metawards.run

metawards.run(help: bool = None, version: bool = None, dry_run: bool = None, silent: bool = False, auto_load: bool = False, config: str = None, input: _Union[str, VariableSet, VariableSets] = None, line: int = None, repeats: int = None, seed: int = None, additional: _Union[str, _List[str]] = None, output: str = None, disease: _Union[str, Disease] = None, model: _Union[str, Wards, Ward] = None, demographics: _Union[str, Demographics, Demographic] = None, start_date: _Union[str, date] = None, start_day: int = None, parameters: _Union[str, Parameters] = None, repository: str = None, population: int = None, nsteps: int = None, user_variables: _Union[str, VariableSet] = None, iterator: str = None, extractor: str = None, mixer: str = None, mover: str = None, star_as_E: bool = None, star_as_R: bool = None, disable_star: bool = None, UV: float = None, debug: bool = None, debug_level: int = None, outdir_scheme: str = None, nthreads: int = None, nprocs: int = None, hostfile: str = None, cores_per_node: int = None, auto_bzip: bool = None, no_auto_bzip: bool = None, force_overwrite_output: bool = None, profile: bool = None, no_profile: bool = None, mpi: bool = None, scoop: bool = None) → _Union[str, 'pandas.DataFrame'][source]

Run a MetaWards simulation

Parameters

  • silent (bool) – Run without printing the output to the screen

  • dry_run (bool) – Don’t run anything - just print what will be run

  • help (bool) – Whether or not to print the full help

  • version (bool) – Whether or not to print the metawards version info

  • output (str) – The name of the directory in which to write the output. If this is not set, then a new, random-named directory will be used.

  • force_overwrite_output (bool) – Force overwriting the output directory - this will remove any existing directory before running

  • auto_load (bool) – Whether or not to automatically load and return a pandas dataframe of the output/results.csv.bz2 file. If pandas is available then this defaults to True, otherwise False

  • disease (Disease or str) – The disease to model (or the filename of the json file containing the disease, or name of the disease)

  • model (Ward, Wards or str) – The network wards to run (of the filename of the json file containing the network, or name of the network))

  • parameters (There are many more) –

  • to (based on the arguments) –

  • --help. (metawards) –

  • of (Please set "help" to True to print out a full list) –

  • arguments (help for all of the) –

    returns

    results – The file containing the output results (output/results.csv.bz2), or, if auto_load is True, the pandas.DataFrame containing those results

    rtype

    str or pandas.DataFrame