Frequentist and Bayesian linear regression for large data sets. Useful when the data does not fit into memory (for both frequentist and Bayesian regression), to make running time manageable (mainly for Bayesian regression), and to reduce the total running time because of reduced or less severe memory-spillover into the virtual memory. This is an implementation of Merge & Reduce for linear regression as described in Geppert, L.N., Ickstadt, K., Munteanu, A., & Sohler, C. (2020). Streaming statistical models via Merge & Reduce'. International Journal of Data Science and Analytics, 1-17, <doi:10.1007/s41060-020-00226-0>.

Calculates mean cumulative count (MCC) to estimate the expected cumulative number of recurrent events per person over time in the presence of competing risks and censoring. Implements both the Dong-Yasui equation method and sum of cumulative incidence method described in Dong, et al. (2015) <doi:10.1093/aje/kwu289>. Supports inverse probability weighting for causal inference as outlined in Gaber, et al. (2023) <doi:10.1093/aje/kwad031>. Provides S3 methods for printing, summarizing, plotting, and extracting results. Handles grouped analyses and integrates with ggplot2 <https://ggplot2.tidyverse.org/> for visualization.

This package provides functions to support compatibility between Maelstrom R packages and Opal environment. Opal is the OBiBa core database application for biobanks. It is used to build data repositories that integrates data collected from multiple sources. Opal Maelstrom is a specific implementation of this software. This Opal client is specifically designed to interact with Opal Maelstrom distributions to perform operations on the R server side. The user must have adequate credentials. Please see <https://opaldoc.obiba.org/> for complete documentation.

Semi-parametric approach for sparse canonical correlation analysis which can handle mixed data types: continuous, binary and truncated continuous. Bridge functions are provided to connect Kendall's tau to latent correlation under the Gaussian copula model. The methods are described in Yoon, Carroll and Gaynanova (2020) <doi:10.1093/biomet/asaa007> and Yoon, Mueller and Gaynanova (2021) <doi:10.1080/10618600.2021.1882468>.

An interface to build machine learning models for classification and regression problems. mikropml implements the ML pipeline described by TopçuoÄ lu et al. (2020) <doi:10.1128/mBio.00434-20> with reasonable default options for data preprocessing, hyperparameter tuning, cross-validation, testing, model evaluation, and interpretation steps. See the website <https://www.schlosslab.org/mikropml/> for more information, documentation, and examples.

Advanced methods for a valuable quantitative environmental risk assessment using Bayesian inference of survival and reproduction Data. Among others, it facilitates Bayesian inference of the general unified threshold model of survival (GUTS). See our companion paper Baudrot and Charles (2021) <doi:10.21105/joss.03200>, as well as complementary details in Baudrot et al. (2018) <doi:10.1021/acs.est.7b05464> and Delignette-Muller et al. (2017) <doi:10.1021/acs.est.6b05326>.

The estimation of the parameters in mixed Poisson models.

This package provides a comprehensive framework for calculating unbiased distances in datasets containing mixed-type variables (numerical and categorical). The package implements a general formulation that ensures multivariate additivity and commensurability, meaning that variables contribute equally to the overall distance regardless of their type, scale, or distribution. Supports multiple distance measures including Gower's distance, Euclidean distance, Manhattan distance, and various categorical variable distances such as simple matching, Eskin, occurrence frequency, and association-based distances. Provides tools for variable scaling (standard deviation, range, robust range, and principal component scaling), and handles both independent and association-based category dissimilarities. Implements methods to correct for biases that typically arise from different variable types, distributions, and number of categories. Particularly useful for cluster analysis, data visualization, and other distance-based methods when working with mixed data. Methods based on van de Velden et al. (2024) <doi:10.48550/arXiv.2411.00429> "Unbiased mixed variables distance".

This package provides various functions for parameter estimation of one-dimensional stable distributions and their mixtures. It implements a diverse set of estimation methods, including quantile-based approaches, regression methods based on the empirical characteristic function (empirical, kernel, and recursive), and maximum likelihood estimation. For mixture models, it provides stochastic expectationâ maximization (SEM) algorithms and Bayesian estimation methods using sampling and importance sampling to overcome the long burn-in period of Markov Chain Monte Carlo (MCMC) strategies. The package also includes tools and statistical tests for analyzing whether a dataset follows a stable distribution. Some of the implemented methods are described in Hajjaji, O., Manou-Abi, S. M., and Slaoui, Y. (2024) <doi:10.1080/02664763.2024.2434627>.

Summarize multiple biomarker responses of aquatic organisms to contaminants using Cliffâ s delta, as described in Pham & Sokolova (2023) <doi:10.1002/ieam.4676>.

