Utilities for Scheduling Functions to Execute Later with Event Loops

Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied. The functions are scheduled in an event loop.

'2bit' 'C' Library

A trimmed down copy of the "kent-core source tree" turned into a 'C' library for manipulation of '.2bit' files. See < https://genome.ucsc.edu/FAQ/FAQformat.html#format7> for a quick overview of the '2bit' format. The "kent-core source tree" can be found here: < https://github.com/ucscGenomeBrowser/kent-core/>. Only the '.c' and '.h' files from the source tree that are related to manipulation of '.2bit' files were kept. Note that the package is primarily useful to developers of other R packages who wish to use the '2bit' 'C' library in their own 'C'/'C++' code.

'Rcpp'-Based Helper Functions to Pass 'Int64' and 'nanotime' Values Between 'R' and 'C++'

'Int64' values can be created and accessed via the 'bit64' package and its 'integer64' class which package the 'int64' representation cleverly into a 'double'. The 'nanotime' packages builds on this to support nanosecond-resolution timestamps. This packages helps conversions between 'R' and 'C++' via several helper functions provided via a single header file. A complete example client package is included as an illustration.

R and C++11

Rcpp11 includes a header only C++11 library that facilitates integration between R and modern C++.

RUV-III-C

Variations of Remove Unwanted Variation-III (RUV-III) known as RUV-III-C (RUV-III Complete). RUV-III performs normalisation using negative control variables and replication. RUV-III-C extends this method to cases where the data contains missing values, by applying RUV-III to complete subsets of the data. Originally designed for SWATH-MS proteomics datasets. Poulos et al. (2020) .

Interpolation From C

Simple interpolation methods designed to be used from C code. Supports constant, linear and spline interpolation. An R wrapper is included but this package is primarily designed to be used from C code using 'LinkingTo'. The spline calculations are classical cubic interpolation, e.g., Forsythe, Malcolm and Moler (1977) .

R and C++ Interfaces to 'spdlite' C++ Header Library for Logging

The lightweight header-only C++-20 logging library 'spdlite', a lighter version of 'spdlog' and also written by Gabi Melman, provides most of the features of the larger version, and also includes 'fmt' as a fallback if std::format() is not selected.

Markov Chain Monte Carlo (MCMC) Package

Contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ written in the Scythe Statistical Library Version 1.0.3. All models return 'coda' mcmc objects that can then be summarized using the 'coda' package. Some useful utility functions such as density functions, pseudo-random number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization are provided.

Multiple Precision Arithmetic

Multiple Precision Arithmetic (big integers and rationals, prime number tests, matrix computation), "arithmetic without limitations" using the C library GMP (GNU Multiple Precision Arithmetic).

T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation

An R wrapper around the fast T-distributed Stochastic Neighbor Embedding implementation by Van der Maaten (see < https://github.com/lvdmaaten/bhtsne/> for more information on the original implementation).