This package implements parametric modal Autoregressive Integrated Moving Average (ARIMA) and seasonal ARIMA (SARIMA) models utilizing the Skewed Distribution (SKD) family, in which the conditional mode, rather than the conditional mean, follows the (seasonal) ARIMA recursion. Current distributions supported are the Skew-Normal, Skewed Student-t, and Skewed Laplace. The parameters are estimated by maximum likelihood using analytical gradients. Includes residual diagnostics, simulation envelopes, automatic order selection, joint and marginal modal forecasts, exact and parametric bootstrap prediction intervals, and classical asymptotic inference via the Fisher Information matrix. Methods are described in Galarza, C.E., Lachos, V.H., Cabral, C.R.B., & Castro, L.M. (2017) <doi:10.1002/sta4.140>.

This package implements Bayesian brain mapping with population-derived priors, including the original model described in Mejia et al. (2020) <doi:10.1080/01621459.2019.1679638>, the model with spatial priors described in Mejia et al. (2022) <doi:10.1080/10618600.2022.2104289>, and the model with population-derived priors on functional connectivity described in Mejia et al. (2025) <doi:10.1093/biostatistics/kxaf022>. Population-derived priors are based on templates representing established brain network maps, for example derived from independent component analysis (ICA), parcellations, or other methods. Model estimation is based on expectation-maximization or variational Bayes algorithms. Includes direct support for CIFTI', GIFTI', and NIFTI neuroimaging file formats.

There are various functions for managing and cleaning data before the application of different approaches. This includes identifying and erasing sudden jumps in dendrometer data not related to environmental change, identifying the time gaps of recordings, and changing the temporal resolution of data to different frequencies. Furthermore, the package calculates daily statistics of dendrometer data, including the daily amplitude of tree growth. Various approaches can be applied to separate radial growth from daily cyclic shrinkage and expansion due to uptake and loss of stem water. In addition, it identifies periods of consecutive days with user-defined climatic conditions in daily meteorological data, then check what trees are doing during that period.

This package provides tools for constructing and auditing longitudinal decision paths from panel data. Implements a decision infrastructure framework for representing institutional AI systems as generators of time-ordered binary decision sequences. Provides functions to build path objects from panel data, summarise per-unit descriptors (dosage, switching rate, onset, duration, longest run), compute the Decision Reliability Index (DRI) following Cronbach (1951) <doi:10.1007/BF02310555>, estimate Shannon decision-path entropy following Shannon (1948) <doi:10.1002/j.1538-7305.1948.tb01338.x>, classify systems by infrastructure type (static, periodic, continuous, human-in-the-loop), and evaluate subgroup disparities in decision exposure and stability. Applications include education, policy, health, and organisational research.

This package provides functions to access data from public RESTful APIs including World Bank API', and Nager.Date API', covering Mexico's economic indicators, population statistics, literacy rates, and official public holidays. The package also includes curated datasets related to Mexico such as air quality monitoring stations, pollution zones, income surveys, postal abbreviations, election studies, forest productivity and demographic data by state. It supports research and analysis focused on Mexico by integrating reliable global APIs with structured national datasets drawn from open and academic sources. For more information on the APIs, see: World Bank API <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392>, and Nager.Date API <https://date.nager.at/Api>.

Fit Bayesian time series models using Stan for full Bayesian inference. A wide range of distributions and models are supported, allowing users to fit Seasonal ARIMA, ARIMAX, Dynamic Harmonic Regression, GARCH, t-student innovation GARCH models, asymmetric GARCH, Random Walks, stochastic volatility models for univariate time series. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their beliefs. Model fit can easily be assessed and compared with typical visualization methods, information criteria such as loglik, AIC, BIC WAIC, Bayes factor and leave-one-out cross-validation methods. References: Hyndman (2017) <doi:10.18637/jss.v027.i03>; Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.

