This package provides functions for estimating probabilistic latent feature models with a disjunctive, conjunctive or additive mapping rule on (aggregated) binary three-way data.

Reviews other packages during code review by looking at their dependencies, code style, code complexity, and how internally defined functions interact with one another.

The Penn World Table 8.x provides information on relative levels of income, output, inputs, and productivity for 167 countries between 1950 and 2011.

This package implements entrywise splitting cross-validation (ECV) and its penalized variant (pECV) for selecting the number of factors in generalized factor models.

This package provides a set of functions for computing potential evapotranspiration and several widely used drought indices including the Standardized Precipitation-Evapotranspiration Index (SPEI).

Generalization of the classification and regression tree (CART) model that partitions subjects into terminal nodes and tailors machine learning model to each terminal node.

Generating realizations of a fractal Brownian function on uniform 1D & 2D grid with classic and generic versions of the Voss algorithm (random sequential additions).

XMRs combine X-Bar control charts and Moving Range control charts. These functions also will recalculate the reference lines when significant change has occurred.

This package provides an interface to the Nexus class library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. It provides elements of the file that can be used to build phylogenetic objects such as ape's phylo or phylobase's phylo4(d). This functionality is demonstrated with read_newick_phylo() and read_nexus_phylo().

STG is a method for feature selection in neural network. The procedure is based on probabilistic relaxation of the l0 norm of features, or the count of the number of selected features. The framework simultaneously learns either a nonlinear regression or classification function while selecting a small subset of features. Read more: Yamada et al. (2020) <https://proceedings.mlr.press/v119/yamada20a.html>.

This package provides functions for studying realized genetic relatedness between people. Users will be able to simulate inheritance patterns given pedigree structures, generate SNP marker data given inheritance patterns, and estimate realized relatedness between pairs of individuals using SNP marker data. See Wang (2017) <doi:10.1534/genetics.116.197004>. This work was supported by National Institutes of Health grants R37 GM-046255.

Applies methods used to estimate animal homerange, but instead of geospatial coordinates, we use isotopic coordinates. The estimation methods include: 1) 2-dimensional bivariate normal kernel utilization density estimator, 2) bivariate normal ellipse estimator, and 3) minimum convex polygon estimator, all applied to stable isotope data. Additionally, functions to determine niche area, polygon overlap between groups and levels (confidence contours) and plotting capabilities.

This package provides various statistical methods for designing and analyzing two-stage randomized controlled trials using the methods developed by Imai, Jiang, and Malani (2021) <doi:10.1080/01621459.2020.1775612> and (2022+) <doi:10.48550/arXiv.2011.07677>. The package enables the estimation of direct and spillover effects, conduct hypotheses tests, and conduct sample size calculation for two-stage randomized controlled trials.

Robust kernel center matrix, robust kernel cross-covariance operator for kernel unsupervised methods, kernel canonical correlation analysis, influence function of identifying significant outliers or atypical objects from multimodal datasets. Alam, M. A, Fukumizu, K., Wang Y.-P. (2018) <doi:10.1016/j.neucom.2018.04.008>. Alam, M. A, Calhoun, C. D., Wang Y.-P. (2018) <doi:10.1016/j.csda.2018.03.013>.

Evaluates R source codes by variable and/or functions names. Similar source codes should deliver similarity coefficients near one. Since neither the frequency nor the order of the used names is considered, a manual inspection of the R source code is required to check for similarity. Possible use cases include detection of code clones for improving software quality and of plagiarism amongst students assignments.

This is an R package for doublet annotation of single cell RNA sequencing data. scds provides methods to annotate doublets in scRNA-seq data computationally.

This is a package for detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.

This package provides a close to zero dependency package to draw and display Venn diagrams up to 7 sets, and any Boolean union of set intersections.

This package loads electrophysiology data from ABF2 files, as created by Axon Instruments/Molecular Devices software. Only files recorded in gap-free mode are currently supported.

This package provides tools for maximum a posteriori estimation for linear and generalized linear mixed-effects models in a Bayesian setting. It extends the lme4 package.

raylib is a high-level library for video game programming. It aims to abstract away platform and graphics details, allowing you to focus on writing your game.

Create and evaluate models using tidymodels and h2o <https://h2o.ai/>. The package enables users to specify h2o as an engine for several modeling methods.

Collection of tools to make R more convenient. Includes tools to summarize data using statistics not available with base R and manipulate objects for analyses.

Time series regression using dynamic linear models fit using MCMC. See Scott and Varian (2014) <DOI:10.1504/IJMMNO.2014.059942>, among many other sources.