This package provides tools for reshaping, plotting, and manipulating matrices of orthogonal polynomials.

This package provides a system for fast, accurate, and flexible whole genome bisulfite sequencing (WGBS) data analysis of two-condition comparisons. Principal Component BiSulfite, PCBS', assigns methylated loci eigenvector values from the treatment-delineating principal component in lieu of running millions of pairwise statistical tests, which dramatically increases analysis flexibility and reduces computational requirements. Methods: <https://katlande.github.io/PCBS/articles/Differential_Methylation.html>.

This package provides tools for calculating and viewing topological properties of phylogenetic trees.

Proportional hazards estimation in the presence of a partially monotone likelihood has difficulties, in that finite estimators do not exist. These difficulties are related to those arising from logistic and multinomial regression. References for methods are given in the separate function documents. Supported by grant NSF DMS 1712839.

Conduct permutation One-Way or Two-Way Analysis of Variance in R. Use different permutation types for two-way designs.

This package provides a versatile R visualization package that empowers researchers with comprehensive visualization tools for seamlessly mapping peptides to protein sequences, identifying distinct domains and regions of interest, accentuating mutations, and highlighting post-translational modifications, all while enabling comparisons across diverse experimental conditions. Potential applications of PepMapViz include the visualization of cross-software mass spectrometry results at the peptide level for specific protein and domain details in a linearized format and post-translational modification coverage across different experimental conditions; unraveling insights into disease mechanisms. It also enables visualization of Major histocompatibility complex-presented peptide clusters in different antibody regions predicting immunogenicity in antibody drug development.

Given a project schedule and associated costs, this package calculates the earned value to date. It is an implementation of Project Management Body of Knowledge (PMBOK) methodologies (reference Project Management Institute. (2021). A guide to the Project Management Body of Knowledge (PMBOK guide) (7th ed.). Project Management Institute, Newtown Square, PA, ISBN 9781628256673 (pdf)).

Simulate via Markov chain Monte Carlo (hit-and-run algorithm) a Dirichlet distribution conditioned to satisfy a finite set of linear equality and inequality constraints (hence to lie in a convex polytope that is a subset of the unit simplex).

An integrative toolbox of word embedding research that provides: (1) a collection of pre-trained static word vectors in the .RData compressed format <https://psychbruce.github.io/WordVector_RData.pdf>; (2) a group of functions to process, analyze, and visualize word vectors; (3) a range of tests to examine conceptual associations, including the Word Embedding Association Test <doi:10.1126/science.aal4230> and the Relative Norm Distance <doi:10.1073/pnas.1720347115>, with permutation test of significance; and (4) a set of training methods to locally train (static) word vectors from text corpora, including Word2Vec <doi:10.48550/arXiv.1301.3781>, GloVe <doi:10.3115/v1/D14-1162>, and FastText <doi:10.48550/arXiv.1607.04606>.

Supports analysis of aerobiological data. Available features include determination of pollen season limits, replacement of outliers (Kasprzyk and Walanus (2014) <doi:10.1007/s10453-014-9332-8>), calculation of growing degree days (Baskerville and Emin (1969) <doi:10.2307/1933912>), and determination of the base temperature for growing degree days (Yang et al. (1995) <doi:10.1016/0168-1923(94)02185-M).

Statistical power analysis for designs including t-tests, correlations, multiple regression, ANOVA, mediation, and logistic regression. Functions accompany Aberson (2019) <doi:10.4324/9781315171500>.

Most of the time floating point arithmetic does approximately the right thing. When adding sums or having products of numbers that greatly differ in magnitude, the floating point arithmetic may be incorrect. This package implements the Kahan (1965) sum <doi:10.1145/363707.363723>, Neumaier (1974) sum <doi:10.1002/zamm.19740540106>, pairwise-sum (adapted from NumPy', See Castaldo (2008) <doi:10.1137/070679946> for a discussion of accuracy), and arbitrary precision sum (adapted from the fsum in Python ; Shewchuk (1997) <https://people.eecs.berkeley.edu/~jrs/papers/robustr.pdf>). In addition, products are changed to long double precision for accuracy, or changed into a log-sum for accuracy.

This package provides a user-friendly interface for creating and managing empirical crowd-sourcing studies via API access to <https://www.prolific.co>.

The Prize-Collecting Steiner Tree problem asks to find a subgraph connecting a given set of vertices with the most expensive nodes and least expensive edges. Since it is proven to be NP-hard, exact and efficient algorithm does not exist. This package provides convenient functionality for obtaining an approximate solution to this problem using loopy belief propagation algorithm.

Survey sampling using permanent random numbers (PRN's). A solution to the problem of unknown overlap between survey samples, which leads to a low precision in estimates when the survey is repeated or combined with other surveys. The PRN solution is to supply the U(0, 1) random numbers to the sampling procedure, instead of having the sampling procedure generate them. In Lindblom (2014) <doi:10.2478/jos-2014-0047>, and therein cited papers, it is shown how this is carried out and how it improves the estimates. This package supports two common fixed-size sampling procedures (simple random sampling and probability-proportional-to-size sampling) and includes a function for transforming the PRN's in order to control the sample overlap.

Extends the S3 generic function knit_print() in knitr to automatically print some objects using an appropriate format such as Markdown or LaTeX. For example, data frames are automatically printed as tables, and the help() pages can also be rendered in knitr documents.

Access a variety of PubMed data through a single, user-friendly interface, including abstracts, bibliometrics from iCite', pubtations from PubTator3', and full-text records from PMC'.

Wrangle and annotate different types of political texts. It also introduces Urgency Analysis, a new method for the analysis of urgency in political texts.

This package implements the Phylogeny-Guided Microbiome OTU-Specific Association Test method, which boosts the testing power by adaptively borrowing information from phylogenetically close OTUs (operational taxonomic units) of the target OTU. This method is built on a kernel machine regression framework and allows for flexible modeling of complex microbiome effects, adjustments for covariates, and can accommodate both continuous and binary outcomes.

Construct and analyze projection matrix models from a demography study of marked individuals classified by age or stage. The package covers methods described in Matrix Population Models by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak (2002).

Power analysis and sample size determination for moderation, mediation, and moderated mediation in models fitted by structural equation modelling using the lavaan package by Rosseel (2012) <doi:10.18637/jss.v048.i02> or by multiple regression. The package manymome by Cheung and Cheung (2024) <doi:10.3758/s13428-023-02224-z> is used to specify the indirect paths or conditional indirect paths to be tested.

Estimate specification models for the state-dependent level of an optimal quantile/expectile forecast. Wald Tests and the test of overidentifying restrictions are implemented. Plotting of the estimated specification model is possible. The package contains two data sets with forecasts and realizations: the daily accumulated precipitation at London, UK from the high-resolution model of the European Centre for Medium-Range Weather Forecasts (ECMWF, <https://www.ecmwf.int/>) and GDP growth Greenbook data by the US Federal Reserve. See Schmidt, Katzfuss and Gneiting (2015) <arXiv:1506.01917> for more details on the identification and estimation of a directive behind a point forecast.

Useful for preparing and cleaning data. It includes functions to center data, reverse coding, dummy code and effect code data, and more.

Statically determine and visualize the function dependencies within and across packages. This may be useful for managing function dependencies across a code base of multiple R packages.