This package provides access to granular sub-national income data from the MCC-PIK Database Of Sub-national Economic Output (DOSE). The package downloads and processes the data from its open repository on Zenodo (<https://zenodo.org/records/13773040>). Functions are provided to fetch data at multiple geographic levels, match coordinates to administrative regions, and access associated geometries.

This package provides functions for obtaining p-values (for hypothesis tests), confidence intervals, and multivariate confidence sets. In particular, the method is compatible with differentially private dataset, as long as the privacy mechanism is known. For more details, see Awan and Wang (2024), "Simulation-based, Finite-sample Inference for Privatized Data", <doi:10.48550/arXiv.2303.05328>.

This package provides methods for low-rank tensor regression with tensor-valued predictors and scalar covariates. Model estimation is performed using stochastic optimization with random-walk updates for low-rank factor matrices. Computationally intensive components for coefficient estimation and prediction are implemented in C++ via Rcpp'. The package also includes tools for cross-validation and prediction error assessment.

The employment of the Wavelet decomposition technique proves to be highly advantageous in the modelling of noisy time series data. Wavelet decomposition technique using the "haar" algorithm has been incorporated to formulate a hybrid Wavelet KNN (K-Nearest Neighbour) model for time series forecasting, as proposed by Anjoy and Paul (2017) <DOI:10.1007/s00521-017-3289-9>.

Extremely fast hashing of R objects using xxHash'. R objects are hashed via the standard serialization mechanism in R. Raw byte vectors and strings can be handled directly for compatibility with hashes created on other systems. This implementation is a wrapper around the xxHash C library which is available from <https://github.com/Cyan4973/xxHash>.

This package vendors an assortment of useful header-only C++ libraries. Bioconductor packages can use these libraries in their own C++ code by LinkingTo this package without introducing any additional dependencies. The use of a central repository avoids duplicate vendoring of libraries across multiple R packages, and enables better coordination of version updates across cohorts of interdependent C++ libraries.

This package provides a convenient way to analyze and visualize PICRUSt2 output with pre-defined plots and functions. It allows for generating statistical plots about microbiome functional predictions and offers customization options. It features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. It streamlines the PICRUSt2 analysis and visualization process.

This package provides a collection of functions helpful in learning the basic tenets of Bayesian statistical inference. It contains functions for summarizing basic one and two parameter posterior distributions and predictive distributions. It contains MCMC algorithms for summarizing posterior distributions defined by the user. It also contains functions for regression models, hierarchical models, Bayesian tests, and illustrations of Gibbs sampling.

This package provides interactive plotting functions for use within RStudio. The manipulate function accepts a plotting expression and a set of controls (e.g. slider, picker, checkbox, or button) which are used to dynamically change values within the expression. When a value is changed using its corresponding control the expression is automatically re-executed and the plot is redrawn.

The CommonMark specification defines a rationalized version of markdown syntax. This package uses the cmark reference implementation for converting markdown text into various formats including HTML, LaTeX and groff man. In addition, it exposes the markdown parse tree in XML format. The latest version of this package also adds support for Github extensions including tables, autolinks and strikethrough text.

This package provides a Shiny application for visualization, exploration, comparison, and filtering of CRISPR screens analyzed with MAGeCK RRA or MLE. Features include interactive plots with on-click labeling, full customization of plot aesthetics, data upload and/or download, and much more. Quickly and easily explore your CRISPR screen results and generate publication-quality figures in seconds.

This package provides functionality for performing divergence analysis as presented in Dinalankara et al, "Digitizing omics profiles by divergence from a baseline", PANS 2018. This allows the user to simplify high dimensional omics data into a binary or ternary format which encapsulates how the data is divergent from a specified baseline group with the same univariate or multivariate features.

This package allows to estimate missing values in DNA methylation data. methyLImp method is based on linear regression since methylation levels show a high degree of inter-sample correlation. Implementation is parallelised over chromosomes since probes on different chromosomes are usually independent. Mini-batch approach to reduce the runtime in case of large number of samples is available.

