'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.

R and C++11

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

'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.

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.

Template Model Builder: A General Random Effect Tool Inspired by 'ADMB'

With this tool, a user should be able to quickly implement complex random effect models through simple C++ templates. The package combines 'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain an efficient implementation of the applied Laplace approximation with exact derivatives. Key features are: Automatic sparseness detection, parallelism through 'BLAS' and parallel user templates.

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.

C/C++ Source Code to Trigger Address and Undefined Behaviour Sanitizers

Recent gcc and clang compiler versions provide functionality to test for memory violations and other undefined behaviour; this is often referred to as "Address Sanitizer" (or 'ASAN') and "Undefined Behaviour Sanitizer" ('UBSAN'). The Writing R Extension manual describes this in some detail in Section 4.3 title "Checking Memory Access". This feature has to be enabled in the corresponding binary, eg in R, which is somewhat involved as it also required a current compiler toolchain which is not yet widely available, or in the case of Windows, not available at all (via the common Rtools mechanism). As an alternative, pre-built Docker containers such as the Rocker container 'r-devel-san' or the multi-purpose container 'r-debug' can be used. This package then provides a means of testing the compiler setup as the known code failures provides in the sample code here should be detected correctly, whereas a default build of R will let the package pass. The code samples are based on the examples from the Address Sanitizer Wiki at < https://github.com/google/sanitizers/wiki>.

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).