This package provides a suite of open-source R functions designed to produce standard metrics for forest management and ecology from forest inventory data. The overarching goal is to minimize potential inconsistencies introduced by the algorithms used to compute and summarize core forest metrics. Learn more about the purpose of the package and the specific algorithms used in the package at <https://github.com/kearutherford/BerkeleyForestsAnalytics>.

This package implements a unified interface for benchmarking meta-analytic publication bias correction methods through simulation studies (see BartoÅ¡ et al., 2025, <doi:10.48550/arXiv.2510.19489>). It provides 1) predefined data-generating mechanisms from the literature, 2) functions for running meta-analytic methods on simulated data, 3) pre-simulated datasets and pre-computed results for reproducible benchmarks, 4) tools for visualizing and comparing method performance.

This package creates complex heatmaps for single cell RNA-seq data that simultaneously display gene expression levels (as color intensity) and expression percentages (as circle sizes). Supports gene grouping, cell type annotations, and time point comparisons. Built on top of ComplexHeatmap and integrates with Seurat objects. For more details see Gu (2022) <doi:10.1002/imt2.43> and Hao (2024) <doi:10.1038/s41587-023-01767-y>.

This package may optionally be used by students at Carmel High School in Indiana in the United States to write physics lab reports for FW physics courses. As many students are beginners at LaTeX, it also attempts to simplify the report-writing process by offering macros for commonly used notation and by automatically formatting the documents for students who will only use TeX for mathematics and not typesetting.

The main function of the package is to perform backward selection of fixed effects, forward fitting of the random effects, and post-hoc analysis using parallel capabilities. Other functionality includes the computation of ANOVAs with upper- or lower-bound p-values and R-squared values for each model term, model criticism plots, data trimming on model residuals, and data visualization. The data to run examples is contained in package LCF_data.

tidySingleCellExperiment is an adapter that abstracts the SingleCellExperiment container in the form of a tibble'. This allows *tidy* data manipulation, nesting, and plotting. For example, a tidySingleCellExperiment is directly compatible with functions from tidyverse packages `dplyr` and `tidyr`, as well as plotting with `ggplot2` and `plotly`. In addition, the package provides various utility functions specific to single-cell omics data analysis (e.g., aggregation of cell-level data to pseudobulks).

This package provides a simple pytest plugin to run tests concurrently. The main goal of pytest-run-parallel is to discover thread-safety issues that could exist when using C libraries, this is of vital importance after PEP703, which provides a path for a CPython implementation without depending on the Global Interpreter Lock (GIL), thus allowing for proper parallelism in programs that make use of the CPython interpreter.

Illumina HumanWGv2 annotation data (chip illuminaHumanv2BeadID) assembled using data from public repositories to be used with data summarized from bead-level data with numeric ArrayAddressIDs as keys. Illumina probes with a No match or Bad quality score were removed prior to annotation. See http://www.compbio.group.cam.ac.uk/Resources/Annotation/index.html and Barbosa-Morais et al (2010) A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Research.

pytest-random-order is a Pytest plugin that randomizes the order of tests. This can be useful to detect a test that passes just because it happens to run after an unrelated test that leaves the system in a favourable state. The plugin allows user to control the level of randomness they want to introduce and to disable reordering on subsets of tests. Tests can be rerun in a specific order by passing a seed value reported in a previous test run.

Execute the self-controlled case series (SCCS) design using observational data in the OMOP Common Data Model. Extracts all necessary data from the database and transforms it to the format required for SCCS. Age and season can be modeled using splines assuming constant hazard within calendar months. Event-dependent censoring of the observation period can be corrected for. Many exposures can be included at once (MSCCS), with regularization on all coefficients except for the exposure of interest. Includes diagnostics for all major assumptions of the SCCS.

It computes full conformal, split conformal and multi-split conformal prediction regions when the response variable is multivariate (i.e. dimension is greater than one). Moreover, the package also contains plot functions to visualize the output of the full and split conformal functions. To guarantee consistency, the package structure mimics the univariate package conformalInference by Ryan Tibshirani. See Lei, Gâ sell, Rinaldo, Tibshirani, & Wasserman (2018) <doi:10.1080/01621459.2017.1307116> for full and split conformal prediction in regression, and Barber, Candès, Ramdas, & Tibshirani (2023) <doi:10.1214/23-AOS2276> for extensions beyond exchangeability.