This package implements several algorithms for bundling edges in networks and flow and metro map layouts. This includes force directed edge bundling <doi:10.1111/j.1467-8659.2009.01450.x>, a flow algorithm based on Steiner trees<doi:10.1080/15230406.2018.1437359> and a multicriteria optimization method for metro map layouts <doi:10.1109/TVCG.2010.24>.

This package provides a collection of functions that would help one to build features based on external data. Very useful for Data Scientists in data to day work. Many functions create features using parallel computation. Since the nitty gritty of parallel computation is hidden under the hood, the user need not worry about creating clusters and shutting them down.

This package provides an interface to the system-level grep utility for efficiently reading, filtering, and aggregating data from multiple flat files. By pre-filtering data at the command line before it enters the R environment, the package reduces memory overhead and improves ingestion speed. Includes functions for counting records across large file systems and supports recursive directory searching.

R lists, especially nested lists, can be very difficult to visualize or represent. Sometimes str() is not enough, so this suite of htmlwidgets is designed to help see, understand, and maybe even modify your R lists. The function reactjson() requires a package reactR that can be installed from CRAN or <https://github.com/timelyportfolio/reactR>.

Efficient calculation of pseudo-ranks and (pseudo)-rank based test statistics. In case of equal sample sizes, pseudo-ranks and mid-ranks are equal. When used for inference mid-ranks may lead to paradoxical results. Pseudo-ranks are in general not affected by such a problem. See Happ et al. (2020, <doi:10.18637/jss.v095.c01>) for details.

For biparental, three and four-way crosses Identity by Descent (IBD) probabilities can be calculated using Hidden Markov Models and inheritance vectors following Lander and Green (<https://www.jstor.org/stable/29713>) and Huang (<doi:10.1073/pnas.1100465108>). One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris.

This package provides bindings to Tree-sitter', an incremental parsing system for programming tools. Tree-sitter builds concrete syntax trees for source files of any language, and can efficiently update those syntax trees as the source file is edited. It also includes a robust error recovery system that provides useful parse results even in the presence of syntax errors.

Create dense vector representation of words and documents using quanteda'. Implements Word2vec (Mikolov et al., 2013) <doi:10.48550/arXiv.1310.4546>, Doc2vec (Le & Mikolov, 2014) <doi:10.48550/arXiv.1405.4053> and Latent Semantic Analysis (Deerwester et al., 1990) <doi:10.1002/(SICI)1097-4571(199009)41:6%3C391::AID-ASI1%3E3.0.CO;2-9>.

Computes confidence intervals for nonlinear functions of model parameters (e.g., product of k coefficients) in single-level and multilevel structural equation models. Methods include the distribution of the product, Monte Carlo simulation, and bootstrap methods. It also performs the Model-Based Constrained Optimization (MBCO) procedure for hypothesis testing of indirect effects. References: Tofighi, D., and MacKinnon, D. P. (2011). RMediation: An R package for mediation analysis confidence intervals. Behavior Research Methods, 43, 692-700. <doi:10.3758/s13428-011-0076-x>; Tofighi, D., and Kelley, K. (2020). Improved inference in mediation analysis: Introducing the model-based constrained optimization procedure. Psychological Methods, 25(4), 496-515. <doi:10.1037/met0000259>; Tofighi, D. (2020). Bootstrap Model-Based Constrained Optimization Tests of Indirect Effects. Frontiers in Psychology, 10, 2989. <doi:10.3389/fpsyg.2019.02989>.

Psupertime is supervised pseudotime for single cell RNAseq data. It uses single cell RNAseq data, where the cells have a known ordering. This ordering helps to identify a small number of genes which place cells in that known order. It can be used for discovery of relevant genes, for identification of subpopulations, and characterization of further unknown or differently labelled data.

Smithay aims to provide building blocks to create wayland compositors in Rust. While not being a full-blown compositor, it'll provide objects and interfaces implementing common functionalities that pretty much any compositor will need, in a generic fashion.

It supports the wayland, wayland-protocols, and some external extensions, such as wlr-protocols and plasma-wayland-protocols.