This package contains datasets and several smaller functions suitable for analysis of interval-censored data. The package complements the book Bogaerts, Komárek and Lesaffre (2017, ISBN: 978-1-4200-7747-6) "Survival Analysis with Interval-Censored Data: A Practical Approach" <https://www.routledge.com/Survival-Analysis-with-Interval-Censored-Data-A-Practical-Approach-with/Bogaerts-Komarek-Lesaffre/p/book/9781420077476>. Full R code related to the examples presented in the book can be found at <https://ibiostat.be/online-resources/icbook/supplemental>. Packages mentioned in the "Suggests" section are used in those examples.

It computes arbitrary products moments (mean vector and variance-covariance matrix), for some double truncated (and folded) multivariate distributions. These distributions belong to the family of selection elliptical distributions, which includes well known skewed distributions as the unified skew-t distribution (SUT) and its particular cases as the extended skew-t (EST), skew-t (ST) and the symmetric student-t (T) distribution. Analogous normal cases unified skew-normal (SUN), extended skew-normal (ESN), skew-normal (SN), and symmetric normal (N) are also included. Density, probabilities and random deviates are also offered for these members.

The unique function of this package allows representing in a single graph the relative occurrence and co-occurrence of events measured in a sample. As examples, the package was applied to describe the occurrence and co-occurrence of different species of bacterial or viral symbionts infecting arthropods at the individual level. The graphics allows determining the prevalence of each symbiont and the patterns of multiple infections (i.e. how different symbionts share or not the same individual hosts). We named the package after the famous painter as the graphical output recalls Mondrianâ s paintings.

Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history. See K. Bartoszek, J, Pienaar, P. Mostad, S. Andersson, T. F. Hansen (2012) <doi:10.1016/j.jtbi.2012.08.005> and K. Bartoszek, and J. Tredgett Clarke, J. Fuentes-Gonzalez, V. Mitov, J. Pienaar, M. Piwczynski, R. Puchalka, K. Spalik, K. L. Voje (2024) <doi:10.1111/2041-210X.14376>. The suggested PCMBaseCpp package (which significantly speeds up the likelihood calculations) can be obtained from <https://github.com/venelin/PCMBaseCpp/>.

DNA methylation is an important epigenetic process that regulates gene activity through chemical modifications of DNA without changing its sequence. OpEnCAST is a plant-specific ensemble-based prediction package that identifies 4mC, 5mC and 6mA methylation sites directly from DNA sequences. It combines multiple machine learning algorithms trained on monocot (Oryza sp.) and dicot (Arabidopsis sp.) reference models to deliver accurate predictions. This methodology is being inspired by the ensemble algorithm for methylation prediction developed by Wang et al. (2022) <doi:10.1186/s12859-022-04756-1>.

Fitting models for, and simulation of, trend locally stationary wavelet (TLSW) time series models, which take account of time-varying trend and dependence structure in a univariate time series. The TLSW model, and its estimation, is described in McGonigle, Killick and Nunes (2022a) <doi:10.1111/jtsa.12643>, (2022b) <doi:10.1214/22-EJS2044>. Further information regarding the use of the package, along with detailed examples, can be found in McGonigle, Killick and Nunes (2025) <doi:10.18637/jss.v115.i10>. New users will likely want to start with the TLSW function.

Using site polymorphism is one of the ways to cluster DNA/protein sequences but it is possible for the sequences with the same polymorphism on a single site to be genetically distant. This package is aimed at clustering sequences using site polymorphism and their corresponding phylogenetic trees. By considering their location on the tree, only the structurally adjacent sequences will be clustered. However, the adjacent sequences may not necessarily have the same polymorphism. So a branch-and-bound like algorithm is used to minimize the entropy representing the purity of site polymorphism of each cluster.

SBGNview is a tool set for pathway based data visalization, integration and analysis. SBGNview is similar and complementary to the widely used Pathview, with the following key features: 1. Pathway definition by the widely adopted Systems Biology Graphical Notation (SBGN); 2. Supports multiple major pathway databases beyond KEGG (Reactome, MetaCyc, SMPDB, PANTHER, METACROP) and user defined pathways; 3. Covers 5,200 reference pathways and over 3,000 species by default; 4. Extensive graphics controls, including glyph and edge attributes, graph layout and sub-pathway highlight; 5. SBGN pathway data manipulation, processing, extraction and analysis.

