Weighted-L2 FPOP Maidstone et al. (2017) <doi:10.1007/s11222-016-9636-3> and pDPA/FPSN Rigaill (2010) <arXiv:1004.0887> algorithm for detecting multiple changepoints in the mean of a vector. Also includes a few model selection functions using Lebarbier (2005) <doi:10.1016/j.sigpro.2004.11.012> and the capsushe package.

Perform variable selection in settings with possibly missing data based on extrinsic (algorithm-specific) and intrinsic (population-level) variable importance. Uses a Super Learner ensemble to estimate the underlying prediction functions that give rise to estimates of variable importance. For more information about the methods, please see Williamson and Huang (2024) <doi:10.1515/ijb-2023-0059>.

Implementations of the algorithms present article Generalized Spatial-Time Sequence Miner, original title (Castro, Antonio; Borges, Heraldo ; Pacitti, Esther ; Porto, Fabio ; Coutinho, Rafaelli ; Ogasawara, Eduardo . Generalização de Mineração de Sequências Restritas no Espaço e no Tempo. In: XXXVI SBBD - Simpósio Brasileiro de Banco de Dados, 2021 <doi:10.5753/sbbd.2021.17891>).

This package provides a visualization suite primarily designed for single-cell RNA-sequencing data analysis applications but well-suited for other purposes as well. It introduces novel plots to represent two-variable and frequency data and optimizes some commonly used plotting options (e.g., correlation, network, density, alluvial and volcano plots) for ease of usage and flexibility.

Functions, data sets, analyses and examples from the book A Handbook of Statistical Analyses Using R (Brian S. Everitt and Torsten Hothorn, Chapman & Hall/CRC, 2006). The first chapter of the book, which is entitled An Introduction to R'', is completely included in this package, for all other chapters, a vignette containing all data analyses is available.

This package implements an S4 distribution system and estimation methods for parameters of common distribution families. The common d, p, q, r function family for each distribution is enriched with the ll, e, and v counterparts, computing the log-likelihood, performing estimation, and calculating the asymptotic variance - covariance matrix, respectively. Parameter estimation is performed analytically whenever possible.

Auxiliary package for better/faster analytics, visualization, data mining, and machine learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling, Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or data scientist to get quick and robust results, without the need of repetitive coding or advanced R programming skills.

Performing multiple-class cluster correspondence analysis(MCCCA). The main functions are create.MCCCAdata() to create a list to be applied to MCCCA, MCCCA() to apply MCCCA, and plot.mccca() for visualizing MCCCA result. Methods used in the package refers to Mariko Takagishi and Michel van de Velden (2022)<doi:10.1080/10618600.2022.2035737>.

Transforms, calculates, and presents results from the Mental Health Quality of Life Questionnaire (MHQoL), a measure of health-related quality of life for individuals with mental health conditions. Provides scoring functions, summary statistics, and visualization tools to facilitate interpretation. For more details see van Krugten et al.(2022) <doi:10.1007/s11136-021-02935-w>.

This package provides a generalization of principal component analysis for integrative analysis. The method finds principal components that describe single matrices or that are common to several matrices. The solutions are sparse. Rank of solutions is automatically selected using cross validation. The method is described in Kallus et al. (2019) <doi:10.48550/arXiv.1911.04927>.

Posterior distribution of case-control fine-mapping. Specifically, Bayesian variable selection for single-nucleotide polymorphism (SNP) data using the normal-gamma prior. Alenazi A.A., Cox A., Juarez M,. Lin W-Y. and Walters, K. (2019) Bayesian variable selection using partially observed categorical prior information in fine-mapping association studies, Genetic Epidemiology. <doi:10.1002/gepi.22213>.

Algorithms for ordinal causal discovery. This package aims to enable users to discover causality for observational ordinal categorical data with greedy and exhaustive search. See Ni, Y., & Mallick, B. (2022) <https://proceedings.mlr.press/v180/ni22a/ni22a.pdf> "Ordinal Causal Discovery. Proceedings of the 38th Conference on Uncertainty in Artificial Intelligence, (UAI 2022), PMLR 180:1530â 1540".

Computes power and level tables for goodness-of-fit tests for the normal, Laplace, and uniform distributions. Generates output in LaTeX format to facilitate reporting and reproducibility. Explanatory graphs help visualize the statistical power of test statistics under various alternatives. For more details, see Lafaye De Micheaux and Tran (2016) <doi:10.18637/jss.v069.i03>.

