Create engaging population and point plots charts in R. ggpop allows users to represent population data and points proportionally using customizable icons, facilitating the creation of circular representative population charts as well as any point-plots.

Generates experiments - simulating structured or experimental data as: completely randomized design, randomized block design, latin square design, factorial and split-plot experiments (Ferreira, 2008, ISBN:8587692526; Naes et al., 2007 <doi:10.1002/qre.841>; Rencher et al., 2007, ISBN:9780471754985; Montgomery, 2001, ISBN:0471316490).

Includes a collection of geographical analysis functions aimed primarily at ecology and conservation science studies, allowing processing of both point and raster data. Now integrates SPECTRE (<https://biodiversityresearch.org/spectre/>), a dataset of global geospatial threat data, developed by the authors.

In statistical modeling, there is a wide variety of regression models for categorical dependent variables (nominal or ordinal data); yet, there is no software embracing all these models together in a uniform and generalized format. Following the methodology proposed by Peyhardi, Trottier, and Guédon (2015) <doi:10.1093/biomet/asv042>, we introduce GLMcat', an R package to estimate generalized linear models implemented under the unified specification (r, F, Z). Where r represents the ratio of probabilities (reference, cumulative, adjacent, or sequential), F the cumulative cdf function for the linkage, and Z, the design matrix. The package accompanies the paper "GLMcat: An R Package for Generalized Linear Models for Categorical Responses" in the Journal of Statistical Software, Volume 114, Issue 9 (see <doi:10.18637/jss.v114.i09>).

This package provides functions for constructing Transformed and Relative Lorenz curves with survey sampling weights. Given a variable of interest measured in two groups with scaled survey weights so that their hypothetical populations are of equal size, tlorenz() computes the proportion of members of the group with smaller values (ordered from smallest to largest) needed for their sum to match the sum of the top qth percentile of the group with higher values. rlorenz() shows the fraction of the total value of the group with larger values held by the pth percentile of those in the group with smaller values. Fd() is a survey weighted cumulative distribution function and Eps() is a survey weighted inverse cdf used in rlorenz(). Ramos, Graubard, and Gastwirth (2025) <doi:10.1093/jrsssa/qnaf044>.

This package performs end-to-end analysis of gene clustersâ such as photosynthesis, carbon/nitrogen/sulfur cycling, carotenoid, antibiotic, or viral marker genes (e.g., capsid, polymerase, integrase)â from genomes and metagenomes. It parses Basic Local Alignment Search Tool (BLAST) results in tab-delimited format produced by tools like NCBI BLAST+ and Diamond BLASTp, filters Open Reading Frames (ORFs) by length, detects contiguous clusters of reference genes, optionally extracts genomic coordinates, merges functional annotations, and generates publication-ready arrow plots. The package works seamlessly with or without the coding sequences input and skips plotting when no functional groups are found. For more details see Li et al. (2023) <doi:10.1038/s41467-023-42193-7>.

This package provides a ggplot2 extension for creating 3D figures. Provides 3D geoms, stats, and a coord_3d() coordinate system supporting rotation, perspective, and lighting.

This package provides a variety of multivariable data summary statistics and constructions have been proposed, either to generalize univariable analogs or to exploit multivariable properties. Notable among these are the bivariate peelings surveyed by Green (1981, ISBN:978-0-471-28039-2), the bag-and-bolster plots proposed by Rousseeuw &al (1999) <doi:10.1080/00031305.1999.10474494>, and the minimum spanning trees used by Jolliffe (2002) <doi:10.1007/b98835> to represent high-dimensional relationships among data in a low-dimensional plot. Additionally, biplots of singular value--decomposed tabular data, such as from principal components analysis, make use of vectors, calibrated axes, and other representations of variable elements to complement point markers for case elements; see Gabriel (1971) <doi:10.1093/biomet/58.3.453> and Gower & Harding (1988) <doi:10.1093/biomet/75.3.445> for original proposals. Because they treat the abscissa and ordinate as commensurate or the data elements themselves as point masses or unit vectors, these multivariable tools can be thought of as belonging to geometric data analysis; see Podani (2000, ISBN:90-5782-067-6) for techniques and applications and Le Roux & Rouanet (2005) <doi:10.1007/1-4020-2236-0> for foundations. gggda extends Wickham's (2010) <doi:10.1198/jcgs.2009.07098> layered grammar of graphics with statistical transformation ("stat") and geometric construction ("geom") layers for many of these tools, as well as convenience coordinate systems to emphasize intrinsic geometry of the data.

This package provides functions to read in the geometry format under the Neuroimaging Informatics Technology Initiative ('NIfTI'), called GIFTI <https://www.nitrc.org/projects/gifti/>. These files contain surfaces of brain imaging data.

Testing, Implementation and Forecasting of Grey Model (GM(1, 1)). For method details see Hsu, L. and Wang, C. (2007). <doi:10.1016/j.techfore.2006.02.005>.

Kernel regularized least squares, also known as kernel ridge regression, is a flexible machine learning method. This package implements this method by providing a smooth term for use with mgcv and uses random sketching to facilitate scalable estimation on large datasets. It provides additional functions for calculating marginal effects after estimation and for use with ensembles ('SuperLearning'), double/debiased machine learning ('DoubleML'), and robust/clustered standard errors ('sandwich'). Chang and Goplerud (2024) <doi:10.1017/pan.2023.27> provide further details.

