Examples: visualization, C++, networks, data cleaning, html widgets, ropensci.

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leidenbase — by Brent Ewing, 4 months ago

R and C/C++ Wrappers to Run the Leiden find_partition() Function

An R to C/C++ interface that runs the Leiden community detection algorithm to find a basic partition (). It runs the equivalent of the 'leidenalg' find_partition() function, which is given in the 'leidenalg' distribution file 'leiden/src/functions.py'. This package includes the required source code files from the official 'leidenalg' distribution and functions from the R 'igraph' package. The 'leidenalg' distribution is available from < https://github.com/vtraag/leidenalg/> and the R 'igraph' package is available from < https://igraph.org/r/>. The Leiden algorithm is described in the article by Traag et al. (2019) . Leidenbase includes code from the packages: igraph version 0.9.8 with license GPL (>= 2), leidenalg version 0.8.10 with license GPL 3.

gmp — by Antoine Lucas, 2 months ago

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).

MCMCpack — by Jong Hee Park, 2 months ago

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.

deSolve — by Thomas Petzoldt, 4 months ago

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.

CsChange — by Zhicheng Du, a year ago

Testing for Change in C-Statistic

Calculate the confidence interval and p value for change in C-statistic. The adjusted C-statistic is calculated by using formula as "Somers' Dxy rank correlation"/2+0.5. The confidence interval was calculated by using the bootstrap method. The p value was calculated by using the Z testing method. Please refer to the article of Peter Ganz et al. (2016) .

rapidxmlr — by David Cooley, 5 years ago

'Rapidxml' C++ Header Files

Provides XML parsing capability through the 'Rapidxml' 'C++' header-only library.

RcppArray — by Jon Clayden, 5 months ago

'Rcpp' Meets 'C++' Arrays

Interoperability between 'Rcpp' and the 'C++11' array and tuple types. Linking to this package allows fixed-length 'std::array' objects to be converted to and from equivalent R vectors, and 'std::tuple' objects converted to lists, via the as() and wrap() functions. There is also experimental support for 'std::span' from 'C++20'.

sanitizers — by Dirk Eddelbuettel, 10 months ago

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>.

BayesXsrc — by Nikolaus Umlauf, 14 days ago

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.

chicane — by Syed Haider, 2 years ago

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.