The ptools (power tools) library extends Ruby's core File class with many additional methods modelled after common POSIX tools, such as File.which for finding executables, File.tail to print the last lines of a file, File.wc to count words, and so on.

This package provides a collection of functions to simulate luminescence production in dosimetric materials using Monte Carlo methods. Implemented are models for delocalised transitions (e.g., Chen and McKeever (1997) <doi:10.1142/2781>), localised transitions (e.g., Pagonis et al. (2019) <doi:10.1016/j.jlumin.2018.11.024>) and tunnelling transitions (Jain et al. (2012) <doi:10.1088/0953-8984/24/38/385402> and Pagonis et al. (2019) <doi:10.1016/j.jlumin.2018.11.024>). Supported stimulation methods are thermal luminescence (TL), continuous-wave optically stimulated luminescence (CW-OSL), linearly-modulated optically stimulated luminescence (LM-OSL), linearly-modulated infrared stimulated luminescence (LM-IRSL), and isothermal luminescence (ITL or ISO-TL).

This package provides Lipsum is a lorem ipsum text generation library. It generates pseudo-random Latin text. Use this if you need filler or dummy text for your application. The text is generated using a simple Markov chain, which you can instantiate to generate your own pieces of pseudo-random text.

Dissects a package environment or covr coverage object in order to cross reference tested code with the lines that are evaluated, as well as linking those evaluated lines to the documentation that they are described within. Connecting these three pieces of information provides a mechanism of linking tests to documented behaviors.

Transforms your uncalibrated Machine Learning scores to well-calibrated prediction estimates that can be interpreted as probability estimates. The implemented BBQ (Bayes Binning in Quantiles) model is taken from Naeini (2015, ISBN:0-262-51129-0). Please cite this paper: Schwarz J and Heider D, Bioinformatics 2019, 35(14):2458-2465.

The beta-binomial test is used for significance analysis of independent samples by Pham et al. (2010) <doi:10.1093/bioinformatics/btp677>. The inverted beta-binomial test is used for paired sample testing, e.g. pre-treatment and post-treatment data, by Pham and Jimenez (2012) <doi:10.1093/bioinformatics/bts394>.

Implement DiSTATIS and CovSTATIS (three-way multidimensional scaling). DiSTATIS and CovSTATIS are used to analyze multiple distance/covariance matrices collected on the same set of observations. These methods are based on Abdi, H., Williams, L.J., Valentin, D., & Bennani-Dosse, M. (2012) <doi:10.1002/wics.198>.

This package provides a foreach parallel adapter for parabar backends. This package offers a minimal implementation of the %dopar% operator, enabling users to run foreach loops in parallel, leveraging the parallel and progress-tracking capabilities of the parabar package. Learn more about parabar and doParabar at <https://parabar.mihaiconstantin.com>.

We propose an objective Bayesian algorithm for searching the space of Gaussian directed acyclic graph (DAG) models. The algorithm proposed makes use of moment fractional Bayes factors (MFBF) and thus it is suitable for learning sparse graph. The algorithm is implemented by using Armadillo: an open-source C++ linear algebra library.

This package provides functions for analysing and modelling extreme events in financial time Series. The topics include: (i) data pre-processing, (ii) explorative data analysis, (iii) peak over threshold modelling, (iv) block maxima modelling, (v) estimation of VaR and CVaR, and (vi) the computation of the extreme index.

Kiener distributions K1, K2, K3, K4 and K7 to characterize distributions with left and right, symmetric or asymmetric fat tails in market finance, neuroscience and other disciplines. Two algorithms to estimate with a high accuracy distribution parameters, quantiles, value-at-risk and expected shortfall. Include power hyperbolas and power hyperbolic functions.

The GeneCycle package implements the approaches of Wichert et al. (2004) <doi:10.1093/bioinformatics/btg364>, Ahdesmaki et al. (2005) <doi:10.1186/1471-2105-6-117> and Ahdesmaki et al. (2007) <DOI:10.1186/1471-2105-8-233> for detecting periodically expressed genes from gene expression time series data.

Uses several types of indicator saturation and automated General-to-Specific (GETS) modelling from the gets package and applies it to panel data. This allows the detection of structural breaks in panel data, operationalising a reverse causal approach of causal inference, see Pretis and Schwarz (2022) <doi:10.2139/ssrn.4022745>.

This package provides methods for model selection, estimation, bootstrap inference, and simulation for the multilevel factor model, based on the principal component estimation and generalised canonical correlation approach. Details can be found in "Generalised Canonical Correlation Estimation of the Multilevel Factor Model." Lin and Shin (2023) <doi:10.2139/ssrn.4295429>.

Note that imageData has been superseded by growthPheno'. The package growthPheno incorporates all the functionality of imageData and has functionality not available in imageData', but some imageData functions have been renamed. The imageData package is no longer maintained, but is retained for legacy purposes.

Import, processing, validation, and visualization of personal light exposure measurement data from wearable devices. The package implements features such as the import of data and metadata files, conversion of common file formats, validation of light logging data, verification of crucial metadata, calculation of common parameters, and semi-automated analysis and visualization.

Nonparametric approach to estimate the location of block boundaries (change-points) of non-overlapping blocks in a random symmetric matrix which consists of random variables whose distribution changes from block to block. BRAULT Vincent, OUADAH Sarah, SANSONNET Laure and LEVY-LEDUC Celine (2017) <doi:10.1016/j.jmva.2017.12.005>.

Wrapper of the Petfinder API <https://www.petfinder.com/developers/v2/docs/> that implements methods for interacting with and extracting data from the Petfinder database. The Petfinder REST API allows access to the Petfinder database, one of the largest online databases of adoptable animals and animal welfare organizations across North America.

Reconstruct pedigrees from genotype data, by optimising the likelihood over all possible pedigrees subject to given restrictions. Tailor-made plots facilitate evaluation of the output. This package is part of the pedsuite ecosystem for pedigree analysis. In particular, it imports pedprobr for calculating pedigree likelihoods and forrel for estimating pairwise relatedness.

Integration of two data sources referred to the same target population which share a number of variables. Some functions can also be used to impute missing values in data sets through hot deck imputation methods. Methods to perform statistical matching when dealing with data from complex sample surveys are available too.

Useful to visualize the Poissoneity (an independent Poisson statistical framework, where each RNA measurement for each cell comes from its own independent Poisson distribution) of Unique Molecular Identifier (UMI) based single cell RNA sequencing (scRNA-seq) data, and explore cell clustering based on model departure as a novel data representation.

This package provides function for small area estimation at area level using averaging pseudo area level model for variables of interest. A dataset produced by data generation is also provided. This package estimates small areas at the village level and then aggregates them to the sub-district, region, and provincial levels.

This package provides tools for measuring similarity among documents and detecting passages which have been reused. Implements shingled n-gram, skip n-gram, and other tokenizers; similarity/dissimilarity functions; pairwise comparisons; minhash and locality sensitive hashing algorithms; and a version of the Smith-Waterman local alignment algorithm suitable for natural language.

Computes a zonohedron from real vector generators. The package also computes zonogons (2D zonotopes) and zonosegs (1D zonotopes). An elementary S3 class for matroids is included, which supports matroids with rank 3, 2, and 1. Optimization methods are taken from Heckbert (1985) <https://www.cs.cmu.edu/~ph/zono.ps.gz>.