An implementation of several functions for feature extraction in ordinal time series datasets. Specifically, some of the features proposed by Weiss (2019) <doi:10.1080/01621459.2019.1604370> can be computed. These features can be used to perform inferential tasks or to feed machine learning algorithms for ordinal time series, among others. The package also includes some interesting datasets containing financial time series. Practitioners from a broad variety of fields could benefit from the general framework provided by otsfeatures'.

Estimates optimal number of biomarkers for two-group classification based on microarray data.

The optimal level of significance is calculated based on a decision-theoretic approach. The optimal level is chosen so that the expected loss from hypothesis testing is minimized. A range of statistical tests are covered, including the test for the population mean, population proportion, and a linear restriction in a multiple regression model. The details are covered in Kim and Choi (2020) <doi:10.1111/abac.12172>, and Kim (2021) <doi:10.1080/00031305.2020.1750484>.

An optimized method for distribution-preserving class-proportional down-sampling of bio-medical data <doi:10.1371/journal.pone.0255838>.

Oblique random survival forests incorporate linear combinations of input variables into random survival forests (Ishwaran, 2008 <DOI:10.1214/08-AOAS169>). Regularized Cox proportional hazard models (Simon, 2016 <DOI:10.18637/jss.v039.i05>) are used to identify optimal linear combinations of input variables.

An implementation of the Rapid Assessment Method for Older People or RAM-OP <https://www.helpage.org/resource/rapid-assessment-method-for-older-people-ramop-manual/>. It provides various functions that allow the user to design and plan the assessment and analyse the collected data. RAM-OP provides accurate and reliable estimates of the needs of older people.

We consider the problem of estimating two isotonic regression curves g1* and g2* under the constraint that they are ordered, i.e. g1* <= g2*. Given two sets of n data points y_1, ..., y_n and z_1, ..., z_n that are observed at (the same) deterministic design points x_1, ..., x_n, the estimates are obtained by minimizing the Least Squares criterion L(a, b) = sum_i=1^n (y_i - a_i)^2 w1(x_i) + sum_i=1^n (z_i - b_i)^2 w2(x_i) over the class of pairs of vectors (a, b) such that a and b are isotonic and a_i <= b_i for all i = 1, ..., n. We offer two different approaches to compute the estimates: a projected subgradient algorithm where the projection is calculated using a PAVA as well as Dykstra's cyclical projection algorithm.

We provide two algorithms for monitoring change points with online matrix-valued time series, under the assumption of a two-way factor structure. The algorithms are based on different calculations of the second moment matrices. One is based on stacking the columns of matrix observations, while another is by a more delicate projected approach. A well-known fact is that, in the presence of a change point, a factor model can be rewritten as a model with a larger number of common factors. In turn, this entails that, in the presence of a change point, the number of spiked eigenvalues in the second moment matrix of the data increases. Based on this, we propose two families of procedures - one based on the fluctuations of partial sums, and one based on extreme value theory - to monitor whether the first non-spiked eigenvalue diverges after a point in time in the monitoring horizon, thereby indicating the presence of a change point. This package also provides some simple functions for detecting and removing outliers, imputing missing entries and testing moments. See more details in He et al. (2021)<doi:10.48550/arXiv.2112.13479>.

It implements functions for simulation and estimation of the ordinal latent block model (OLBM), as described in Corneli, Bouveyron and Latouche (2019).

An implementation of DuMouchel's (1999) <doi:10.1080/00031305.1999.10474456> Bayesian data mining method for the market basket problem. Calculates Empirical Bayes Geometric Mean (EBGM) and posterior quantile scores using the Gamma-Poisson Shrinker (GPS) model to find unusually large cell counts in large, sparse contingency tables. Can be used to find unusually high reporting rates of adverse events associated with products. In general, can be used to mine any database where the co-occurrence of two variables or items is of interest. Also calculates relative and proportional reporting ratios. Builds on the work of the PhViD package, from which much of the code is derived. Some of the added features include stratification to adjust for confounding variables and data squashing to improve computational efficiency. Includes an implementation of the EM algorithm for hyperparameter estimation loosely derived from the mederrRank package.

Several Oceanographic data sets are provided for use by the oce package and for other purposes.