An interactive platform for clustering analysis and teaching based on the shiny web application framework. Supports multiple popular clustering algorithms including k-means, hierarchical clustering, DBSCAN (Density-Based Spatial Clustering of Applications with Noise), PAM (Partitioning Around Medoids), GMM (Gaussian Mixture Model), and spectral clustering. Users can upload datasets or use built-in ones, visualize clustering results using dimensionality reduction methods such as Principal Component Analysis (PCA) and t-distributed Stochastic Neighbor Embedding (t-SNE), evaluate clustering quality via silhouette plots, and explore method-specific visualizations and guides. For details on implemented methods, see: Reynolds (2009, ISBN:9781598296975) for GMM; Luxburg (2007) <doi:10.1007/s11222-007-9033-z> for spectral clustering.

This package provides a workflow based on scTenifoldNet to perform in-silico knockout experiments using single-cell RNA sequencing (scRNA-seq) data from wild-type (WT) control samples as input. First, the package constructs a single-cell gene regulatory network (scGRN) and knocks out a target gene from the adjacency matrix of the WT scGRN by setting the geneâ s outdegree edges to zero. Then, it compares the knocked out scGRN with the WT scGRN to identify differentially regulated genes, called virtual-knockout perturbed genes, which are used to assess the impact of the gene knockout and reveal the geneâ s function in the analyzed cells.

Allows the user to apply the Bayes Linear approach to finite population with the Simple Random Sampling - BLE_SRS() - and the Stratified Simple Random Sampling design - BLE_SSRS() - (both without replacement), to the Ratio estimator (using auxiliary information) - BLE_Ratio() - and to categorical data - BLE_Categorical(). The Bayes linear estimation approach is applied to a general linear regression model for finite population prediction in BLE_Reg() and it is also possible to achieve the design based estimators using vague prior distributions. Based on Gonçalves, K.C.M, Moura, F.A.S and Migon, H.S.(2014) <https://www150.statcan.gc.ca/n1/en/catalogue/12-001-X201400111886>.

These functions were developed to support statistical analysis on functional covariance operators. The package contains functions to: - compute 2-Wasserstein distances between Gaussian Processes as in Masarotto, Panaretos & Zemel (2019) <doi:10.1007/s13171-018-0130-1>; - compute the Wasserstein barycenter (Frechet mean) as in Masarotto, Panaretos & Zemel (2019) <doi:10.1007/s13171-018-0130-1>; - perform analysis of variance testing procedures for functional covariances and tangent space principal component analysis of covariance operators as in Masarotto, Panaretos & Zemel (2022) <arXiv:2212.04797>. - perform a soft-clustering based on the Wasserstein distance where functional data are classified based on their covariance structure as in Masarotto & Masarotto (2023) <doi:10.1111/sjos.12692>.

This package provides tools for simulating, analysing, and fitting mobility-based SEAIR (Susceptible-Exposed-Asymptomatic-Infectious-Recovered) compartmental epidemic models with heterogeneous individual mobility. Each individual carries a fixed mobility trait that scales susceptibility and infectiousness through a rank-one kernel, extending the mobility-based compartmental framework of Jiang et al. (2025) <doi:10.1137/24M1691557> by adding a latent stage and a behavioural split between asymptomatic and symptomatic infectiousness. Provides a numerical solver for the underlying partial differential equation system, closed-form computation of the basic reproduction number R0 and the final epidemic size, and a parametric least-squares routine for recovering the mobility distribution from an observed aggregate symptomatic time series.

Reduction-based techniques for cost-sensitive multi-class classification, in which each observation has a different cost for classifying it into one class, and the goal is to predict the class with the minimum expected cost for each new observation. Implements Weighted All-Pairs (Beygelzimer, A., Langford, J., & Zadrozny, B., 2008, <doi:10.1007/978-0-387-79361-0_1>), Weighted One-Vs-Rest (Beygelzimer, A., Dani, V., Hayes, T., Langford, J., & Zadrozny, B., 2005, <https://dl.acm.org/citation.cfm?id=1102358>) and Regression One-Vs-Rest. Works with arbitrary classifiers taking observation weights, or with regressors. Also implements cost-proportionate rejection sampling for working with classifiers that don't accept observation weights.

