This package performs analysis of one-way multivariate data, for small samples using Nonparametric techniques. Using approximations for ANOVA Type, Wilks Lambda, Lawley Hotelling, and Bartlett Nanda Pillai Test statics, the package compares the multivariate distributions for a single explanatory variable. The comparison is also performed using a permutation test for each of the four test statistics. The package also performs an all-subsets algorithm regarding variables and regarding factor levels.

This package provides methods to estimate finite-population parameters under nonresponse that is not missing at random (NMAR, nonignorable). Incorporates auxiliary information and user-specified response models, and supports independent samples and complex survey designs via objects from the survey package. Provides diagnostics and optional variance estimates. For methodological background see Qin, Leung and Shao (2002) <doi:10.1198/016214502753479338> and Riddles, Kim and Im (2016) <doi:10.1093/jssam/smv047>.

This package provides functions for implementing different versions of the OSCV method in the kernel regression and density estimation frameworks. The package mainly supports the following articles: (1) Savchuk, O.Y., Hart, J.D. (2017). Fully robust one-sided cross-validation for regression functions. Computational Statistics, <doi:10.1007/s00180-017-0713-7> and (2) Savchuk, O.Y. (2017). One-sided cross-validation for nonsmooth density functions, <arXiv:1703.05157>.

Implementation of commonly used penalized functional linear regression models, including the Smooth and Locally Sparse (SLoS) method by Lin et al. (2016) <doi:10.1080/10618600.2016.1195273>, Nested Group bridge Regression (NGR) method by Guan et al. (2020) <doi:10.1080/10618600.2020.1713797>, Functional Linear Regression That's interpretable (FLIRTI) by James et al. (2009) <doi:10.1214/08-AOS641>, and the Penalized B-spline regression method.

This package provides a toolbox for making R functions and capabilities more accessible to students and professionals from Epidemiology and Public Health related disciplines. Includes a function to report coefficients and confidence intervals from models using robust standard errors (when available), functions that expand ggplot2 plots and functions relevant for introductory papers in Epidemiology or Public Health. Please note that use of the provided data sets is for educational purposes only.

This package provides methods for regression with high-dimensional predictors and univariate or maltivariate response variables. It considers the decomposition of the coefficient matrix that leads to the best approximation to the signal part in the response given any rank, and estimates the decomposition by solving a penalized generalized eigenvalue problem followed by a least squares procedure. Ruiyan Luo and Xin Qi (2017) <doi:10.1016/j.jmva.2016.09.005>.

Comprehensive set of tools for analyzing and manipulating functional data with non-uniform lengths. This package addresses two common scenarios in functional data analysis: Variable Domain Data, where the observation domain differs across samples, and Partially Observed Data, where observations are incomplete over the domain of interest. VDPO enhances the flexibility and applicability of functional data analysis in R'. See Amaro et al. (2024) <doi:10.48550/arXiv.2401.05839>.

An interface to the BaM (Bayesian Modeling) engine, a Fortran'-based executable aimed at estimating a model with a Bayesian approach and using it for prediction, with a particular focus on uncertainty quantification. Classes are defined for the various building blocks of BaM inference (model, data, error models, Markov Chain Monte Carlo (MCMC) samplers, predictions). The typical usage is as follows: (1) specify the model to be estimated; (2) specify the inference setting (dataset, parameters, error models...); (3) perform Bayesian-MCMC inference; (4) read, analyse and use MCMC samples; (5) perform prediction experiments. Technical details are available (in French) in Renard (2017) <https://hal.science/hal-02606929v1>. Examples of applications include Mansanarez et al. (2019) <doi:10.1029/2018WR023389>, Le Coz et al. (2021) <doi:10.1002/hyp.14169>, Perret et al. (2021) <doi:10.1029/2020WR027745>, Darienzo et al. (2021) <doi:10.1029/2020WR028607> and Perret et al. (2023) <doi:10.1061/JHEND8.HYENG-13101>.

The Reproducible Open Coding Kit ('ROCK', and this package, rock') was developed to facilitate reproducible and open coding, specifically geared towards qualitative research methods. It was developed to be both human- and machine-readable, in the spirit of MarkDown and YAML'. The idea is that this makes it relatively easy to write other functions and packages to process ROCK files. The rock package contains functions for basic coding and analysis, such as collecting and showing coded fragments and prettifying sources, as well as a number of advanced analyses such as the Qualitative Network Approach and Qualitative/Unified Exploration of State Transitions. The ROCK and this rock package are described in the ROCK book (ZörgÅ & Peters, 2022; <https://rockbook.org>), in ZörgÅ & Peters (2024) <doi:10.1080/21642850.2022.2119144> and Peters, ZörgÅ and van der Maas (2022) <doi:10.31234/osf.io/cvf52>, and more information and tutorials are available at <https://rock.science>.

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

mist (Methylation Inference for Single-cell along Trajectory) is a hierarchical Bayesian framework for modeling DNA methylation trajectories and performing differential methylation (DM) analysis in single-cell DNA methylation (scDNAm) data. It estimates developmental-stage-specific variations, identifies genomic features with drastic changes along pseudotime, and, for two phenotypic groups, detects features with distinct temporal methylation patterns. mist uses Gibbs sampling to estimate parameters for temporal changes and stage-specific variations.

