To provide a comprehensive analysis of high dimensional longitudinal data,this package provides analysis for any combination of 1) simultaneous variable selection and estimation, 2) mean regression or quantile regression for heterogeneous data, 3) cross-sectional or longitudinal data, 4) balanced or imbalanced data, 5) moderate, high or even ultra-high dimensional data, via computationally efficient implementations of penalized generalized estimating equations.

Convert the chip ID of GPL2025 <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL2025> to GeneBank Accession and ENTREZID <http://www.ncbi.nlm.nih.gov/gene>.

Detecting spatial associations via spatial stratified heterogeneity, accounting for spatial dependencies, interpretability, complex interactions, and robust stratification. In addition, it supports the spatial stratified heterogeneity family described in Lv et al. (2025)<doi:10.1111/tgis.70032>.

Computes probabilities related to group sequential designs for normally distributed test statistics. Enables to derive critical boundaries, power, drift, and confidence intervals of such designs. Supports the alpha spending approach by Lan-DeMets (1994) <doi:10.1002/sim.4780131308>.

Computes the probability density, survival function, the hazard rate functions and generates random samples from the GTDL distribution given by Mackenzie, G. (1996) <doi:10.2307/2348408>. The likelihood estimates, the randomized quantile (Louzada, F., et al. (2020) <doi:10.1109/ACCESS.2020.3040525>) residuals and the normally transformed randomized survival probability (Li,L., et al. (2021) <doi:10.1002/sim.8852>) residuals are obtained for the GTDL model.

Extended techniques for generalized linear models (GLMs), especially for binary responses, including parametric links and heteroscedastic latent variables.

Estimates generalized additive latent and mixed models using maximum marginal likelihood, as defined in Sorensen et al. (2023) <doi:10.1007/s11336-023-09910-z>, which is an extension of Rabe-Hesketh and Skrondal (2004)'s unifying framework for multilevel latent variable modeling <doi:10.1007/BF02295939>. Efficient computation is done using sparse matrix methods, Laplace approximation, and automatic differentiation. The framework includes generalized multilevel models with heteroscedastic residuals, mixed response types, factor loadings, smoothing splines, crossed random effects, and combinations thereof. Syntax for model formulation is close to lme4 (Bates et al. (2015) <doi:10.18637/jss.v067.i01>) and PLmixed (Rockwood and Jeon (2019) <doi:10.1080/00273171.2018.1516541>).

Implement a coherent and flexible protocol for animal color tagging. GenTag provides a simple computational routine with low CPU usage to create color sequences for animal tag. First, a single-color tag sequence is created from an algorithm selected by the user, followed by verification of the combination uniqueness. Three methods to produce color tag sequences are provided. Users can modify the main function core to allow a wide range of applications.

The gRbase package provides graphical modelling features used by e.g. the packages gRain', gRim and gRc'. gRbase implements graph algorithms including (i) maximum cardinality search (for marked and unmarked graphs). (ii) moralization, (iii) triangulation, (iv) creation of junction tree. gRbase facilitates array operations, gRbase implements functions for testing for conditional independence. gRbase illustrates how hierarchical log-linear models may be implemented and describes concept of graphical meta data. The facilities of the package are documented in the book by Højsgaard, Edwards and Lauritzen (2012, <doi:10.1007/978-1-4614-2299-0>) and in the paper by Dethlefsen and Højsgaard, (2005, <doi:10.18637/jss.v014.i17>). Please see citation("gRbase") for citation details.

This package implements the Rank In Similarity Graph Edge-count two-sample test (RISE) for high-dimensional and non-Euclidean data. The method constructs similarity-based graphs, such as k-nearest neighbor graph (k-NNG), k-minimum spanning tree (k-MST), and k-minimum distance non-bipartite pairing (k-MDP), and evaluates rank-based within-sample edge counts with asymptotic and permutation p-values. For methodological details, see Zhou and Chen (2023) <https://proceedings.mlr.press/v195/zhou23a.html>.

Easy access to official spatial data sets of Brazil. The package offers a wide range of spatial data sets available at various geographic scales and for various years with harmonized attributes, projection and fixed topology. All functions allow for seamless integration sf, DuckDB and Arrow.

Make 2D and 3D plots of linear programming (LP), integer linear programming (ILP), or mixed integer linear programming (MILP) models with up to three objectives. Plots of both the solution and criterion space are possible. For instance the non-dominated (Pareto) set for bi-objective LP/ILP/MILP programming models (see vignettes for an overview). The package also contains an function for checking if a point is inside the convex hull.

Streamlines downloading and cleaning biodiversity data from Integrated Digitized Biocollections (iDigBio) and the Global Biodiversity Information Facility (GBIF).

Writes SAS code to get predicted values from every tree of a gbm.object.

Facilitates efficient visualization of Relative Synonymous Codon Usage patterns across species. Based on analytical outputs from codonW', MEGA', and Phylosuite', it supports multi-species RSCU comparisons and allows users to explore visual analysis of structurally similar datasets.

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.

This package provides a tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from GENEActiv <https://activinsights.com/>, binary (.gt3x) and .csv-export data from Actigraph <https://ametris.com/> devices, and binary (.cwa) and .csv-export data from Axivity <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format. Also the package allows for external function embedding.

Cross-validated eigenvalues are estimated by splitting a graph into two parts, the training and the test graph. The training graph is used to estimate eigenvectors, and the test graph is used to evaluate the correlation between the training eigenvectors and the eigenvectors of the test graph. The correlations follow a simple central limit theorem that can be used to estimate graph dimension via hypothesis testing, see Chen et al. (2021) <doi:10.48550/arXiv.2108.03336> for details.

This package provides tools for specifying and evaluating standard and truncated probability distributions, with support for log-space computation and joint distribution specification. It enables Bayesian computation for cognition models and includes utilities for density calculation, sampling, and visualisation, facilitating prior distribution specification and model assessment in hierarchical Bayesian frameworks.

Approximate frequentist inference for generalized linear mixed model analysis with expectation propagation used to circumvent the need for multivariate integration. In this version, the random effects can be any reasonable dimension. However, only probit mixed models with one level of nesting are supported. The methodology is described in Hall, Johnstone, Ormerod, Wand and Yu (2018) <arXiv:1805.08423v1>.

Facilitates the citation of R packages used in analysis projects. Scans project for packages used, gets their citations, and produces a document with citations in the preferred bibliography format, ready to be pasted into reports or manuscripts. Alternatively, grateful can be used directly within an R Markdown or Quarto document.

Gradient-Enhanced Kriging as an emulator for computer experiments based on Maximum-Likelihood estimation.

This package contains the implementation of a binary large margin classifier based on Gabriel Graph. References for this method can be found in L.C.B. Torres et al. (2015) <doi:10.1049/el.2015.1644>.

Quantification, analysis, and visualization of urban greenness within city networks using data from OpenStreetMap <https://www.openstreetmap.org>.