Interface to the 'C++' Library 'Pf'

Builds and runs 'c++' code for classes that encapsulate state space model, particle filtering algorithm pairs. Algorithms include the Bootstrap Filter from Gordon et al. (1993) , the generic SISR filter, the Auxiliary Particle Filter from Pitt et al (1999) , and a variety of Rao-Blackwellized particle filters inspired by Andrieu et al. (2002) . For more details on the 'c++' library 'pf', see Brown (2020) .

Distribution of the 'BayesX' C++ Sources

'BayesX' performs Bayesian inference in structured additive regression (STAR) models. The R package BayesXsrc provides the 'BayesX' command line tool for easy installation. A convenient R interface is provided in package R2BayesX.

Matching Algorithms in R and C++

Computes matching algorithms quickly using Rcpp. Implements the Gale-Shapley Algorithm to compute the stable matching for two-sided markets, such as the stable marriage problem and the college-admissions problem. Implements Irving's Algorithm for the stable roommate problem. Implements the top trading cycle algorithm for the indivisible goods trading problem.

Wrapper for 'lz-string' 'C++' Library

Provide access to the 'lz-string' < http://pieroxy.net/blog/pages/lz-string/index.html> 'C++' library for Lempel-Ziv (LZ) based compression and decompression of strings.

'C++' Standard Template Library Containers

Use 'C++' Standard Template Library containers interactively in R. Includes sets, unordered sets, multisets, unordered multisets, maps, unordered maps, multimaps, unordered multimaps, stacks, queues, priority queues, vectors, deques, forward lists, and lists.

C++ Standard Library Vectors in R

Allows the creation and manipulation of C++ std::vector's in R.

Global Optimization by Differential Evolution in C++

An efficient C++ based implementation of the 'DEoptim' function which performs global optimization by differential evolution. Its creation was motivated by trying to see if the old approximation "easier, shorter, faster: pick any two" could in fact be extended to achieving all three goals while moving the code from plain old C to modern C++. The initial version did in fact do so, but a good part of the gain was due to an implicit code review which eliminated a few inefficiencies which have since been eliminated in 'DEoptim'.

'C++' Header Files from 'Abseil'

Wraps the 'Abseil' 'C++' library for use by R packages. Original files are from < https://github.com/abseil/abseil-cpp>. Patches are located at < https://github.com/doccstat/abseil-r/tree/main/local/patches>.

Solving Ax = b Nimbly in C++

Routines for solving large systems of linear equations and eigenproblems in R. Direct and iterative solvers from the Eigen C++ library are made available. Solvers include Cholesky, LU, QR, and Krylov subspace methods (Conjugate Gradient, BiCGSTAB). Dense and sparse problems are supported.

Capture Hi-C Analysis Engine

Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.