Compute Buishand Range Test, Pettit Test, SNHT, Student t-test, and Mann-Whitney Rank Test, to identify breakpoints in series. For all functions NA is allowed. Since all of the mention methods identify only one breakpoint in a series, a general function to look for N breakpoint is given. Also, the Yamamoto test for climate jump is available. Alexandersson, H. (1986) <doi:10.1002/joc.3370060607>, Buishand, T. (1982) <doi:10.1016/0022-1694(82)90066-X>, Hurtado, S. I., Zaninelli, P. G., & Agosta, E. A. (2020) <doi:10.1016/j.atmosres.2020.104955>, Mann, H. B., Whitney, D. R. (1947) <doi:10.1214/aoms/1177730491>, Pettitt, A. N. (1979) <doi:10.2307/2346729>, Ruxton, G. D., jul (2006) <doi:10.1093/beheco/ark016>, Yamamoto, R., Iwashima, T., Kazadi, S. N., & Hoshiai, M. (1985) <doi:10.2151/jmsj1965.63.6_1157>.

This package provides an Markov-Chain-Monte-Carlo algorithm for Bayesian t-tests on the effect size. The underlying Gibbs sampler is based on a two-component Gaussian mixture and approximates the posterior distributions of the effect size, the difference of means and difference of standard deviations. A posterior analysis of the effect size via the region of practical equivalence is provided, too. For more details about the Gibbs sampler see Kelter (2019) <arXiv:1906.07524>.

Functional differences between the cerebral hemispheres are a fundamental characteristic of the human brain. Researchers interested in studying these differences often infer underlying hemispheric dominance for a certain function (e.g., language) from laterality indices calculated from observed performance or brain activation measures . However, any inference from observed measures to latent (unobserved) classes has to consider the prior probability of class membership in the population. The provided functions implement a Bayesian model for predicting hemispheric dominance from observed laterality indices (Sorensen and Westerhausen, Laterality: Asymmetries of Body, Brain and Cognition, 2020, <doi:10.1080/1357650X.2020.1769124>).

Prognostic Enrichment is a clinical trial strategy of evaluating an intervention in a patient population with a higher rate of the unwanted event than the broader patient population (R. Temple (2010) <DOI:10.1038/clpt.2010.233>). A higher event rate translates to a lower sample size for the clinical trial, which can have both practical and ethical advantages. This package is a tool to help evaluate biomarkers for prognostic enrichment of clinical trials.

Consider an at-most-K-stage group sequential design with only an upper bound for the last analysis and non-binding lower bounds.With binary endpoint, two kinds of test can be applied, asymptotic test based on normal distribution and exact test based on binomial distribution. This package supports the computation of boundaries and conditional power for single-arm group sequential test with binary endpoint, via either asymptotic or exact test. The package also provides functions to obtain boundary crossing probabilities given the design.

BEAST2 (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. BEAST2 is a command-line tool. This package provides a way to call BEAST2 from an R function call.

Generates different posterior distributions of adjusted odds ratio under different priors of sensitivity and specificity, and plots the models for comparison. It also provides estimations for the specifications of the models using diagnostics of exposure status with a non-linear mixed effects model. It implements the methods that are first proposed in <doi:10.1016/j.annepidem.2006.04.001> and <doi:10.1177/0272989X09353452>.

Nowcasting right-truncated epidemiological data is critical for timely public health decision-making, as reporting delays can create misleading impressions of declining trends in recent data. This package provides nowcasting methods based on using empirical delay distributions and uncertainty from past performance. It is also designed to be used as a baseline method for developers of new nowcasting methods. For more details on the performance of the method(s) in this package applied to case studies of COVID-19 and norovirus, see our recent paper at <https://wellcomeopenresearch.org/articles/10-614>. The package supports standard data frame inputs with reference date, report date, and count columns, as well as the direct use of reporting triangles, and is compatible with epinowcast objects. Alongside an opinionated default workflow, it has a low-level pipe-friendly modular interface, allowing context-specific workflows. It can accommodate a wide spectrum of reporting schedules, including mixed patterns of reference and reporting (daily-weekly, weekly-daily). It also supports sharing delay distributions and uncertainty estimates between strata, as well as custom uncertainty models and delay estimation methods.

Response surface methods for drug synergy analysis. Available methods include generalized and classical Loewe formulations as well as Highest Single Agent methodology. Response surfaces can be plotted in an interactive 3-D plot and formal statistical tests for presence of synergistic effects are available. Implemented methods and tests are described in the article "BIGL: Biochemically Intuitive Generalized Loewe null model for prediction of the expected combined effect compatible with partial agonism and antagonism" by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas, Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017) <doi:10.1038/s41598-017-18068-5>.

This package implements an S3 class based on data.table to store and process efficiently ethomics (high-throughput behavioural) data.

Implementations in cpp of the BayesProject algorithm (see G. Hahn, P. Fearnhead, I.A. Eckley (2020) <doi:10.1007/s11222-020-09966-2>) which implements a fast approach to compute a projection direction for multivariate changepoint detection, as well as the sum-cusum and max-cusum methods, and a wild binary segmentation wrapper for all algorithms.

