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Run temporal dynamics on a hypergraph network

Manual page for Run temporal dynamics on a hypergraph network version 1.0

Run temporal dynamics on a hypergraph network [--output value] [--remove-files value] [--edges-file value] [--algorithm value] [--sampler value] [--tmax value] [--use-qs value] [--n-samples value] [--time-scale value] [--initial-fraction value] [--initial-number value] --beta1 value [--par-b value] [--par-theta value] [--export-states value] [--seed value] [--verbose value] [--verbose-level value] [--help] [--markdown] [--version]

Sep 2025

Short description

This program runs a temporal dynamics on a hypergraph network, using the Gillespie algorithm. The network can be read from a file or generated as a small example. The dynamics can be configured with various parameters.

Command line options:

Required switches:

  • --beta1 value, -b1 value Infection rate parameter beta1

Optional switches:

  • --output value, -o value default value ./output Output prefix for result files

  • --remove-files value, -rm value default value false Remove existing output files before running

  • --edges-file value, -e value File containing the edge list of the network as input

  • --algorithm value, -a value , value in: HB_OGA,NB_OGA default value HB_OGA Dynamics algorithm to use

  • --sampler value, -s value , value in: rejection_maxheap,btree default value rejection_maxheap Sampler choice

  • --tmax value, -t value default value 1000.0 Maximum simulation time

  • --use-qs value, -qs value default value false Use Quasi-Stationary method

  • --n-samples value, -ns value default value 10 Number of samples to average over

  • --time-scale value, -ts value , value in: powerlaw,uniform default value powerlaw Time scale to use

  • --initial-fraction value, -if value default value 1.0 Initial fraction of infected nodes

  • --initial-number value, -in value default value 0 Initial number of infected nodes (overrides initial-fraction)

  • --par-b value, -pb value default value 0.5 Dynamical parameter b

  • --par-theta value, -pt value default value 0.5 Dynamical parameter theta

  • --export-states value, -es value default value false Export the states of nodes and edges at the end of each sample (be careful with large networks)

  • --seed value, -rs value default value 42 Random seed for the dynamics

  • --verbose value, -vv value default value true Enable verbose logging

  • --verbose-level value, -vl value , value in: error,warning,info,debug default value info Logging level

  • --help, -h Print this help message

  • --markdown, -md Save this help message in a Markdown file

  • --version, -v Print version