The tidySummarizedExperiment package provides a set of tools for creating and manipulating tidy data representations of SummarizedExperiment objects. SummarizedExperiment is a widely used data structure in bioinformatics for storing high-throughput genomic data, such as gene expression or DNA sequencing data. The tidySummarizedExperiment package introduces a tidy framework for working with SummarizedExperiment objects. It allows users to convert their data into a tidy format, where each observation is a row and each variable is a column. This tidy representation simplifies data manipulation, integration with other tidyverse packages, and enables seamless integration with the broader ecosystem of tidy tools for data analysis.

This package provides methods for Neutrosophic Analysis of Variance (NANOVA) for split-plot and strip-plot experimental designs using interval-valued observations. The package computes neutrosophic sums of squares, mean squares, interval-valued F-statistics, significance tests, and Least Significant Difference (LSD) based multiple comparisons for main plot, sub plot, horizontal factor, vertical factor, and interaction effects. For crisp data, users may provide identical lower and upper response values to obtain results equivalent to classical analysis of variance. The basic idea of neutrosophic statistics is obtained from Smarandache (2014) <https://fs.unm.edu/NeutrosophicStatistics.pdf>, while the analysis procedures implemented in this package are newly developed.

Fits Gaussian Mixtures by applying evolution. As fitness function a mixture of the chi square test for distributions and a novel measure for approximating the common area under curves between multiple Gaussians is used. The package presents an alternative to the commonly used Likelihood Maximization as is used in Expectation Maximization. The algorithm and applications of this package are published under: Lerch, F., Ultsch, A., Lotsch, J. (2020) <doi:10.1038/s41598-020-57432-w>. The evolution is based on the GA package: Scrucca, L. (2013) <doi:10.18637/jss.v053.i04> while the Gaussian Mixture Logic stems from AdaptGauss': Ultsch, A, et al. (2015) <doi:10.3390/ijms161025897>.

Human Resource Machine is a puzzle game for nerds. In each level, your boss gives you a job. Automate it by programming your little office worker. If you succeed, you'll be promoted up to the next level for another year of work in the vast office building. Congratulations!

Don't worry if you've never programmed before - programming is just puzzle solving. If you strip away all the 1's and 0's and scary squiggly brackets, programming is simple, logical, beautiful, and something that anyone can understand and have fun with! Are you already an expert? There will be extra challenges for you.

Have fun! Management is watching.

• Learn to program inside a giant computer made of humans. You'll be taught everything you need to know.

• Already an expert? Each level comes with Optimization Challenges - difficult (and optional) challenges that test how well your solution optimizes for program size and execution speed.

• From the creators of Little Inferno and World of Goo.

Computes experimental designs for two-arm experiments with covariates using multiple methods, including: (0) complete randomization and randomization with forced-balance; (1) greedy optimization of a balance objective function via pairwise switching; (2) numerical optimization via gurobi'; (3) rerandomization; (4) Karp's method for one covariate; (5) exhaustive enumeration for small sample sizes; (6) binary pair matching using nbpMatching'; (7) binary pair matching plus method (1) to further optimize balance; (8) binary pair matching plus method (3) to further optimize balance; (9) Hadamard designs; and (10) simultaneous multiple kernels. For the greedy, rerandomization, and related methods, three objective functions are supported: Mahalanobis distance, standardized sums of absolute differences, and kernel distances via the kernlab library. This package is the result of a stream of research that can be found in Krieger, A. M., Azriel, D. A., and Kapelner, A. (2019). "Nearly Random Designs with Greatly Improved Balance." Biometrika 106(3), 695-701 <doi:10.1093/biomet/asz026>. Krieger, A. M., Azriel, D. A., and Kapelner, A. (2023). "Better experimental design by hybridizing binary matching with imbalance optimization." Canadian Journal of Statistics, 51(1), 275-292 <doi:10.1002/cjs.11685>.

React package for shallow rendering.

Affymetrix rta10 annotation data (chip rta10transcriptcluster) assembled using data from public repositories.

This package provides an implementation of the RDF4J Rio API, which reads and writes TriG.

This package provides an Rcmdr "plug-in" based on the TeachingDemos package, and is primarily for illustrative purposes.

Convert CommonJS modules to ES2015

TypeScript definitions for istanbul-reports

Convert CommonJS modules to ES2015

Datasets to support COPDSexaulDimorphism Package.