This package provides tools designed to perform and evaluate cluster analysis (including Tocher's algorithm), discriminant analysis and path analysis (standard and under collinearity), as well as some useful miscellaneous tools for dealing with sample size and optimum plot size calculations. A test for seed sample heterogeneity is now available. Mantel's permutation test can be found in this package. A new approach for calculating its power is implemented. biotools also contains tests for genetic covariance components. Heuristic approaches for performing non-parametric spatial predictions of generic response variables and spatial gene diversity are implemented.

General optimisation and specific tools for the parameter estimation (i.e. calibration) of complex models, including stochastic ones. It implements generic functions that can be used for fitting any type of models, especially those with non-differentiable objective functions, with the same syntax as base::optim. It supports multiple phases estimation (sequential parameter masking), constrained optimization (bounding box restrictions) and automatic parallel computation of numerical gradients. Some common maximum likelihood estimation methods and automated construction of the objective function from simulated model outputs is provided. See <https://roliveros-ramos.github.io/calibrar/> for more details.

Statistical methods for retrospectively detecting changes in location and/or dispersion of univariate and multivariate variables. Data values are assumed to be independent, can be individual (one observation at each instant of time) or subgrouped (more than one observation at each instant of time). Control limits are computed, often using a permutation approach, so that a prescribed false alarm probability is guaranteed without making any parametric assumptions on the stable (in-control) distribution. See G. Capizzi and G. Masarotto (2018) <doi:10.1007/978-3-319-75295-2_1> for an introduction to the package.

This package provides a shiny-based front end (the ExPanD app) and a set of functions for exploratory data analysis. Run as a web-based app, ExPanD enables users to assess the robustness of empirical evidence without providing them access to the underlying data. You can export a notebook containing the analysis of ExPanD and/or use the functions of the package to support your exploratory data analysis workflow. Refer to the vignettes of the package for more information on how to use ExPanD and/or the functions of this package.

The EM algorithm is a powerful tool for computing maximum likelihood estimates with incomplete data. This package will help to applying EM algorithm based on triangular and trapezoidal fuzzy numbers (as two kinds of incomplete data). A method is proposed for estimating the unknown parameter in a parametric statistical model when the observations are triangular or trapezoidal fuzzy numbers. This method is based on maximizing the observed-data likelihood defined as the conditional probability of the fuzzy data; for more details and formulas see Denoeux (2011) <doi:10.1016/j.fss.2011.05.022>.

This package provides tools for simulating mathematical models of infectious disease dynamics. Epidemic model classes include deterministic compartmental models, stochastic individual-contact models, and stochastic network models. Network models use the robust statistical methods of exponential-family random graph models (ERGMs) from the Statnet suite of software packages in R. Standard templates for epidemic modeling include SI, SIR, and SIS disease types. EpiModel features an API for extending these templates to address novel scientific research aims. Full methods for EpiModel are detailed in Jenness et al. (2018, <doi:10.18637/jss.v084.i08>).

Bayesian (and some likelihoodist) functions as alternatives to hypothesis-testing functions in R base using a user interface patterned after those of R's hypothesis testing functions. See McElreath (2016, ISBN: 978-1-4822-5344-3), Gelman and Hill (2007, ISBN: 0-521-68689-X) (new edition in preparation) and Albert (2009, ISBN: 978-0-387-71384-7) for good introductions to Bayesian analysis and Pawitan (2002, ISBN: 0-19-850765-8) for the Likelihood approach. The functions in the package also make extensive use of graphical displays for data exploration and model comparison.

Identifying labeled compounds in a 13C-tracer experiment in non-targeted fashion is a cumbersome process. This package facilitates such type of analyses by providing high level quality control plots, deconvoluting and evaluating spectra and performing a multitude of tests in an automatic fashion. The main idea is to use changing intensity ratios of ion pairs from peak list generated with xcms as candidates and evaluate those against base peak chromatograms and spectra information within the raw measurement data automatically. The functionality is described in Hoffmann et al. (2018) <doi:10.1021/acs.analchem.8b00356>.

