Accumulating into a Workspace

The default function that is always called by extract() is metawards.extractors.output_core().

This core extractor performs the bulk of the work of accumulating all of the infection data into a single metawards.Workspace object.

This metawards.Workspace object contains;

inf_tot(): The total population size at each of the different disease stages from the work infections.
pinf_tot(): The total population size at each of the different disease stages from the play infections.
n_inf_wards(): The number of wards with at least one member for each disease stage.
total_inf_ward(): The size of the infected population in each ward (the prevalence).
total_new_inf_ward(): The number of new infections on this day in each ward.
incidence(): The incidence of infection in each ward.

Output incidence

This Workspace contains data that can be easily output, e.g. the metawards.extractors.output_incidence() supplied extractor writes the incidence to a file called incidence.dat.bz2. For example, you can call this from your population.py extractor by changing it to read;

from metawards.utils import Console

def output_population(population, output_dir, **kwargs):
    Console.debug("Hello output_population")

    # create an output file called 'population.dat'
    popfile = output_dir.open("population.dat",
                              headers=["day", "date", "S", "E",
                                       "I", "R"])

    # write the population to this file
    popfile.write(f"{population.day} {population.date.isoformat()} "
                f"{population.susceptibles} {population.latent} "
                f"{population.total} {population.recovereds}\n")


def extract_population(population, **kwargs):
    Console.debug("hello extract_population")

    from metawards.extractors import output_incidence

    if population.day % 2 == 0:
        return [output_population, output_incidence]
    else:
        return [output_incidence]

Note

See how we are calling output_incidence on every day, but output_population only on even days.

If you run this extractor using

metawards --extractor population

You will now see that you get a file called incidence.dat.bz2 in the output directory. This will be a big matrix of mostly zeroes, as no infection has been seeded.

Default outputs

The default extractor is extract_default(). This returns;

output_basic(): Writes out basic information to the files NumberWardsInfected.dat, TotalInfections.dat etc.
output_dispersal(): Calculates and writes out the geographic disperal of the outbreak to MeanXY.dat, VarXY.day and Dispersal.dat
output_prevalence(): Writes the (large) prevalence matrix to prevalence.dat.
output_incidence(): Writes the (large) incidence matrix to incidence.dat.

You can use extract_default() either by not supplying an extractor via the --extractor command line argument, or by specifying --extract-default.

Have a go using;

metawards --extractor extract_default

As well as extract_default(), there is also extract_small() (only extracting the “small” files), “meth:extract_large (extract everything, including producing large trajectory files) and extract_none() (extract nothing - useful if you want to restrict output only to results.csv.bz2).