The geographical complexity of individual variables can be characterized by the differences in local attribute variables, while the common geographical complexity of multiple variables can be represented by fluctuations in the similarity of vectors composed of multiple variables. In spatial regression tasks, the goodness of fit can be improved by incorporating a geographical complexity representation vector during modeling, using a geographical complexity-weighted spatial weight matrix, or employing local geographical complexity kernel density. Similarly, in spatial sampling tasks, samples can be selected more effectively by using a method that weights based on geographical complexity. By optimizing performance in spatial regression and spatial sampling tasks, the spatial bias of the model can be effectively reduced.

Gain seamless access to origin-destination (OD) data from the Spanish Ministry of Transport, hosted at <https://www.transportes.gob.es/ministerio/proyectos-singulares/estudios-de-movilidad-con-big-data/opendata-movilidad>. This package simplifies the management of these large datasets by providing tools to download zone boundaries, handle associated origin-destination data, and process it efficiently with the duckdb database interface. Local caching minimizes repeated downloads, streamlining workflows for researchers and analysts. Methods described in Kotov et al. (2026) <doi:10.1177/23998083251415040>. Extensive documentation is available at <https://ropenspain.github.io/spanishoddata/index.html>, offering guides on creating static and dynamic mobility flow visualizations and transforming large datasets into analysis-ready formats.

This package provides functions for estimating uncertainty in the number of fatalities in the Uppsala Conflict Data Program (UCDP) data. The package implements a parametric reported-value Gumbel mixture distribution that accounts for the uncertainty in the number of fatalities in the UCDP data. The model is based on information from a survey on UCDP coders and how they view the uncertainty of the number of fatalities from UCDP events. The package provides functions for making random draws of fatalities from the mixture distribution, as well as to estimate percentiles, quantiles, means, and other statistics of the distribution. Full details on the survey and estimation procedure can be found in Vesco et al (2024).

This package provides a set of fast and convenient functions to help conducting accessibility analyses. Given a pre-computed travel cost matrix and a land use dataset (containing for example the location of jobs, healthcare and population), the package allows one to calculate accessibility levels, and accessibility poverty and inequality. The package covers the majority of the most commonly used accessibility measures (such as cumulative opportunities, gravity-based and floating catchment areas methods), some cutting edge measures proposed in the literature (e.g. balancing cost and constrained accessibility) as well as the most frequently used inequality and poverty metrics (such as the Palma ratio, the concentration and Theil indices and the FGT family of measures).

This package provides tools to conduct Monte Carlo simulations under different conditions (e.g., varying sample size, data normality) for structural equation models (SEMs). Data can be simulated based on user-defined factor loadings and correlations, with optional non-normality added via Fleishman's power method (1978) <doi:10.1007/BF02293811>. Once generated, models can be estimated using lavaan'. This package facilitates testing model performance across multiple simulation scenarios. When data generation is completed (or when generated data sets are given) model tests can also be run. Please cite as "Orçan, F. (2021). MonteCarloSEM An R Package to Simulate Data for SEM. International Journal of Assessment Tools in Education, 8 (3), 704-713.".

This package provides functions for generating partially replicated (p-rep) test-control designs for early generation varietal trials conducted across multiple environments. The package implements three construction methods for obtaining p-rep test-control designs with one or more control treatments. The package extends the partially replicated design framework of Vinaykumar et al. (2026) <doi:10.1007/s12355-025-01684-1> to accommodate test-control comparisons in breeding trials. Functions are provided for generating randomized and non-randomized layouts and for displaying the design parameters and treatment allocations for each environment. The proposed designs are useful for large-scale varietal evaluation trials where a large number of test lines are assessed under limited experimental resources.