Normative data are often used to estimate the relative position of a raw test score in the population. This package allows for deriving regression-based normative data. It includes functions that enable the fitting of regression models for the mean and residual (or variance) structures, test the model assumptions, derive the normative data in the form of normative tables or automatic scoring sheets, and estimate confidence intervals for the norms. This package accompanies the book Van der Elst, W. (2024). Regression-based normative data for psychological assessment. A hands-on approach using R. Springer Nature.

Dealing with neutrosophic data of the form N=D+I(where N is a Neutrosophic number ,D is the determinant part of the number and I is the indeterminacy part) using the neutrosophic two way anova test keeps the type I error low. This algorithm calculates the fisher statistics when we have a neutrosophic data, also tests two hypothesizes, first is to test differences between treatments, and second is to test differences between sectors. For more information see Miari, Mahmoud; Anan, Mohamad Taher; Zeina, Mohamed Bisher(2022) <https://www.americaspg.com/articleinfo/21/show/1058>.

The comprehensive knowledge of epigenetic modifications in plants, encompassing histone modifications in regulating gene expression, is not completely ingrained. It is noteworthy that histone deacetylation and histone H3 lysine 27 trimethylation (H3K27me3) play a role in repressing transcription in eukaryotes. In contrast, histone acetylation (H3K9ac) and H3K4me3 have been inevitably linked to the stimulation of gene expression, which significantly influences plant development and plays a role in plant responses to biotic and abiotic stresses. To our knowledge this the first multiclass classifier for predicting histone modification in plants. <doi:10.1186/s12864-019-5489-4>.

Datetimes and timestamps are invariably an imprecise notation, with any partial representation implying some amount of uncertainty. To handle this, parttime provides classes for embedding partial missingness as a central part of its datetime classes. This central feature allows for more ergonomic use of datetimes for challenging datetime computation, including calculations of overlapping date ranges, imputations, and more thoughtful handling of ambiguity that arises from uncertain time zones. This package was developed first and foremost with pharmaceutical applications in mind, but aims to be agnostic to application to accommodate general use cases just as conveniently.

The goal of PlotFTIR is to easily and quickly kick-start the production of journal-quality Fourier Transform Infra-Red (FTIR) spectral plots in R using ggplot2'. The produced plots can be published directly or further modified by ggplot2 functions. L'objectif de PlotFTIR est de démarrer facilement et rapidement la production des tracés spectraux de spectroscopie infrarouge à transformée de Fourier (IRTF) de qualité journal dans R à l'aide de ggplot2'. Les tracés produits peuvent être publiés directement ou modifiés davantage par les fonctions ggplot2'.

Researchers working with Qualitative Comparative Analysis (QCA) can use the package to estimate power of a sufficient term using permutation tests. A term can be anything: A condition, conjunction or disjunction of any combination of these. The package further allows users to plot the estimation results and to estimate the number of cases required to achieve a certain level of power, given a prespecified null and alternative hypothesis. Reference for the article introducing power estimation for QCA is: Rohlfing, Ingo (2018) <doi:10.1017/pan.2017.30> (ungated version: <doi:10.17605/OSF.IO/PC4DF>).

Dual interfaces, graphical and programmatic, designed for intuitive applications of Multilevel Regression and Poststratification (MRP). Users can apply the method to a variety of datasets, from electronic health records to sample survey data, through an end-to-end Bayesian data analysis workflow. The package provides robust tools for data cleaning, exploratory analysis, flexible model building, and insightful result visualization. For more details, see Si et al. (2020) <https://www150.statcan.gc.ca/n1/en/pub/12-001-x/2020002/article/00003-eng.pdf?st=iF1_Fbrh> and Si (2025) <doi:10.1214/24-STS932>.

It allows to rapidly compute, bootstrap and plot up to fourth-order Sobol'-based sensitivity indices using several state-of-the-art first and total-order estimators. Sobol indices can be computed either for models that yield a scalar as a model output or for systems of differential equations. The package also provides a suit of benchmark tests functions and several options to obtain publication-ready figures of the model output uncertainty and sensitivity-related analysis. An overview of the package can be found in Puy et al. (2022) <doi:10.18637/jss.v102.i05>.