This package provides a inferential analysis method for detecting differentially expressed CpG sites in MeDIP-seq data. It uses statistical framework and EM algorithm, to identify differentially expressed CpG sites. The methods on this package are described in the article Methylation-level Inferences and Detection of Differential Methylation with Medip-seq Data by Yan Zhou, Jiadi Zhu, Mingtao Zhao, Baoxue Zhang, Chunfu Jiang and Xiyan Yang (2018, pending publication).

This package provides tools for compositional and other sample-level ecological analyses and visualizations tailored for single-cell RNA-seq data. SETA includes functions for taxonomizing celltypes, normalizing data, performing statistical tests, and visualizing results. Several tutorials are included to guide users and introduce them to key concepts. SETA is meant to teach users about statistical concepts underlying ecological analysis methods so they can apply them to their own single-cell data.

This package performs the two-sample Ansariâ Bradley test (Ansari & Bradley, 1960 <https://www.jstor.org/stable/2237814>) for univariate, distinct data in the presence of missing values, as described in Zeng et al. (2025) <doi:10.48550/arXiv.2509.20332>. This method does not make any assumptions about the missingness mechanisms and controls the Type I error regardless of the missing values by taking all possible missing values into account.

This package provides an approach which is based on the methodology of the Burden of Communicable Diseases in Europe (BCoDE) and can be used for large and small samples such as individual countries. The Burden of Healthcare-Associated Infections (BHAI) is estimated in disability-adjusted life years, number of infections as well as number of deaths per year. Results can be visualized with various plotting functions and exported into tables.

This package provides correlation-based penalty estimators for both linear and logistic regression models by implementing a new regularization method that incorporates correlation structures within the data. This method encourages a grouping effect where strongly correlated predictors tend to be in or out of the model together. See Tutz and Ulbricht (2009) <doi:10.1007/s11222-008-9088-5> and Algamal and Lee (2015) <doi:10.1016/j.eswa.2015.08.016>.

This package performs classical age-depth modelling of dated sediment deposits - prior to applying more sophisticated techniques such as Bayesian age-depth modelling. Any radiocarbon dated depths are calibrated. Age-depth models are constructed by sampling repeatedly from the dated levels, each time drawing age-depth curves. Model types include linear interpolation, linear or polynomial regression, and a range of splines. See Blaauw (2010) <doi:10.1016/j.quageo.2010.01.002>.

This package implements parametric (Direct) regression methods for modeling cumulative incidence functions (CIFs) in the presence of competing risks. Methods include the direct Gompertz-based approach and generalized regression models as described in Jeong and Fine (2006) <doi:10.1111/j.1467-9876.2006.00532.x> and Jeong and Fine (2007) <doi:10.1093/biostatistics/kxj040>. The package facilitates maximum likelihood estimation, variance computation, with applications to clinical trials and survival analysis.

Create high-performance clinical reporting tables (TLGs) from ADaM-like inputs. The package provides a consistent, programmatic API to generate common tables such as demographics, adverse event incidence, and laboratory summaries, using data.table for fast aggregation over large populations. Functions support flexible target-variable selection, stratification by treatment, and customizable summary statistics, and return tidy, machine-readable results ready to render with downstream table/formatting packages in analysis pipelines.

Training and prediction functions are provided for the Extreme Learning Machine algorithm (ELM). The ELM use a Single Hidden Layer Feedforward Neural Network (SLFN) with random generated weights and no gradient-based backpropagation. The training time is very short and the online version allows to update the model using small chunk of the training set at each iteration. The only parameter to tune is the hidden layer size and the learning function.

The Forecast Linear Augmented Projection (flap) method reduces forecast variance by adjusting the forecasts of multivariate time series to be consistent with the forecasts of linear combinations (components) of the series by projecting all forecasts onto the space where the linear constraints are satisfied. The forecast variance can be reduced monotonically by including more components. For a given number of components, the flap method achieves maximum forecast variance reduction among linear projections.

Fitting and analyzing a Joint Trait Distribution Model. The Joint Trait Distribution Model is implemented in the Bayesian framework using conjugate priors and posteriors, thus guaranteeing fast inference. In particular the package computes joint probabilities and multivariate confidence intervals, and enables the investigation of how they depend on the environment through partial response curves. The method implemented by the package is described in Poggiato et al. (2023) <doi:10.1111/geb.13706>.

This package provides functions to fit quantile regression models for hierarchical data (2-level nested designs) as described in Geraci and Bottai (2014, Statistics and Computing) <doi:10.1007/s11222-013-9381-9>. A vignette is given in Geraci (2014, Journal of Statistical Software) <doi:10.18637/jss.v057.i13> and included in the package documents. The packages also provides functions to fit quantile models for independent data and for count responses.

This package provides a complement to all editions of *Modern Data Science with R* (ISBN: 978-0367191498, publisher URL: <https://www.routledge.com/Modern-Data-Science-with-R/Baumer-Kaplan-Horton/p/book/9780367191498>). This package contains data and code to complete exercises and reproduce examples from the text. It also facilitates connections to the SQL database server used in the book. All editions of the book are supported by this package.