Import classification results from the RDP Classifier (Ribosomal Database Project), USEARCH sintax, vsearch sintax and the QIIME2 (Quantitative Insights into Microbial Ecology) classifiers into phyloseq tax_table objects.

High dimensional survival data analysis with Markov Chain Monte Carlo(MCMC). Currently supports frailty data analysis. Allows for Weibull and Exponential distribution. Includes function for interval censored data.

Quantify stratigraphic disorder using the metrics defined by Burgess (2016) <doi:10.2110/jsr.2016.10>. Contains a range of utility tools to construct and manipulate stratigraphic columns.

Provide utilities to work with solar time, i.e. where noon is exactly when sun culminates. Provides functions for computing sun position and times of sunrise and sunset.

This package provides functions for the computationally efficient simulation of dynamic networks estimated with the statistical framework of temporal exponential random graph models, implemented in the tergm package.

This package provides a Shiny application for the interactive visualisation and analysis of networks that also provides a web interface for collecting social media data using vosonSML'.

This package provides a WebSocket client interface for R. WebSocket is a protocol for low-overhead real-time communication: <https://en.wikipedia.org/wiki/WebSocket>.

Use BridgeDb functions and load identifier mapping databases in R. It uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files.

This package provides a fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.

The polyester package simulates RNA-seq reads from differential expression experiments with replicates. The reads can then be aligned and used to perform comparisons of methods for differential expression.

This package provides the functionality to set configuration options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected.

This package provides tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead.

This package provides a Wrapper around the SVDLIBC library for (truncated) singular value decomposition of a sparse matrix. Currently, only sparse real matrices in Matrix package format are supported.

This package provides an interface to the rich display capabilities of Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a running IRkernel session.

This package provides a utility library intended at providing configurable reader macros for common tasks such as accessors, hash-tables, sets, uiop:run-program, arrays and a few others.

Infer log-linear Poisson Graphical Model with an auxiliary data set. Hot-deck multiple imputation method is used to improve the reliability of the inference with an auxiliary dataset. Standard log-linear Poisson graphical model can also be used for the inference and the Stability Approach for Regularization Selection (StARS) is implemented to drive the selection of the regularization parameter. The method is fully described in <doi:10.1093/bioinformatics/btx819>.

Process phylogenetic trees with tropical support vector machine and principal component analysis defined with tropical geometry. Details about tropical support vector machine are available in : Tang, X., Wang, H. & Yoshida, R. (2020) <arXiv:2003.00677>. Details about tropical principle component analysis are available in : Page, R., Yoshida, R. & Zhang L. (2020) <doi:10.1093/bioinformatics/btaa564> and Yoshida, R., Zhang, L. & Zhang, X. (2019) <doi:10.1007/s11538-018-0493-4>.

Implemented fast and memory-efficient Notch-filter, Welch-periodogram, discrete wavelet spectrogram for minutes of high-resolution signals, fast 3D convolution, image registration, 3D mesh manipulation; providing fundamental toolbox for intracranial Electroencephalography (iEEG) pipelines. Documentation and examples about RAVE project are provided at <https://rave.wiki>, and the paper by John F. Magnotti, Zhengjia Wang, Michael S. Beauchamp (2020) <doi:10.1016/j.neuroimage.2020.117341>; see citation("ravetools") for details.

Detecting outliers using robust methods, i.e. the Median Absolute Deviation (MAD) for univariate outliers; Leys, Ley, Klein, Bernard, & Licata (2013) <doi:10.1016/j.jesp.2013.03.013> and the Mahalanobis-Minimum Covariance Determinant (MMCD) for multivariate outliers; Leys, C., Klein, O., Dominicy, Y. & Ley, C. (2018) <doi:10.1016/j.jesp.2017.09.011>. There is also the more known but less robust Mahalanobis distance method, only for comparison purposes.

This package provides fast algorithms for the Theil-Sen estimator, Siegel's repeated median slope estimator, and Passing-Bablok regression. The implementation is based on algorithms by Dillencourt et al. (1992) <doi:10.1142/S0218195992000020> and Matousek et al. (1998) <doi:10.1007/PL00009190>. The implementations are detailed in Raymaekers (2023) <doi:10.32614/RJ-2023-012> and Raymaekers J., Dufey F. (2022) <arXiv:2202.08060>. All algorithms run in quasilinear time.

This package provides a collection of tools for antitrust practitioners, including the ability to calibrate different consumer demand systems and simulate the effects of mergers under different competitive regimes.

This package provides functions to calculate the assortment of vertices in social networks. This can be measured on both weighted and binary networks, with discrete or continuous vertex values.

Making probabilistic projections of life expectancy for all countries of the world, using a Bayesian hierarchical model <doi:10.1007/s13524-012-0193-x>. Subnational projections are also supported.

Fits Bayesian grouped weighted quantile sum (BGWQS) regressions for one or more chemical groups with binary outcomes. Wheeler DC et al. (2019) <doi:10.1016/j.sste.2019.100286>.