The modeling and prediction of graph-associated time series(GATS) based on continuous time quantum walk. This software is mainly used for feature extraction, modeling, prediction and result evaluation of GATS, including continuous time quantum walk simulation, feature selection, regression analysis, time series prediction, and series fit calculation. A paper is attached to the package for reference.

Simulates and plots quantities of interest (relative hazards, first differences, and hazard ratios) for linear coefficients, multiplicative interactions, polynomials, penalised splines, and non-proportional hazards, as well as stratified survival curves from Cox Proportional Hazard models. It also simulates and plots marginal effects for multiplicative interactions. Methods described in Gandrud (2015) <doi:10.18637/jss.v065.i03>.

This package provides functions to non-parametrically estimate the off-pulse interval of a source function originating from a pulsar. The technique is based on a sequential application of P-values obtained from goodness-of-fit tests for the uniform distribution, such as the Kolmogorov-Smirnov, Cramer-von Mises, Anderson-Darling and Rayleigh goodness-of-fit tests.

This statistical method uses the nearest neighbor algorithm to estimate absolute distances between single cells based on a chosen constellation of surface proteins, with these distances being a measure of the similarity between the two cells being compared. Based on Sen, N., Mukherjee, G., and Arvin, A.M. (2015) <DOI:10.1016/j.ymeth.2015.07.008>.

Based on STATA xtsum command, it is used to compute summary statistics for a panel data set. It generates overall, between-group, and within-group statistics for specified variables in a panel data set, as presented in S. Porter (2023) <https://stephenporter.org/files/xtsum_handout.pdf>, StataCorp (2023) <https://www.stata.com/manuals/xtxtsum.pdf>.

Relative, generalized, and Erreygers corrected concentration index; plot Lorenz curves; and decompose health inequalities into contributing factors. The package currently works with (generalized) linear models, survival models, complex survey models, and marginal effects probit models. originally forked by Brecht Devleesschauwer from the decomp package (no longer on CRAN), rineq is now maintained by Kaspar Walter Meili. Compared to the earlier rineq version on github by Brecht Devleesschauwer (<https://github.com/brechtdv/rineq>), the regression tree functionality has been removed. Improvements compared to earlier versions include improved plotting of decomposition and concentration, added functionality to calculate the concentration index with different methods, calculation of robust standard errors, and support for the decomposition analysis using marginal effects probit regression models. The development version is available at <https://github.com/kdevkdev/rineq>.

This package provides an R interface for the Bureau of Economic Analysis (BEA) API (see <http://www.bea.gov/API/bea_web_service_api_user_guide.htm> for more information) that serves two core purposes - 1. To Extract/Transform/Load data [beaGet()] from the BEA API as R-friendly formats in the user's work space [transformation done by default in beaGet() can be modified using optional parameters; see, too, bea2List(), bea2Tab()]. 2. To enable the search of descriptive meta data [beaSearch()]. Other features of the library exist mainly as intermediate methods or are in early stages of development. Important Note - You must have an API key to use this library. Register for a key at <http://www.bea.gov/API/signup/index.cfm> .

Numerous functions for cohort-based analyses, either for prediction or causal inference. For causal inference, it includes Inverse Probability Weighting and G-computation for marginal estimation of an exposure effect when confounders are expected. We deal with binary outcomes, times-to-events, competing events, and multi-state data. For multistate data, semi-Markov model with interval censoring may be considered, and we propose the possibility to consider the excess of mortality related to the disease compared to reference lifetime tables. For predictive studies, we propose a set of functions to estimate time-dependent receiver operating characteristic (ROC) curves with the possible consideration of right-censoring times-to-events or the presence of confounders. Finally, several functions are available to assess time-dependent ROC curves or survival curves from aggregated data.

The package is focused on the detection of correlation between expressed genes and selected epigenomic signals (i.e. enhancers obtained from ChIP-seq data) either within topologically associated domains (TADs) or between chromatin contact loop anchors. Various parameters can be controlled to investigate the influence of external factors and visualization plots are available for each analysis step.

This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package. Support for reproducibility of the whole analysis is provided by means of a template report which gets automatically compiled and can be stored/shared.

This package builds on the Epimods framework which facilitates finding weighted subnetworks ("modules") on Illumina Infinium 27k arrays using the SpinGlass algorithm, as implemented in the iGraph package. We have created a class of gene centric annotations associated with p-values and effect sizes and scores from any researchers prior statistical results to find functional modules.