Finds subsets of sets of genotypes with a high Heterozygosity, and Mean of Transformed Kinships (MTK), measures that can indicate a subset would be beneficial for rare-trait discovery and genome-wide association scanning, respectively.

Constructs gains tables and lift charts for prediction algorithms. Gains tables and lift charts are commonly used in direct marketing applications. The method is described in Drozdenko and Drake (2002), "Optimal Database Marketing", Chapter 11.

The gasanalyzer R package offers methods for importing, preprocessing, and analyzing data related to photosynthetic characteristics (gas exchange, chlorophyll fluorescence and isotope ratios). It translates variable names into a standard format, and can recalculate derived, physiological quantities using imported or predefined equations. The package also allows users to assess the sensitivity of their results to different assumptions used in the calculations. See also Tholen (2024) <doi:10.1093/aobpla/plae035>.

Group Sequential Operating Characteristics for Clinical, Bayesian two-arm Trials with known Sigma and Normal Endpoints, as described in Gerber and Gsponer (2016) <doi: 10.18637/jss.v069.i11>.

Process in-situ Gamma-Ray Spectrometry for Luminescence Dating. This package allows to import, inspect and correct the energy shifts of gamma-ray spectra. It provides methods for estimating the gamma dose rate by the use of a calibration curve as described in Mercier and Falguères (2007). The package only supports Canberra CNF and TKA and Kromek SPE files.

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.

Spatial data plus the power of the ggplot2 framework means easier mapping when input data are already in the form of spatial objects.

An R interface to the GPTZero API (<https://gptzero.me/docs>). Allows users to classify text into human and computer written with probabilities. Formats the data into data frames where each sentence is an observation. Paragraph-level and document-level predictions are organized to align with the sentences.

Allows plotting data on bathymetric maps using ggplot2'. Plotting oceanographic spatial data is made as simple as feasible, but also flexible for custom modifications. Data that contain geographic information from anywhere around the globe can be plotted on maps generated by the basemap() or qmap() functions using ggplot2 layers separated by the + operator. The package uses spatial shape- ('sf') and raster ('stars') files, geospatial packages for R to manipulate, and the ggplot2 package to plot these files. The package ships with low-resolution spatial data files and higher resolution files for detailed maps are stored in the ggOceanMapsLargeData repository on GitHub and downloaded automatically when needed.

This package provides a template for a geometallurgical database and a fast and easy interface for accessing it.

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>).

This package provides adaptive association tests for SNP level, gene level and pathway level analyses.

This package provides functions for performing polygon geometry with grid grobs. This allows complex shapes to be defined by combining simpler shapes.

The multiple contrast tests for univariate were proposed by Munko, Ditzhaus, Pauly, Smaga, and Zhang (2023) <doi:10.48550/arXiv.2306.15259>. Recently, they were extended to the multivariate functional data in Munko, Ditzhaus, Pauly, and Smaga (2024) <doi:10.48550/arXiv.2406.01242>. These procedures enable us to evaluate the overall hypothesis regarding equality, as well as specific hypotheses defined by contrasts. In particular, we can perform post hoc tests to examine particular comparisons of interest. Different experimental designs are supported, e.g., one-way and multi-way analysis of variance for functional data.

This package provides a collection of tools which extract a model documentation from GAMS code and comments. In order to use the package you need to install pandoc and pandoc-citeproc first (<https://pandoc.org/>).

Downloads and aggregates data for Brazilian government issued bonds directly from the website of Tesouro Direto <https://www.tesourodireto.com.br/>.

The classical Markowitz's mean-variance portfolio formulation ignores heavy tails and skewness. High-order portfolios use higher order moments to better characterize the return distribution. Different formulations and fast algorithms are proposed for high-order portfolios based on the mean, variance, skewness, and kurtosis. The package is based on the papers: R. Zhou and D. P. Palomar (2021). "Solving High-Order Portfolios via Successive Convex Approximation Algorithms." <arXiv:2008.00863>. X. Wang, R. Zhou, J. Ying, and D. P. Palomar (2022). "Efficient and Scalable High-Order Portfolios Design via Parametric Skew-t Distribution." <arXiv:2206.02412>.

High throughput toxicokinetics ("HTTK") is the combination of 1) chemical-specific in vitro measurements or in silico predictions and 2) generic mathematical models, to predict absorption, distribution, metabolism, and excretion by the body. HTTK methods have been described by Pearce et al. (2017) (<doi:10.18637/jss.v079.i04>) and Breen et al. (2021) (<doi:10.1080/17425255.2021.1935867>). Here we provide examples (vignettes) applying HTTK to solve various problems in bioinformatics, toxicology, and exposure science. In accordance with Davidson-Fritz et al. (2025) (<doi:10.1371/journal.pone.0321321>), whenever a new HTTK model is developed, the code to generate the figures evaluating that model is added as a new vignettte.

Using Dirichlet-Multinomial distribution to provide several functions for formal hypothesis testing, power and sample size calculations for human microbiome experiments.

This package contains functions to construct high-dimensional orthogonal maximin distance designs in two, four, eight, and sixteen levels from rotating the Kronecker product of sub-Hadamard matrices.

Focuses on data processing and visualization in hydrology and climate forecasting. Main function includes data extraction, data downscaling, data resampling, gap filler of precipitation, bias correction of forecasting data, flexible time series plot, and spatial map generation. It is a good pre- processing and post-processing tool for hydrological and hydraulic modellers.

We provide extensions to the classical dataset "Example 4: Death by the kick of a horse in the Prussian Army" first used by Ladislaus von Bortkeiwicz in his treatise on the Poisson distribution "Das Gesetz der kleinen Zahlen", <DOI:10.1017/S0370164600019453>. As well as an extended time series for the horse-kick death data, we also provide, in parallel, deaths by falling from a horse and by drowning.

Calculate an optimal embedding of a set of data points into low-dimensional hyperbolic space. This uses the strain-minimizing hyperbolic embedding of Keller-Ressel and Nargang (2019), see <arXiv:1903.08977>.

Historical borrowing in clinical trials can improve precision and operating characteristics. This package supports a hierarchical model and a mixture model to borrow historical control data from other studies to better characterize the control response of the current study. It also quantifies the amount of borrowing through benchmark models (independent and pooled). Some of the methods are discussed by Viele et al. (2013) <doi:10.1002/pst.1589>.