.g. cached results are saved using saveRDS() and readRDS()).

Projection pursuit is used to find interesting low-dimensional projections of high-dimensional data by optimizing an index over all possible projections. The spinebil package contains methods to evaluate the performance of projection pursuit index functions using tour methods. A paper describing the methods can be found at <doi:10.1007/s00180-020-00954-8>.

Fits Bayesian hierarchical piecewise regression models with multiple logistic-smoothed change-points. Non-linear parameters (change-point locations and transition sharpness) and linear parameters can each be conditioned on covariates and factors via flexible design matrices. A random-intercept structure is supported for any parameter. Spike-and-slab regularization is supported for selecting the number of breakpoints. Posterior inference uses a Metropolis-within-Gibbs sampler implemented in Rust for speed. Methods are based on the smooth transition piecewise regression model of Bacon and Watts (1971) <doi:10.2307/2334389> and variable selection spike-and-slab priors of Kuo and Mallick (1998) <https://www.jstor.org/stable/25053023>.

Computation of sparse eigenvectors of a matrix (aka sparse PCA) with running time 2-3 orders of magnitude lower than existing methods and better final performance in terms of recovery of sparsity pattern and estimation of numerical values. Can handle covariance matrices as well as data matrices with real or complex-valued entries. Different levels of sparsity can be specified for each individual ordered eigenvector and the method is robust in parameter selection. See vignette for a detailed documentation and comparison, with several illustrative examples. The package is based on the paper: K. Benidis, Y. Sun, P. Babu, and D. P. Palomar (2016). "Orthogonal Sparse PCA and Covariance Estimation via Procrustes Reformulation," IEEE Transactions on Signal Processing <doi:10.1109/TSP.2016.2605073>.

Find non-linear formulas that fits your input data. You can systematically explore and memorize the possible formulas and it's cross-validation performance, in an incremental fashion. Three main interoperable search functions are available: 1) random.search() performs a random exploration, 2) genetic.search() employs a genetic optimization algorithm, 3) comb.search() combines best results of the first two. For more details see Tomasoni et al. (2026) <doi:10.1208/s12248-026-01232-z>.

Multi-stage selection is practiced in numerous fields of life and social sciences and particularly in breeding. A special characteristic of multi-stage selection is that candidates are evaluated in successive stages with increasing intensity and effort, and only a fraction of the superior candidates is selected and promoted to the next stage. For the optimum design of such selection programs, the selection gain plays a crucial role. It can be calculated by integration of a truncated multivariate normal (MVN) distribution. While mathematical formulas for calculating the selection gain and the variance among selected candidates were developed long time ago, solutions for numerical calculation were not available. This package can also be used for optimizing multi-stage selection programs for a given total budget and different costs of evaluating the candidates in each stage.