This package implements the GALAHAD algorithm (Geometry-Adaptive Lyapunov-Assured Hybrid Optimizer), updated in version 2 to replace the hard-clamp positivity constraint of v1 with a numerically smooth softplus reparameterization, add rho-based trust-region adaptation (actual vs. predicted objective reduction), extend convergence detection to include both absolute and relative function-stall criteria, and enrich the per-iteration history with Armijo backtrack counts and trust-region quality ratios. Parameters constrained to be positive (rates, concentrations, scale parameters) are handled in a transformed z-space via the softplus map so that gradients remain well-defined at the constraint boundary. A two-partition API (positive / euclidean) replaces the three-way T/P/E partition of v1; the legacy form is still accepted for backwards compatibility. Designed for biological modeling problems (germination, dose-response, prion RT-QuIC, survival) where rates, concentrations, and unconstrained coefficients coexist. Developed at the Minnesota Center for Prion Research and Outreach (MNPRO), University of Minnesota. Based on Conn et al. (2000) <doi:10.1137/1.9780898719857>, Barzilai and Borwein (1988) <doi:10.1093/imanum/8.1.141>, Xu and An (2024) <doi:10.48550/arXiv.2409.14383>, Polyak (1969) <doi:10.1016/0041-5553(69)90035-4>, Nocedal and Wright (2006, ISBN:978-0-387-30303-1), and Dugas et al. (2009) <https://www.jmlr.org/papers/v10/dugas09a.html>.

This package implements general unilateral loading estimator for two-layer latent factor models with smooth, element-wise factor transformations. We provide data simulation, loading estimation,finite-sample error bounds, and diagnostic tools for zero-mean and sub-Gaussian assumptions. A unified interface is given for evaluating estimation accuracy and cosine similarity. The philosophy of the package is described in Guo G. (2026) <doi:10.1016/j.apm.2025.116280>.

We provide an efficient implementation for two-step multi-source transfer learning algorithms in high-dimensional generalized linear models (GLMs). The elastic-net penalized GLM with three popular families, including linear, logistic and Poisson regression models, can be fitted. To avoid negative transfer, a transferable source detection algorithm is proposed. We also provides visualization for the transferable source detection results. The details of methods can be found in "Tian, Y., & Feng, Y. (2023). Transfer learning under high-dimensional generalized linear models. Journal of the American Statistical Association, 118(544), 2684-2697.".

We consider the ultrahigh-dimensional and error-prone data. Our goal aims to estimate the precision matrix and identify the graphical structure of the random variables with measurement error corrected. We further adopt the estimated precision matrix to the linear discriminant function to do classification for multi-label classes.

Two arms clinical trials required sample size is calculated in the comprehensive parametric context. The calculation is based on the type of endpoints(continuous/binary/time-to-event/ordinal), design (parallel/crossover), hypothesis tests (equality/noninferiority/superiority/equivalence), trial arms noncompliance rates and expected loss of follow-up. Methods are described in: Chow SC, Shao J, Wang H, Lokhnygina Y (2017) <doi:10.1201/9781315183084>, Wittes, J (2002) <doi:10.1093/epirev/24.1.39>, Sato, T (2000) <doi:10.1002/1097-0258(20001015)19:19%3C2689::aid-sim555%3E3.0.co;2-0>, Lachin J M, Foulkes, M A (1986) <doi:10.2307/2531201>, Whitehead J(1993) <doi:10.1002/sim.4780122404>, Julious SA (2023) <doi:10.1201/9780429503658>.

Creating, exploring, analyzing, and manipulating General Transit Feed Specification (GTFS) files, which represent public transportation schedules and geographic data. The package allows users to filter data by routes, trips, stops, service dates, and time, generate spatial visualizations, and perform detailed analyses of transit networks, including headway, dwell times, route frequencies, service span, scheduled vehicle-hours, and trip duration. Methods follow common public transport planning and operation concepts described in Ceder (2007, ISBN:978-0-7506-6166-6), Vuchic (2005, ISBN:978-0-471-63265-8), and Vuchic (2007, ISBN:978-0-471-75823-5).

This package provides a native R implementation of grammatical evolution (GE). GE facilitates the discovery of programs that can achieve a desired goal. This is done by performing an evolutionary optimisation over a population of R expressions generated via a user-defined context-free grammar (CFG) and cost function.

This package provides a Gibbs sampler corresponding to a Group Inverse-Gamma Gamma (GIGG) regression model with adjustment covariates. Hyperparameters in the GIGG prior specification can either be fixed by the user or can be estimated via Marginal Maximum Likelihood Estimation. Jonathan Boss, Jyotishka Datta, Xin Wang, Sung Kyun Park, Jian Kang, Bhramar Mukherjee (2021) <arXiv:2102.10670>.

The aim of this package is to offer more variability of graphics based on the self-organizing maps.

This package provides functions and necessary JavaScript bindings to quickly transfer spatial data from R memory or remote URLs to the browser for use in interactive HTML widgets created with the htmlwidgets R package. Leverages GeoArrow (<https://geoarrow.org/>) data representation for data stored in local R memory which is generally faster than traditional GeoJSON by minimising the amount of copy, serialization and deserialization steps necessary for the data transfer. Furthermore, provides functionality and JavaScript bindings to consume GeoParquet (<https://geoparquet.org/>) files from remote URLs in the browser.

This package creates ideal data for all distributions in the generalized linear model framework.

Draw geospatial objects by clicks on the map. This packages can help data analyst who want to check their own geospatial hypothesis but has no ready-made geospatial objects.

Estimating trait heritability and handling overfitting. This package includes a collection of functions for (1) estimating genetic variance-covariances and calculate trait heritability; and (2) handling overfitting by calculating the variance components and the heritability through cross validation.