'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) .

Solvers for Initial Value Problems of Differential Equations ('ODE', 'DAE', 'DDE')

Functions that solve initial value problems of a system of first-order ordinary differential equations ('ODE'), of partial differential equations ('PDE'), of differential algebraic equations ('DAE'), and of delay differential equations. The functions provide an interface to the FORTRAN functions 'lsoda', 'lsodar', 'lsode', 'lsodes' of the 'ODEPACK' collection, to the FORTRAN functions 'dvode', 'zvode' and 'daspk' and a C-implementation of solvers of the 'Runge-Kutta' family with fixed or variable time steps. The package contains routines designed for solving 'ODEs' resulting from 1-D, 2-D and 3-D partial differential equations ('PDE') that have been converted to 'ODEs' by numerical differencing.

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) .

C++ Interface to PostgreSQL

Fully DBI-compliant C++-backed interface to PostgreSQL < https://www.postgresql.org/>, an open-source relational database.

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

The mature and widely-used C++ logging library 'spdlog' by Gabi Melman provides many desirable features. This package bundles these header files for easy use by R packages from both their R and C or C++ code. Explicit use via 'LinkingTo:' is also supported. Also see the 'spdl' package which enhanced this package with a consistent R and C++ interface.

Regression Spline Functions and Classes

Constructs basis functions of B-splines, M-splines, I-splines, convex splines (C-splines), periodic splines, natural cubic splines, generalized Bernstein polynomials, their derivatives, and integrals (except C-splines) by closed-form recursive formulas. It also contains a C++ head-only library integrated with Rcpp. See Wang and Yan (2021) for details.

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>.