Utilities designed to make the analysis of field trials easier and more accessible for everyone working in plant breeding. It provides a simple and intuitive interface for conducting single and multi-environmental trial analysis, with minimal coding required. Whether you're a beginner or an experienced user, agriutilities will help you quickly and easily carry out complex analyses with confidence. With built-in functions for fitting Linear Mixed Models, agriutilities is the ideal choice for anyone who wants to save time and focus on interpreting their results. Some of the functions require the R package asreml for the ASReml software, this can be obtained upon purchase from VSN international <https://vsni.co.uk/software/asreml-r/>.

This package provides functions to access data from the BrasilAPI', Nager.Date API', and World Bank API', related to Brazil's postal codes, banks, holidays, company registrations, and economic development data. Additionally, the package includes curated datasets related to Brazil, covering topics such as demographic data (males and females by state and year), river levels, environmental emission factors, film festivals, and yellow fever outbreak records. The package supports research and analysis focused on Brazil by integrating open APIs with high-quality datasets from multiple domains. For more information on the APIs, see: BrasilAPI <https://brasilapi.com.br/>, Nager.Date <https://date.nager.at/Api>, World Bank API <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392>.

Detection of a statistically significant trend in the data provided by the user. This is based on the a signed test based on the binomial distribution. The package returns a trend test value, T, and also a p-value. A T value close to 1 indicates a rising trend, whereas a T value close to -1 indicates a decreasing trend. A T value close to 0 indicates no trend. There is also a command to visualize the trend. A test data set called gtsa_data is also available, which has global mean temperatures for January, April, July, and October for the years 1851 to 2022. Reference: Walpole, Myers, Myers, Ye. (2007, ISBN: 0-13-187711-9).

This package provides specialized color palettes representing phenological transitions and biological lifecycles within Philippine landscapes. Rather than abstract gradients, these scales are anchored to topologically grounded states such as agricultural maturity, seasonal vegetation shifts, and environmental readiness. Palettes are indexed against the Biologische Bundesanstalt, Bundessortenamt und CHemische Industrie (BBCH) scale (Meier, 2023) <https://www.openagrar.de/servlets/MCRFileNodeServlet/openagrar_derivate_00010428/BBCH-Skala_en.pdf> for terrestrial vegetation and the Reef Health Index (RHI) framework (McField and Kramer, 2007) <https://www.healthyreefs.org> for marine ecosystems. This ensures scientific interoperability across archipelagic spatial models, aligning with global standards for ecological state-transition modeling (Schwartz, 2013) <doi:10.1007/978-94-007-6925-0>.

The notion of power index has been widely used in literature to evaluate the influence of individual players (e.g., voters, political parties, nations, stockholders, etc.) involved in a collective decision situation like an electoral system, a parliament, a council, a management board, etc., where players may form coalitions. Traditionally this ranking is determined through numerical evaluation. More often than not however only ordinal data between coalitions is known. The package socialranking offers a set of solutions to rank players based on a transitive ranking between coalitions, including through CP-Majority, ordinal Banzhaf or lexicographic excellence solution summarized by Tahar Allouche, Bruno Escoffier, Stefano Moretti and Meltem à ztürk (2020, <doi:10.24963/ijcai.2020/3>).

Computes bounds and sensitivity parameters as part of sensitivity analysis for selection bias. Different bounds are provided: the SV (Smith and VanderWeele), sharp bounds, AF (assumption-free) bound, GAF (generalized AF), and CAF (counterfactual AF) bounds. The calculation of the sensitivity parameters for the SV, sharp, and GAF bounds assume an additional dependence structure in form of a generalized M-structure. The bounds can be calculated for any structure as long as the necessary assumptions hold. See Smith and VanderWeele (2019) <doi:10.1097/EDE.0000000000001032>, Zetterstrom, Sjölander, and Waernabum (2025) <doi:10.1177/09622802251374168>, Zetterstrom and Waernbaum (2022) <doi:10.1515/em-2022-0108>, and Zetterstrom (2024) <doi:10.1515/em-2023-0033>.