As heavy-tailed error distribution and outliers in the response variable widely exist, models which are robust to data contamination are highly demanded. Here, we develop a novel robust Bayesian variable selection method with elastic net penalty. In particular, the spike-and-slab priors have been incorporated to impose sparsity. An efficient Gibbs sampler has been developed to facilitate computation.The core modules of the package have been developed in C++ and R.

It makes the creation of networks from sequences of RNA, with this is done the abstraction of characteristics of these networks with a methodology of threshold for the purpose of making a classification between the classes of the sequences. There are four data present in the BASiNET package, "sequences", "sequences2", "sequences-predict" and "sequences2-predict" with 11, 10, 11 and 11 sequences respectively. These sequences were taken from the data set used in the article (LI, Aimin; ZHANG, Junying; ZHOU, Zhongyin, 2014) <doi:10.1186/1471-2105-15-311>, these sequences are used to run examples. The BASiNET was published on Nucleic Acids Research, (ITO, Eric; KATAHIRA, Isaque; VICENTE, Fábio; PEREIRA, Felipe; LOPES, Fabrà cio, 2018) <doi:10.1093/nar/gky462>.

Generates nonparametric bootstrap confidence intervals (Efron and Tibshirani, 1993: <doi:10.1201/9780429246593>) for standardized regression coefficients (beta) and other effect sizes, including multiple correlation, semipartial correlations, improvement in R-squared, squared partial correlations, and differences in standardized regression coefficients, for models fitted by lm().

Supervised learning on tabular data with blockwise missing patterns, using the Blockwise Reduced Modeling (BRM) method of Srinivasan, Currim, and Ram (2025) <doi:10.1287/ijds.2022.9016>. BRM partitions the training data into overlapping subsets based on per-row feature-missing patterns, fits one user-supplied learner per subset with minimal imputation, and at prediction time routes each test instance to the best-matching subset model. The interface is learner-agnostic: any fit-and-predict pair can be plugged in, and convenience specifications are provided for linear models, tree models, random forests, and gradient boosting.

This package provides a "Shiny"" web application for creating interactive Bayesian Network models, learning the structure and parameters of Bayesian networks, and utilities for classic network analysis.

This package provides a modular framework for standardized analysis of thermal imaging data in animal experimentation. The package integrates thermographic data import (FLIR, raw, CSV), automated region of interest (ROI) segmentation based on EBImage (Pau et al., 2010 <doi:10.1093/bioinformatics/btq046>), interactive ROI refinement, and high-throughput batch processing.

This package provides a simple interface to switch between two methods for calculating basket trial characteristics, numerical integration ("exact") and Monte Carlo simulation ("simulated") for the basket trial design by Fujikawa et al. 2020 <doi:10.1002/bimj.201800404>. The exact implementation is from the baskexact package, see Baumann (2024) <doi:10.1016/j.softx.2024.101793>. The simulated implementation is from the basksim package, which was developed for Baumann et al. (2024) <doi:10.1080/19466315.2024.2402275>. The package's syntax is compatible with the basksim syntax and easily extendable.

Facilitates scalable spatiotemporally varying coefficient modelling with Bayesian kernelized tensor regression. The important features of this package are: (a) Enabling local temporal and spatial modeling of the relationship between the response variable and covariates. (b) Implementing the model described by Lei et al. (2023) <doi:10.48550/arXiv.2109.00046>. (c) Using a Bayesian Markov Chain Monte Carlo (MCMC) algorithm to sample from the posterior distribution of the model parameters. (d) Employing a tensor decomposition to reduce the number of estimated parameters. (e) Accelerating tensor operations and enabling graphics processing unit (GPU) acceleration with the torch package.

This package provides a build system based on GNU make that creates and maintains (simply) make files in an R session and provides GUI debugging support through Microsoft Visual Code'.

Fit Bayesian models using brms'/'Stan with parsnip'/'tidymodels via bayesian <doi:10.5281/zenodo.4426836>. tidymodels is a collection of packages for machine learning; see Kuhn and Wickham (2020) <https://www.tidymodels.org>). The technical details of brms and Stan are described in Bürkner (2017) <doi:10.18637/jss.v080.i01>, Bürkner (2018) <doi:10.32614/RJ-2018-017>, and Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.

An improved multiple testing procedure for controlling false discovery rates which is developed based on the Bonferroni procedure with integrated estimates from the Benjamini-Hochberg procedure and the Storey's q-value procedure. It controls false discovery rates through controlling the expected number of false discoveries.

This package provides a system to facilitate brand identity management using the brand.yml standard, providing functions to consistently access and apply brand colors, typography, and other visual elements across your R projects.

An interactive document on the topic of binary logistic regression analysis using rmarkdown and shiny packages. Runtime examples are provided in the package function as well as at <https://analyticmodels.shinyapps.io/BinaryLogisticRegressionModelling/>.