Data

Tools

Indexes

Applications

Experiments

Open Source Science

epi-net-sim

epidemiological network-based ABM written in Julia

https://github.com/matsim-vsp/epi-net-sim

Science Score: 52.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization matsim-vsp has institutional domain (www.vsp.tu-berlin.de)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

epidemiological network-based ABM written in Julia

Basic Info
  • Host: GitHub
  • Owner: matsim-vsp
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Size: 105 KB
Statistics
  • Stars: 1
  • Watchers: 11
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created over 2 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Citation

README.md

epi-net-sim

EpiNetSim is an epidemiological network-based ABM toy model written in Julia.

Run Locally

After cloning this repository and navigating into the folder on your terminal, you can run the toy model with the following command: bash julia src/main/julia/run_locally.jl

You can change the input variables in runlocally.jl as needed: - seeds: number of times to run model. - iterations: number of time steps (e.g. days) to simulate. - basesusceptibilities: probability that a susceptible agent will be infected by an infectious agent given contact. Multiple values may be provided in array. - recovery rate: probality an agent will switch from the disease state "Infectious" to the disease state "Recovered". For instance, a value of 0.2 means it will take an average of 5 days for an individual to recover. - networkstructures: network structure connecting agents, options include ["regular", "random", "smallworld", "smallworldreg", "preferential"] - localglobalscenarios: the risk reduction stategy that agents will apply. Options include ["base","global","local1","local2","local1and2","globallocal1","globallocal1and2"] - meandegree: mean degree of network - daysuntilshowingsymtoms: length of "Presymptomatic" state, in which agent can transmit disease but it is not detectable in the context of risk reduction strategies. If set to 0, "Presymptomatic" State is excluded. - outputfolder: custom folder name for storing output files. If missing, a folder will be generated with timestamp as name.

Run on Cluster

For large parameter combinations, it may make sense to run the toy model on a computing cluster. runoncluster.jl is one example of a run script for this purpose. On SLURM-based cluster, the following exemplary shell script can begin the simulation: ```bash

!/bin/sh

SBATCH -N 1

SBATCH -t 01:30:00

module load julia

OUTPUTFOLDERNAME=sensitivityrec0.5

mkdir $OUTPUTFOLDERNAME

for prob in seq 0.1 0.05 .3; do julia runoncluster.jl $prob 0 $OUTPUTFOLDERNAME & julia runoncluster.jl $prob 1 $OUTPUTFOLDERNAME & julia runoncluster.jl $prob 2 $OUTPUTFOLDERNAME & done

wait ```

Owner

  • Name: VSP TU-Berlin
  • Login: matsim-vsp
  • Kind: organization
  • Location: Berlin

Technische Universität Berlin, Transport Systems Planning and Transport Telematics

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: EpiNetSim
doi: 10.5281/zenodo.10602488
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Jakob
    family-names: Rehmann
    email: rehmann@vsp.tu-berlin.de
    affiliation: Technische Universität Berlin
    orcid: 'https://orcid.org/0000-0002-1666-6419'
  - given-names: Sydney
    family-names: Paltra
    email: paltra@vsp.tu-berlin.de
    affiliation: Technische Universität Berlin
    orcid: 'https://orcid.org/0000-0002-4935-8586'
repository-code: 'https://github.com/matsim-vsp/epi-net-sim'
abstract: >-
  EpiNetSim is an epidemiological network-based ABM toy
  model written in Julia.
license: GPL-3.0
commit: 107a59a
version: v0.1
date-released: '2024-01-31'

GitHub Events

Total
Last Year

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 minutes
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • jakobrehmann (3)
Top Labels
Issue Labels
Pull Request Labels