This package provides classes and methods for implementing aquatic ecosystem models, for running these models, and for visualizing their results.

Programmatic interface to the European Centre for Medium-Range Weather Forecasts dataset web services (ECMWF; <https://www.ecmwf.int/>) and Copernicus's Data Stores. Allows for easy downloads of weather forecasts and climate reanalysis data in R. Data stores covered include the Climate Data Store (CDS; <https://cds.climate.copernicus.eu>), Atmosphere Data Store (ADS; <https://ads.atmosphere.copernicus.eu>) and Early Warning Data Store (CEMS; <https://ewds.climate.copernicus.eu>).

An intuitive and user-friendly package designed to aid undergraduate students in understanding and applying econometric methods in their studies, Tailored specifically for Econometrics and Regression Modeling courses, it provides a practical toolkit for modeling and analyzing econometric data with detailed inference capabilities.

This package provides methods to simulate and analyse the size and length of branching processes with an arbitrary offspring distribution. These can be used, for example, to analyse the distribution of chain sizes or length of infectious disease outbreaks, as discussed in Farrington et al. (2003) <doi:10.1093/biostatistics/4.2.279>.

This package provides a plot overlying the niche of multiple species is obtained: 1) to determine the niche conditions which favor a higher species richness, 2) to create a box plot with the range of environmental variables of the species, 3) to obtain a list of species in an area of the niche selected by the user and, 4) to estimate niche overlap among the species.

Implementations of the expected shortfall backtests of Bayer and Dimitriadis (2020) <doi:10.1093/jjfinec/nbaa013> as well as other well known backtests from the literature. Can be used to assess the correctness of forecasts of the expected shortfall risk measure which is e.g. used in the banking and finance industry for quantifying the market risk of investments. A special feature of the backtests of Bayer and Dimitriadis (2020) <doi:10.1093/jjfinec/nbaa013> is that they only require forecasts of the expected shortfall, which is in striking contrast to all other existing backtests, making them particularly attractive for practitioners.

This package provides tools and pre-trained Machine Learning [ML] models for calibration of Agent-Based Models [ABMs] built with the R package epiworldR'. Implements methods described in Najafzadehkhoei, Vega Yon, Modenesi, and Meyer (2025) <doi:10.48550/arXiv.2509.07013>. Users can automatically calibrate ABMs in seconds with pre-trained ML models, effectively focusing on simulation rather than calibration. Bridges a gap by allowing public health practitioners to run their own ABMs without the advanced technical expertise often required by calibration.

Descriptive analysis is essential for publishing medical articles. This package provides an easy way to conduct the descriptive analysis. 1. Both numeric and factor variables can be handled. For numeric variables, normality test will be applied to choose the parametric and nonparametric test. 2. Both two or more groups can be handled. For groups more than two, the post hoc test will be applied, Tukey for the numeric variables and FDR for the factor variables. 3. T test, ANOVA or Fisher test can be forced to apply. 4. Mean and standard deviation can be forced to display.

This framework provides versatile algorithms to efficiently infer confidence intervals for extreme value statistics, such as extreme quantiles and return levels, that are representative of the asymmetric uncertainty spread, using extreme value theory extrapolation and the profile likelihood (see e.g., Coles (2001) <doi:10.1007/978-1-4471-3675-0>). Unlike existing algorithms, the CI endpoints are found without the need for a strict prespecified range, can be covariate-dependent, and can be based on weighted samples. This package is motivated by Zeder et al. (2023) <doi:10.1029/2023GL104090> and by Pasche et al. (2026) <doi:10.1007/s10687-026-00536-9>.

This package provides functions for evaluating and visualizing ecological assessment procedures for surface waters containing physical, chemical and biological assessments in the form of value functions.

Estimates the time-varying reproduction number, rate of spread, and doubling time using a renewal equation approach combined with Bayesian inference via Stan. Supports Gaussian process and random walk priors for modelling changes in transmission over time. Accounts for delays between infection and observation (incubation period, reporting delays), right-truncation in recent data, day-of-week effects, and observation overdispersion. Can estimate relationships between primary and secondary outcomes (e.g., cases to hospitalisations or deaths) and forecast both. Runs across multiple regions in parallel. Based on Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1> and Gostic et al. (2020) <doi:10.1101/2020.06.18.20134858>.

This dataset contains population estimates of all European cities with at least 10,000 inhabitants during the period 1500-1800. These data are adapted from Jan De Vries, "European Urbanization, 1500-1800" (1984).

This package implements forecasting methods for individual electricity load curves, including Kernel Wavelet Functional (KWF), clustered KWF, Generalized Additive Models (GAM), Multivariate Adaptive Regression Splines (MARS), and Long Short-Term Memory (LSTM) models. Provides normalized dataset adapters for iFlex, StoreNet, Smart-Grid Smart-City, Low Carbon London, and REFIT; download and read support for IDEAL and GX; explicit Python backend selection for TensorFlow-based LSTM fits; helpers for daily segmentation and rolling-origin benchmarking; and compact shipped example panels and benchmark-result datasets.

Some wrappers, functions and data sets for for spatial point pattern analysis (mainly based on spatstat'), used in the book "Introduccion al Analisis Espacial de Datos en Ecologia y Ciencias Ambientales: Metodos y Aplicaciones" and in the papers by De la Cruz et al. (2008) <doi:10.1111/j.0906-7590.2008.05299.x> and Olano et al. (2009) <doi:10.1051/forest:2008074>.

