netdiffuseR - Analysis of Diffusion and Contagion Processes on Networks
Empirical statistical analysis, visualization and simulation of diffusion and contagion processes on networks. The package implements algorithms for calculating network diffusion statistics such as transmission rate, hazard rates, exposure models, network threshold levels, infectiousness (contagion), and susceptibility. The package is inspired by work published in Valente, et al., (2015) <DOI:10.1016/j.socscimed.2015.10.001>; Valente (1995) <ISBN: 9781881303213>, Myers (2000) <DOI:10.1086/303110>, Iyengar and others (2011) <DOI:10.1287/mksc.1100.0566>, Burt (1987) <DOI:10.1086/228667>; among others.
Last updated 9 days ago
contagiondiffusion-networknetwork-analysisnetwork-visualization
8.51 score 86 stars 207 scripts 630 downloadsepiworldR - Fast Agent-Based Epi Models
A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.
Last updated 1 days ago
abmagent-based-modelingcovid-19epidemicsepidemiologyr-programmingrpackrpkgseirseir-modelsimulationsirsir-model
8.18 score 8 stars 1 packages 53 scripts 336 downloads
slurmR - A Lightweight Wrapper for 'Slurm'
'Slurm', Simple Linux Utility for Resource Management <https://slurm.schedmd.com/>, is a popular 'Linux' based software used to schedule jobs in 'HPC' (High Performance Computing) clusters. This R package provides a specialized lightweight wrapper of 'Slurm' with a syntax similar to that found in the 'parallel' R package. The package also includes a method for creating socket cluster objects spanning multiple nodes that can be used with the 'parallel' package.
Last updated 1 years ago
bioinformaticshpcslurm
8.03 score 58 stars 1 packages 203 scripts 304 downloads
rgexf - Build, Import, and Export GEXF Graph Files
Create, read, and write 'GEXF' (Graph Exchange 'XML' Format) graph files (used in 'Gephi' and others). Using the 'XML' package, rgexf allows reading and writing GEXF files, including attributes, 'GEXF' visual attributes (such as color, size, and position), network dynamics (for both edges and nodes), and edges' weights. Users can build/handle graphs element-by-element or massively through data frames, visualize the graph on a web browser through 'gexf-js' (a 'javascript' library), and interact with the 'igraph' package.
Last updated 1 months ago
gephigexfgexf-graph-filessocial-networkxml
7.43 score 27 stars 185 scripts 1.4k downloadsnetplot - Beautiful Graph Drawing
A graph visualization engine that emphasizes on aesthetics at the same time providing default parameters that yield out-of-the-box-nice visualizations. The package is built on top of 'The Grid Graphics Package' and seamlessly work with 'igraph' and 'network' objects.
Last updated 6 days ago
graph-visualizationigraphnetscinetwork-analysisnetwork-visualizationsnastatnet
6.85 score 51 stars 69 scripts 481 downloads
fmcmc - A friendly MCMC framework
Provides a friendly (flexible) Markov Chain Monte Carlo (MCMC) framework for implementing Metropolis-Hastings algorithm in a modular way allowing users to specify automatic convergence checker, personalized transition kernels, and out-of-the-box multiple MCMC chains using parallel computing. Most of the methods implemented in this package can be found in Brooks et al. (2011, ISBN 9781420079425). Among the methods included, we have: Haario (2001) <doi:10.1007/s11222-011-9269-5> Adaptive Metropolis, Vihola (2012) <doi:10.1007/s11222-011-9269-5> Robust Adaptive Metropolis, and Thawornwattana et al. (2018) <doi:10.1214/17-BA1084> Mirror transition kernels.
Last updated 1 years ago
adaptivebayesian-inferencemarkov-chain-monte-carlomcmcmetropolis-hastingsparallel-computing
6.79 score 16 stars 1 packages 86 scripts 309 downloads
aphylo - Statistical Inference and Prediction of Annotations in Phylogenetic Trees
Implements a parsimonious evolutionary model to analyze and predict gene-functional annotations in phylogenetic trees as described in Vega Yon et al. (2021) <doi:10.1371/journal.pcbi.1007948>. Focusing on computational efficiency, 'aphylo' makes it possible to estimate pooled phylogenetic models, including thousands (hundreds) of annotations (trees) in the same run. The package also provides the tools for visualization of annotated phylogenies, calculation of posterior probabilities (prediction) and goodness-of-fit assessment featured in Vega Yon et al. (2021).
Last updated 1 years ago
annotationsinferencephylogeneticsrcpparmadillo
5.49 score 6 stars 104 scripts 295 downloads
ergmito - Exponential Random Graph Models for Small Networks
Simulation and estimation of Exponential Random Graph Models (ERGMs) for small networks using exact statistics as shown in Vega Yon et al. (2020) <DOI:10.1016/j.socnet.2020.07.005>. As a difference from the 'ergm' package, 'ergmito' circumvents using Markov-Chain Maximum Likelihood Estimator (MC-MLE) and instead uses Maximum Likelihood Estimator (MLE) to fit ERGMs for small networks. As exhaustive enumeration is computationally feasible for small networks, this R package takes advantage of this and provides tools for calculating likelihood functions, and other relevant functions, directly, meaning that in many cases both estimation and simulation of ERGMs for small networks can be faster and more accurate than simulation-based algorithms.
Last updated 1 years ago
ergmexponential-random-graph-modelsstatistics
5.43 score 9 stars 30 scripts 212 downloads
ABCoptim - Implementation of Artificial Bee Colony (ABC) Optimization
An implementation of Karaboga (2005) Artificial Bee Colony Optimization algorithm <http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf>. This was developed upon the basic version programmed in C and available at the algorithm's official website.
Last updated 1 years ago
artificial-bee-colonyoptimizationr-programmingrcppstochastic-optimizers
4.52 score 29 stars 23 scripts 686 downloadsgooglePublicData - Working with Google's 'Public Data Explorer' DSPL Metadata Files
Provides a collection of functions to set up 'Google Public Data Explorer' <https://www.google.com/publicdata/> data visualization tool with your own data, building automatically the corresponding DataSet Publishing Language file, or DSPL (XML), metadata file jointly with the CSV files. All zip-up and ready to be published in 'Public Data Explorer'.
Last updated 3 years ago
dsplgapmindergooglegoogle-public-dataxml
3.60 score 8 stars 10 scripts 455 downloads