Stochastic Hybrid Models in Dynamic Networks

Simulates stochastic hybrid models for transmission of infectious diseases in dynamic networks. It is a metapopulation model in which each node in the network is a sub-population and disease spreads within nodes and among them, combining two approaches: stochastic simulation algorithm or its approximations (Gillespie DT (2007) ) and individual-based approach, respectively. Movement among nodes are data based and can be irregular. Equations that models spread within nodes are customizable and there are two link types among nodes: migration and influence (commuting).


Version: 0.2.15


hybridModels is a R package to simulate customizable stochastic hybrid models for transmission of diseases in dynamic networks. It is possible to use one of the options below to install the package:

  • Using the function install.packages() for stable versions from CRAN (https://CRAN.R-project.org/package=hybridModels).
install.packages("hybridModels")
  • Making use of the devtools package (Hadley Wickham and Winston Chang (2015). devtools: Tools to Make Developing R Packages Easier. R package version 1.10.0 or higher, http://CRAN.R-project.org/package=devtools).

Through github and devtools

library(devtools)
install_github("fernandosm/hybridModels")

Features

The current version runs:

  • Customizable hybrid model in dynamic networks in which migration is the link type between nodes.

  • Customizable hybrid model in dynamic networks in which influence is the link type between nodes.

  • Find nodes of contact chains (outgoing and ingoing).

  • Calculate contact chains' size (outgoing and ingoing).

  • SI hybrid model without explicit demographics (migration link). It is assumed that the total number of individuals is constant and animals migrate between premises.

  • SI hybrid model without explicit demographics (influence link). It is assumed that the total number of individuals is constant and animals do not migrate between premises, they influence other premises.

In use

Jason Ardila Galvis (email: [email protected]) studies disease spread among animals and, as an exemple, he created an animation (click on the image below) based on results generated by hybridModels package. In this example he made use of fictitius data.

Animated visualization for transmission of infectious diseases in dynamic networks

News

hybridModels 0.2.15

  • adding few short comments

  • adding date option in summary method

  • updating summary documentation

  • updating description field

hybridModels 0.2.14

  • findContactChain: it retrieves chains without selected.node.

  • networkSample: removing unnecessary data.

hybridModels 0.2.13

  • New class and methods to handle customizable models of influence link type.

  • new example with a influence link type.

hybridModels 0.2.12

  • summary - bug fix.

  • roxygen2 warning fix.

hybridModels 0.2.11

  • Documentations mistakes.

  • summary method.

hybridModels 0.2.10

  • Identation and naming mistakes corrected.

hybridModels 0.2.9

  • new column names of example data set (new documentation).

  • adjusting all examples for the new column names.

hybridModels 0.2.8

  • implemantation of findContactChain function.

hybridModels 0.2.7

  • example data have one column name changed.

hybridModels 0.2.6

  • using PSOCK cluster type for all OSs.

hybridModels 0.2.5

  • Considering Mac OS cluster type for parallel functions.

hybridModels 0.2.4

  • faster examples (from SIR to SIS and smaller pops).

  • back to doParallel package.

  • foreach package from Depends to Imports.

  • layout changes data set help.

  • removing unnecessary function.

hybridModels 0.2.3

  • stats package from Depends to Imports.

hybridModels 0.2.2

  • It uses the superseded package: 'doSNOW' since it passes the cran check and the doParallel did not.

hybridModels 0.2.1

  • Changing examples: examples are now using custom equations.

  • plot.HD function: it is possible to customize through ggplot2.

hybridModels 0.2.0

  • hybridModel function: now it includes new class (customMigr).

  • buildModelClass function: now it includes it includes new class (generic function).

  • buildModelClass.customMigr: method to create an object of the class customMigr.

  • simHM.customMigr function: method to run custom models (migration link type).

  • plot.HD function: new plot opstions.

  • networkSample data: new data set

  • nodesCensus data: new data set

hybridModels 0.1.0

  • hybridModel function: now it includes link.type parameter.

  • buildModelClass function: now it includes link.type parameter (generic function).

  • buildModelClass.siWoDemogrMigr: replaces buildModelClass.siWoDemogrMigr method.

  • buildModelClass.siWoDemogrInfl: method to create an object of the class siWoDemogrInfl.

  • simHB function: generic that calls the method based on model's class.

  • simHB.siWoDemogrMigr function: method to run the 'SI without demographics' model of migration link type.

  • simHB.siWoDemogrInfl function: method to run the 'SI without demographics' model of influence link type.

  • plot.HD function: replaces plot.siWoDemogrmethod method.

  • networkSample data: replaces network.sample

  • nodesCensus data: replaces nodes.Info

hybridModels 0.0.1

  • hybridModel function: main function to simulate the spread of diseases using an model.

  • buildModelClass function: generic that calls the method based on model's class.

  • buildModelClass.siWoDemogr: method to create an object of the class siWoDemogr.

  • simHB function: generic that calls the method based on model's class.

  • simHB.siWoDemogr function: method to run the 'SI without demographics' model.

  • plot.siWoDemogr function: method to plot the 'SI without demographics' results.

  • network.sample data: a sample of a dynamic network of traded animals between farms.

  • network.Info data: farms' censitary information.

Reference manual

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install.packages("hybridModels")

0.2.15 by Fernando S. Marques, 5 months ago


https://github.com/fernandosm/hybridModels


Report a bug at https://github.com/fernandosm/hybridModels/issues


Browse source code at https://github.com/cran/hybridModels


Authors: Fernando S. Marques [aut, cre], Jose H. H. Grisi-Filho [aut], Marcos Amaku [aut]


Documentation:   PDF Manual  


GPL (>= 2) license


Imports doParallel, foreach, ggplot2, GillespieSSA, parallel, reshape2, stats, stringr, grid


See at CRAN