This package provides tools for surrogate evaluation in longitudinal studies using state-space models as proposed in Santos Jr. and Parast (2026)<doi:10.48550/arXiv.2604.12882>. The package estimates treatment effects over time with and without adjustment for surrogate information, summarizes the proportion of treatment effect explained by a longitudinal surrogate, quantifies uncertainty via bootstrap resampling, and provides plotting and summary utilities for fitted models.

Facilitates the creation of intuitive figures to describe metabolomics data by utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) hierarchy data, and gathers functional orthology and gene data from the KEGG-REST API.

Bayesian reconstruction of who infected whom during past outbreaks using routinely-collected surveillance data. Inference of transmission trees using genotype, age specific social contacts, distance between cases and onset dates of the reported cases. (Robert A, Kucharski AJ, Gastanaduy PA, Paul P, Funk S. (2020) <doi:10.1098/rsif.2020.0084>).

Use health data in the Observational Medical Outcomes Partnership Common Data Model format in Spark'. Functionality includes creating all required tables and fields and creation of a single reference to the data. Native Spark functionality is supported.

Accesses high resolution raster maps using the OpenStreetMap protocol. Dozens of road, satellite, and topographic map servers are directly supported. Additionally raster maps may be constructed using custom tile servers. Maps can be plotted using either base graphics, or ggplot2. This package is not affiliated with the OpenStreetMap.org mapping project.

Sequential outlier identification for Gaussian mixture models using the distribution of Mahalanobis distances. The optimal number of outliers is chosen based on the dissimilarity between the theoretical and observed distributions of the scaled squared sample Mahalanobis distances. Also includes an extension for Gaussian linear cluster-weighted models using the distribution of studentized residuals. Doherty, McNicholas, and White (2025) <doi:10.48550/arXiv.2505.11668>.

O-statistics, or overlap statistics, measure the degree of community-level trait overlap. They are estimated by fitting nonparametric kernel density functions to each speciesâ trait distribution and calculating their areas of overlap. For instance, the median pairwise overlap for a community is calculated by first determining the overlap of each species pair in trait space, and then taking the median overlap of each species pair in a community. This median overlap value is called the O-statistic (O for overlap). The Ostats() function calculates separate univariate overlap statistics for each trait, while the Ostats_multivariate() function calculates a single multivariate overlap statistic for all traits. O-statistics can be evaluated against null models to obtain standardized effect sizes. Ostats is part of the collaborative Macrosystems Biodiversity Project "Local- to continental-scale drivers of biodiversity across the National Ecological Observatory Network (NEON)." For more information on this project, see the Macrosystems Biodiversity Website (<https://neon-biodiversity.github.io/>). Calculation of O-statistics is described in Read et al. (2018) <doi:10.1111/ecog.03641>, and a teaching module for introducing the underlying biological concepts at an undergraduate level is described in Grady et al. (2018) <http://tiee.esa.org/vol/v14/issues/figure_sets/grady/abstract.html>.

The online principal component method can process the online data set. The philosophy of the package is described in Guo G. (2018) <doi:10.1080/10485252.2018.1531130>.

Conduct sensitivity analysis of omitted variable bias in linear econometric models using the methodology presented in Basu (2025) <doi:10.2139/ssrn.4704246>.

This package provides an end-to-end workflow for integrative analysis of two omics layers using sparse canonical correlation analysis (sCCA), including sample alignment, feature selection, network edge construction, and visualization of gene-metabolite relationships. The underlying methods are based on penalized matrix decomposition and sparse CCA (Witten, Tibshirani and Hastie (2009) <doi:10.1093/biostatistics/kxp008>), with design principles inspired by multivariate integrative frameworks such as mixOmics (Rohart et al. (2017) <doi:10.1371/journal.pcbi.1005752>).

Given a certain coverage level, obtains simultaneous confidence bands for the survival and cumulative hazard functions such that the area between is minimized. Produces an approximate solution based on local time arguments.

An RStudio addin to assist with removing objects from the global environment. Features include removing objects according to name patterns and object type. During the course of an analysis, temporary objects are often created and this tool assists with removing them quickly. This can be useful when memory management within R is important.

OpenTelemetry is a collection of tools, APIs, and SDKs used to instrument, generate, collect, and export telemetry data (metrics, logs, and traces) for analysis in order to understand your software's performance and behavior. This package contains the OpenTelemetry SDK, and exporters. Use this package to export traces, metrics, logs from instrumented R code. Use the otel package to instrument your R code for OpenTelemetry.