Allows the user to animate text within rmarkdown documents and shiny applications. The animations are activated using the Animate.css library. See <https://animate.style/> for more information.

This package performs binary classification via Group Method of Data Handling (GMDH) - type neural network algorithms. There exist two main algorithms available in GMDH() and dceGMDH() functions. GMDH() performs classification via GMDH algorithm for a binary response and returns important variables. dceGMDH() performs classification via diverse classifiers ensemble based on GMDH (dce-GMDH) algorithm. Also, the package produces a well-formatted table of descriptives for a binary response. Moreover, it produces confusion matrix, its related statistics and scatter plot (2D and 3D) with classification labels of binary classes to assess the prediction performance. All GMDH2 functions are designed for a binary response (Dag et al., 2019, <https://download.atlantis-press.com/article/125911202.pdf>).

Designed to simplify geospatial data access from the Statistics Finland Web Feature Service API <https://geo.stat.fi/geoserver/index.html>, the geofi package offers researchers and analysts a set of tools to obtain and harmonize administrative spatial data for a wide range of applications, from urban planning to environmental research. The package contains annually updated time series of municipality key datasets that can be used for data aggregation and language translations.

Generalized Entropy Calibration produces calibration weights using generalized entropy as the objective function for optimization. This approach, as implemented in the GECal package, is based on Kwon, Kim, and Qiu (2024) <doi:10.48550/arXiv.2404.01076>. GECal incorporates design weights into the constraints to maintain design consistency, rather than including them in the objective function itself.

This small collection of functions provides what we call elemental graphics for display of analysis of variance results, David C. Hoaglin, Frederick Mosteller and John W. Tukey (1991, ISBN:978-0-471-52735-0), Paul R. Rosenbaum (1989) <doi:10.2307/2684513>, Robert M. Pruzek and James E. Helmreich <https://jse.amstat.org/v17n1/helmreich.html>. The term elemental derives from the fact that each function is aimed at construction of graphical displays that afford direct visualizations of data with respect to the fundamental questions that drive the particular analysis of variance methods. These functions can be particularly helpful for students and non-statistician analysts. But these methods should be quite generally helpful for work-a-day applications of all kinds, as they can help to identify outliers, clusters or patterns, as well as highlight the role of non-linear transformations of data.

Allows users to fit a cosinor model using the glmmTMB framework. This extends on existing cosinor modeling packages, including cosinor and circacompare', by including a wide range of available link functions and the capability to fit mixed models. The cosinor model is described by Cornelissen (2014) <doi:10.1186/1742-4682-11-16>.

This package provides ggplot2 geoms for visualizing multivariate data using glyphs. The package implements several established glyph designs described in the information visualization literature, including the review by Borgo et al. (2013) <doi:10.2312/conf/EG2013/stars/039-063>.

The gamma-Orthogonal Matching Pursuit (gamma-OMP) is a recently suggested modification of the OMP feature selection algorithm for a wide range of response variables. The package offers many alternative regression models, such linear, robust, survival, multivariate etc., including k-fold cross-validation. References: Tsagris M., Papadovasilakis Z., Lakiotaki K. and Tsamardinos I. (2018). "Efficient feature selection on gene expression data: Which algorithm to use?" BioRxiv. <doi:10.1101/431734>. Tsagris M., Papadovasilakis Z., Lakiotaki K. and Tsamardinos I. (2022). "The gamma-OMP algorithm for feature selection with application to gene expression data". IEEE/ACM Transactions on Computational Biology and Bioinformatics 19(2): 1214--1224. <doi:10.1109/TCBB.2020.3029952>.

This package implements nonparametric density estimation with Averaged Shifted Histogram (ASH), Linear Blend Frequency Polygon (LBFP), and General Linear Blend Frequency Polygon (GLBFP) estimators. The package provides pointwise and grid-based estimation workflows, sparse-prefix grid-count computation, plotting helpers, and plug-in bandwidth selection. Methodological background follows Scott (1992) <doi:10.1002/9780470316849>, Terrell and Scott (1985) <doi:10.1080/01621459.1985.10477163>, and Carbon and Duchesne (2024) <doi:10.1007/s10463-023-00883-5>.

