This package provides a variety of improved shrinkage estimators in the area of statistical analysis: unrestricted; restricted; preliminary test; improved preliminary test; Stein; and positive-rule Stein. More details can be found in chapter 7 of Saleh, A. K. Md. E. (2006) <ISBN: 978-0-471-56375-4>.

Statistical tests for validating multispecies coalescent gene tree simulators, using pairwise distances and rooted triple counts. See Allman ES, Baños HD, Rhodes JA 2023. Testing multispecies coalescent simulators using summary statistics, IEEE/ACM Trans Comput Biol Bioinformat, 20(2):1613â 1618. <doi:10.1109/TCBB.2022.3177956>.

Farmer, J., D. Jacobs (2108) <DOI:10.1371/journal.pone.0196937>. A multivariate nonparametric density estimator based on the maximum-entropy method. Accurately predicts a probability density function (PDF) for random data using a novel iterative scoring function to determine the best fit without overfitting to the sample.

This package provides tools for retrieving and analyzing air quality data from PurpleAir sensors through their API. Functions enable downloading historical measurements, accessing sensor metadata, and managing API request limitations through chunked data retrieval. For more information about the PurpleAir API, see <https://api.purpleair.com/>.

This package contains chart code for monitoring clinical trial safety. Charts can be used as standalone output, but are also designed for use with the safetyGraphics package, which makes it easy to load data and customize the charts using an interactive web-based interface created with Shiny.

This package provides a simple interface to integrate star ratings into your shiny apps. It can be used for customer feedback systems, user reviews, or any application that requires user ratings. shinyRatings offers a straightforward and customisable solution that enhances user engagement and facilitates valuable feedback collection.

This package adductomicsR processes data generated by the second stage of mass spectrometry (MS2) to identify potentially adducted peptides from spectra that has been corrected for mass drift and retention time drift and quantifies level mass spectral peaks from first stage of mass spectrometry (MS1) data.

Functionality for performing a principled reference analysis in the Bayesian normal-normal hierarchical model used for Bayesian meta-analysis, as described in Ott, Plummer and Roos (2021) <doi:10.1002/sim.9076>. Computes a reference posterior, induced by a minimally informative improper reference prior for the between-study (heterogeneity) standard deviation. Determines additional proper anti-conservative (and conservative) prior benchmarks. Includes functions for reference analyses at both the posterior and the prior level, which, given the data, quantify the informativeness of a heterogeneity prior of interest relative to the minimally informative reference prior and the proper prior benchmarks. The functions operate on data sets which are compatible with the bayesmeta package.

Spatio-temporal data from Scotland used in the vignettes accompanying the CARBayes (spatial modelling) and CARBayesST (spatio-temporal modelling) packages. Most of the data relate to the set of 271 Intermediate Zones (IZ) that make up the 2001 definition of the Greater Glasgow and Clyde health board.

This package provides methods and data for color science - color conversions by observer, illuminant, and gamma. Color matching functions and chromaticity diagrams. Color indices, color differences, and spectral data conversion/analysis. This package is deprecated and will someday be removed; for reasons and details please see the README file.

This package provides functions for obtaining the probability of detection, for grab samples selection by using two different methods such as systematic or random based on two-state Markov chain model. For detection probability calculation, we used results from Bhat, U. and Lal, R. (1988) <doi:10.2307/1427041>.

This function performs the two-sample Kuiper test to assess the anomaly of continuous, one-dimensional probability distributions. References used for this method are (1). Kuiper, N. H. (1960). <DOI:10.1016/S1385-7258(60)50006-0> and (2). Paltani, S. (2004). <DOI:10.1051/0004-6361:20034220>.

This package provides tools for spectral clustering of weighted directed networks using motif adjacency matrices. Methods perform well on large and sparse networks, and random sampling methods for generating weighted directed networks are also provided. Based on methodology detailed in Underwood, Elliott and Cucuringu (2020) <arXiv:2004.01293>.

Perform classic chi-squared tests and Ripol et al(1999) binomial confidence interval approach for autopolyploid dominant markers. Also, dominant markers may be generated for families of offspring where either one or both of the parents possess the marker. Missing values and misclassified markers may be generated at random.

This package provides a comprehensive logging framework for R applications that provides hierarchical logging levels, database integration, and contextual logging capabilities. The package supports SQLite storage for persistent logs, provides colour-coded console output for better readability, includes parallel processing support, and implements structured error reporting with JSON formatting.

Dictionary-like reference for computing scoring rules in a wide range of situations. Covers both parametric forecast distributions (such as mixtures of Gaussians) and distributions generated via simulation. Further details can be found in the package vignettes <doi:10.18637/jss.v090.i12>, <doi:10.18637/jss.v110.i08>.

Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages.

A workflow is a combination of a model and preprocessors (e.g, a formula, recipe, etc.). In order to try different combinations of these, an object can be created that contains many workflows. There are functions to create workflows en masse as well as training them and visualizing the results.

This package provides a string allocator for allocating many write-once strings. This library is primarily useful for parsing where you need to repeatedly build many strings, use them, and then throw them away. Instead of allocating many independent strings, this library will put them all in the same buffer.

Given the parameters of a distribution, the package uses the concept of alpha-outliers by Davies and Gather (1993) to flag outliers in a data set. See Davies, L.; Gather, U. (1993): The identification of multiple outliers, JASA, 88 423, 782-792, <doi:10.1080/01621459.1993.10476339> for details.

Enables creation of visualizations using the CanvasXpress framework in R. CanvasXpress is a standalone JavaScript library for reproducible research with complete tracking of data and end-user modifications stored in a single PNG image that can be played back. See <https://www.canvasxpress.org> for more information.

This package provides functions for obtaining estimates of the parameter of the niche preemption model (also known as the geometric series), in particular a maximum likelihood estimator (Graffelman, 2021) <doi:10.1101/2021.01.27.428381>. The niche preemption model is a widely used model in ecology and biodiversity studies.

Utilize the CDF penalty function to estimate a penalized linear model. It enables you to display some graphical representations and determine whether the Karush-Kuhn-Tucker conditions are met. For more details about the theory, please refer to Cuntrera, D., Augugliaro, L., & Muggeo, V. M. (2022) <arXiv:2212.08582>.

Provide various functions and tools to help fit models for estimating treatment effects in stepped wedge cluster randomized trials. Implements methods described in Kenny, Voldal, Xia, and Heagerty (2022) "Analysis of stepped wedge cluster randomized trials in the presence of a time-varying treatment effect", <doi:10.1002/sim.9511>.