Easily export R graphs and statistical output to Microsoft Office / LibreOffice', Latex and HTML Documents, using sensible defaults that result in publication-quality output with simple, straightforward commands. Output to Microsoft Office is in editable DrawingML vector format for graphs, and can use corporate template documents for styling. This enables the production of standardized reports and also allows for manual tidy-up of the layout of R graphs in Powerpoint before final publication. Export of graphs is flexible, and functions enable the currently showing R graph or the currently showing R stats object to be exported, but also allow the graphical or tabular output to be passed as objects. The package relies on package officer for export to Office documents,and output files are also fully compatible with LibreOffice'. Base R', ggplot2 and lattice plots are supported, as well as a wide variety of R stats objects, via wrappers to xtable(), broom::tidy() and stargazer(), including aov(), lm(), glm(), lme(), glmnet() and coxph() as well as matrices and data frames and many more...

Generate citations and references for R packages from CRAN or Bioconductor. Supports RIS and BibTeX formats with automatic DOI retrieval from GitHub repositories and published papers. Includes command-line interface for batch processing.

This data management package provides some helper classes for publicly available data sources (HMD, DESTATIS) in Demography. Similar to ideas developed in the Bioconductor project <https://bioconductor.org> we strive to encapsulate data in easy to use S4 objects. If original data is provided in a text file, the resulting S4 object contains all information from that text file. But the information is somehow structured (header, footer, etc). Further the classes provide methods to make a subset for selected calendar years or selected regions. The resulting subset objects still contain the original header and footer information.

Evaluation Platform in Chronic Obstructive Pulmonary Disease (EPIC) is a Discrete Event Simulation (DES) model that simulates health outcomes of patients with Chronic Obstructive Pulmonary Disease (COPD) based on demographics and individual-level risk factors, based on the model published in Sadatsafavi et al. (2019) <doi:10.1177/0272989X18824098>.

This package provides a conservative, assumption-aware statistical consistency checker for published research results. Parses test statistics, effect sizes, and confidence intervals from text, PDF, HTML, and Word documents across multiple citation styles including American Psychological Association (APA), Harvard, Frontiers, PLOS ONE, Scientific Reports, Nature Human Behaviour, PeerJ, eLife, PNAS, and others. Recomputes effect sizes using all plausible variants when design is ambiguous, and validates internal consistency. Supports t-tests, F-tests/ANOVA, correlations, chi-square, z-tests, regression, and nonparametric tests. Provides statcheck'-compatible API functions for batch processing of files and directories. Explicitly tracks all assumptions and uncertainty in output. Detects decision errors (significance reversals) similar to statcheck'. Note: this package is under active development and results should be independently verified. Use is at the sole responsibility of the user. Contributions and verification reports are welcome.

Training and predict functions for Single Hidden-layer Feedforward Neural Networks (SLFN) using the Extreme Learning Machine (ELM) algorithm. The ELM algorithm differs from the traditional gradient-based algorithms for very short training times (it doesn't need any iterative tuning, this makes learning time very fast) and there is no need to set any other parameters like learning rate, momentum, epochs, etc. This is a reimplementation of the elmNN package using RcppArmadillo after the elmNN package was archived. For more information, see "Extreme learning machine: Theory and applications" by Guang-Bin Huang, Qin-Yu Zhu, Chee-Kheong Siew (2006), Elsevier B.V, <doi:10.1016/j.neucom.2005.12.126>.

This package creates simple or stacked epidemic curves for hourly, daily, weekly or monthly outcome data.

Current layout algorithms such as Kamada Kawai do not take into consideration disjoint clusters in a network, often resulting in a high overlap among the clusters, resulting in a visual â hairballâ that often is uninterpretable. The ExplodeLayout algorithm takes as input (1) an edge list of a unipartite or bipartite network, (2) node layout coordinates (x, y) generated by a layout algorithm such as Kamada Kawai, (3) node cluster membership generated from a clustering algorithm such as modularity maximization, and (4) a radius to enable the node clusters to be â explodedâ to reduce their overlap. The algorithm uses these inputs to generate new layout coordinates of the nodes which â explodesâ the clusters apart, such that the edge lengths within the clusters are preserved, while the edge lengths between clusters are recalculated. The modified network layout with nodes and edges are displayed in two dimensions. The user can experiment with different explode radii to generate a layout which has sufficient separation of clusters, while reducing the overall layout size of the network. This package is a basic version of an earlier version called [epl]<https://github.com/UTMB-DIVA-Lab/epl> that searched for an optimal explode radius, and offered multiple ways to separate clusters in a network (Bhavnani et al(2017) <https://pmc.ncbi.nlm.nih.gov/articles/PMC5543384/>). The example dataset is for a bipartite network, but the algorithm can work also for unipartite networks.

This package provides tools for transforming R expressions. Provides functions for finding, extracting, and replacing patterns in R language objects, similarly to how regular expressions can be used to find, extract, and replace patterns in text. Also provides functions for generating code using specially-formatted template files and for translating R expressions into similar expressions in other programming languages. The package may be helpful for advanced uses of R expressions, such as developing domain-specific languages.

This package provides a set of functions for computing expected permutation matrices given a matrix of likelihoods for each individual assignment. It has been written to accompany the forthcoming paper Computing expectations and marginal likelihoods for permutations'. Publication details will be updated as soon as they are finalized.