Multi-Fidelity emulator for data from computer simulations of the same underlying system but at different input locations and fidelity level, where both the input locations and fidelity level can be continuous. Active Learning can be performed with an implementation of the Integrated Mean Square Prediction Error (IMSPE) criterion developed by Boutelet and Sung (2025, <doi:10.48550/arXiv.2503.23158>).

This package provides functions for the creation, evaluation and test of decision models based in Multi Attribute Utility Theory (MAUT). Can process and evaluate local risk aversion utilities for a set of indexes, compute utilities and weights for the whole decision tree defining the decision model and simulate weights employing Dirichlet distributions under addition constraints in weights.

This package provides probability mass, distribution, quantile, random variate generation, and method-of-moments parameter fitting for the MBBEFD family of distributions used in insurance modeling as described in Bernegger (1997) <doi:10.2143/AST.27.1.563208> without any external dependencies.

Implementations of various robust and flexible model-based clustering methods for data sets with missing values at random (Tong and Tortora, 2025, <doi:10.18637/jss.v115.i03>). Two main models are: Multivariate Contaminated Normal Mixture (MCNM, Tong and Tortora, 2022, <doi:10.1007/s11634-021-00476-1>) and Multivariate Generalized Hyperbolic Mixture (MGHM, Wei et al., 2019, <doi:10.1016/j.csda.2018.08.016>). Mixtures via some special or limiting cases of the multivariate generalized hyperbolic distribution are also included: Normal-Inverse Gaussian, Symmetric Normal-Inverse Gaussian, Skew-Cauchy, Cauchy, Skew-t, Student's t, Normal, Symmetric Generalized Hyperbolic, Hyperbolic Univariate Marginals, Hyperbolic, and Symmetric Hyperbolic. Funding: This work was partially supported by the National Science foundation NSF Grant NO. 2209974.

Used for general multiple mediation analysis with big data sets.

An approach to identify microbiome biomarker for time to event data by discovering microbiome for predicting survival and classifying subjects into risk groups. Classifiers are constructed as a linear combination of important microbiome and treatment effects if necessary. Several methods were implemented to estimate the microbiome risk score such as the LASSO method by Robert Tibshirani (1998) <doi:10.1002/(SICI)1097-0258(19970228)16:4%3C385::AID-SIM380%3E3.0.CO;2-3>, Elastic net approach by Hui Zou and Trevor Hastie (2005) <doi:10.1111/j.1467-9868.2005.00503.x>, supervised principle component analysis of Wold Svante et al. (1987) <doi:10.1016/0169-7439(87)80084-9>, and supervised partial least squares analysis by Inge S. Helland <https://www.jstor.org/stable/4616159>. Sensitivity analysis on the quantile used for the classification can also be accessed to check the deviation of the classification group based on the quantile specified. Large scale cross validation can be performed in order to investigate the mostly selected microbiome and for internal validation. During the evaluation process, validation is accessed using the hazard ratios (HR) distribution of the test set and inference is mainly based on resampling and permutations technique.

Meta-package for statistical and machine learning with a unified interface for model fitting, prediction, performance assessment, and presentation of results. Approaches for model fitting and prediction of numerical, categorical, or censored time-to-event outcomes include traditional regression models, regularization methods, tree-based methods, support vector machines, neural networks, ensembles, data preprocessing, filtering, and model tuning and selection. Performance metrics are provided for model assessment and can be estimated with independent test sets, split sampling, cross-validation, or bootstrap resampling. Resample estimation can be executed in parallel for faster processing and nested in cases of model tuning and selection. Modeling results can be summarized with descriptive statistics; calibration curves; variable importance; partial dependence plots; confusion matrices; and ROC, lift, and other performance curves.

This package provides utility functions for multivariate analysis (factor analysis, discriminant analysis, and others). The package is primary written for the course Multivariate analysis and for the course Computer intensive methods at the masters program of Applied Statistics at University of Ljubljana.

This package provides methods to analyze cluster alternatives based on multi-objective optimization of cluster validation indices. For details see Kraus et al. (2011) <doi:10.1007/s00180-011-0244-6>.

This package contains a set of tools for constructing and coercing into and from the "mdate" class. This date class implements ISO 8601-2:2019(E) and allows regular dates to be annotated to express unspecified date components, approximate or uncertain date components, date ranges, and sets of dates. This is useful for describing and analysing temporal information, whether historical or recent, where date precision may vary.

First- and higher-order likelihood inference in meta-analysis and meta-regression models.

This package provides a method for multivariate ordinal data generation given marginal distributions and correlation matrix based on the methodology proposed by Demirtas (2006) <DOI:10.1080/10629360600569246>.

This toolkit allows performing continuous-time microsimulation for a wide range of life science (demography, social sciences, epidemiology) applications. Individual life-courses are specified by a continuous-time multi-state model as described in Zinn (2014) <doi:10.34196/IJM.00105>.

Combination of either p-values or modified effect sizes from different studies to find differentially expressed genes.