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git2r - Provides Access to Git Repositories

Interface to the 'libgit2' library, which is a pure C implementation of the 'Git' core methods. Provides access to 'Git' repositories to extract data and running some basic 'Git' commands.

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gitgit-clientlibgit2libgit2-library

12.70 score 223 stars 41 dependents 936 scripts 39k downloads

SimInf - A Framework for Data-Driven Stochastic Disease Spread Simulations

Provides an efficient and very flexible framework to conduct data-driven epidemiological modeling in realistic large scale disease spread simulations. The framework integrates infection dynamics in subpopulations as continuous-time Markov chains using the Gillespie stochastic simulation algorithm and incorporates available data such as births, deaths and movements as scheduled events at predefined time-points. Using C code for the numerical solvers and 'OpenMP' (if available) to divide work over multiple processors ensures high performance when simulating a sample outcome. One of our design goals was to make the package extendable and enable usage of the numerical solvers from other R extension packages in order to facilitate complex epidemiological research. The package contains template models and can be extended with user-defined models. For more details see the paper by Widgren, Bauer, Eriksson and Engblom (2019) <doi:10.18637/jss.v091.i12>. The package also provides functionality to fit models to time series data using the Approximate Bayesian Computation Sequential Monte Carlo ('ABC-SMC') algorithm of Toni and others (2009) <doi:10.1098/rsif.2008.0172> or the Particle Markov Chain Monte Carlo ('PMCMC') algorithm of 'Andrieu' and others (2010) <doi:10.1111/j.1467-9868.2009.00736.x>.

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data-drivenepidemiologyhigh-performance-computingmarkov-chainmathematical-modellinggslopenmp

10.24 score 37 stars 202 scripts 368 downloads

rmatio - Read and Write 'Matlab' Files

Read and write 'Matlab' MAT files from R. The 'rmatio' package supports reading MAT version 4, MAT version 5 and MAT compressed version 5. The 'rmatio' package can write version 5 MAT files and version 5 files with variable compression.

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zlib

6.37 score 13 stars 2 dependents 133 scripts 4.6k downloads

EpiContactTrace - Epidemiological Tool for Contact Tracing

Routines for epidemiological contact tracing and visualisation of network of contacts.

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cpp

5.34 score 13 stars 42 scripts 259 downloads