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.

Last updated 1 months ago

gitgit-clientlibgit2libgit2-library

13.95 score 215 stars 47 packages 828 scripts 135k 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>.

Last updated 8 hours ago

data-drivenepidemiologyhigh-performance-computingmarkov-chainmathematical-modelling

9.97 score 33 stars 226 scripts 528 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.

Last updated 2 years ago

5.93 score 10 stars 2 packages 115 scripts 2.5k downloads

EpiContactTrace - Epidemiological Tool for Contact Tracing

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

Last updated 1 months ago

5.71 score 11 stars 39 scripts 618 downloads