Integrates with your RMarkdown documents to automatically publish figures to the <https://GoFigr.io> service. Supports both knitr and interactive execution within RStudio'.

Graph clustering using an agglomerative algorithm to maximize the integrated classification likelihood criterion and a mixture of stochastic block models. The method is described in the article "Model-based clustering of multiple networks with a hierarchical algorithm" by T. Rebafka (2022) <arXiv:2211.02314>.

The official implementation of the Global Livestock Environmental Assessment Model (GLEAM) of the Food and Agriculture Organization of the United Nations (FAO) in R. GLEAM-X provides a modular, transparent framework for simulating livestock production systems and quantifying their environmental impacts. Methodological background: MacLeod et al. (2017) "Invited review: A position on the Global Livestock Environmental Assessment Model (GLEAM)" <doi:10.1017/S1751731117001847>. Further information: <https://www.fao.org/gleam/en/>.

Geoms for placing arrowheads at multiple points along a segment, not just at the end; position function to shift starts and ends of arrows to avoid exactly intersecting points.

Estimation of covariance matrices as solutions of continuous time Lyapunov equations. Sparse coefficient matrix and diagonal noise are estimated with a proximal gradient method for an l1-penalized loss minimization problem. Varando G, Hansen NR (2020) <arXiv:2005.10483>.

This package provides tools for constructing row-column factorial experiment layouts for the estimation of main effects and two-factor interactions in factorial and fractional factorial experiments. The package implements generator-matrix based design construction methods motivated by 2fi-optimal row-column designs, where all main effects are estimable and as many two-factor interactions as possible are unconfounded; see Zhang, Pan and Shi (2025) <doi:10.1016/j.jspi.2024.106192>. It also includes theorem-based constructions, heuristic D-optimal search routines for unsupported or composite-level cases, utilities for building generator matrices, and diagnostic functions for evaluating aliasing and estimability properties of the generated designs.

This package provides functions and a graphical user interface for graphical described multiple test procedures.

This package provides a user-friendly interface for characterizing gene function by disease type and tissue site, integrating curated data from publicly available genomic and proteomic databases to support candidate gene prioritization in experimental workflows.

This package contains the Gene ontology terms and skeleton for the reduced GO directed acyclic graph (DAG) for the organisms Rat and Mouse. The methods are explicitly discussed in the following article : Manjang et al (2020) <doi:10.1038/s41598-020-73326-3>.

This package implements a flexible nonlinear modelling framework for nonstationary generalized extreme value analysis in hydroclimatology following Cannon (2010) <doi:10.1002/hyp.7506>.

This package provides a network-based gene weighting algorithm for pathway enrichment analysis, using either RNA-seq or microarray data. Zhaoyuan Fang, Weidong Tian and Hongbin Ji (2012) <doi:10.1038/cr.2011.149>.

Fast algorithms for robust estimation with large samples of multivariate observations. Estimation of the geometric median, robust k-Gmedian clustering, and robust PCA based on the Gmedian covariation matrix.

Wrappers for functions in the gRain package to emulate some RHugin functionality, allowing the building of Bayesian networks consisting on discrete chance nodes incrementally, through adding nodes, edges and conditional probability tables, the setting of evidence, both hard (boolean) or soft (likelihoods), querying marginal probabilities and normalizing constants, and generating sets of high-probability configurations. Computations will typically not be so fast as they are with RHugin', but this package should assist users without access to Hugin to use code written to use RHugin'.

Implemented are three Wald-type statistic and respective permuted versions for null hypotheses formulated in terms of cumulative hazard rate functions, medians and the concordance measure, respectively, in the general framework of survival factorial designs with possibly heterogeneous survival and/or censoring distributions, for crossed designs with an arbitrary number of factors and nested designs with up to three factors. Ditzhaus, Dobler and Pauly (2020) <doi:10.1177/0962280220980784> Ditzhaus, Genuneit, Janssen, Pauly (2023) <doi:10.1111/biom.13575> Dobler and Pauly (2019) <doi:10.1177/0962280219831316>.

The functionality provided by this package is an expansion of the code of the statebins package, created by B. Rudis (2022), <doi:10.32614/CRAN.package.statebins>. It allows for the creation of square choropleths for the entire world, provided an appropriate specified grid is supplied.