analyzers

analyzers

Analyzers, which record more than a sim records by default, as it runs

For example, the number infected by age or by sex, or who infected whom (ss.infection_log).

Used with: agents and compartments; declared and coded modules

Classes

Name	Description
Analyzer	Base class for analyzers, which record more about a sim than it records by default: for
infection_log	Log who infected whom – see ss.diseases.InfectionLog for detail

Analyzer

analyzers.Analyzer(name=None, label=None, **kwargs)

Base class for analyzers, which record more about a sim than it records by default: for example, a state of the people on each step, read before the next step changes it.

An analyzer records results as any module does: those about the state at the start of each step (stocks) in record_states(), and those about what happened in it (flows) in record_events() (both with self.ti the step’s, as in every module). Its step(), if it has one, is called at the end of each step, after the flows are recorded, when the people are as they are at the next time point.

Examples

class BySex(ss.Analyzer):
    def init_results(self):
        super().init_results()
        self.define_results(ss.Result('infected', columns=['female', 'male'], kind='stock'))

    def record_states(self):
        infected, female = self.sim.diseases.sis.I, self.sim.people.female
        self.results.infected[self.ti] = [np.count_nonzero(infected & female), np.count_nonzero(infected & ~female)]

An analyzer that reads who infected whom sets needs_infection_log = True: each disease then keeps its infection log (disease.infection_log, see ss.infection_log), as with an ss.infection_log in the sim.

Methods

Name	Description
step	Nothing by default: an analyzer usually only records results (see record_states() and record_events())

step

analyzers.Analyzer.step()

Nothing by default: an analyzer usually only records results (see record_states() and record_events())

infection_log

analyzers.infection_log(**kwargs)

Log who infected whom – see ss.diseases.InfectionLog for detail

This analyzer turns on the infection log of each disease, rather than recording anything itself, since who infected whom is known only inside the disease’s transmit() step.

Each entry has the time (t), the person infected (target), who infected them (source), and the route (network). The source is known only for transmission over a network, where each infection is drawn along an edge: seeds have a source of -1, and infections by a mixing pool (ss.MixingPool), a contact matrix, or mixing with everyone (no network) have a source and network of NaN, since they come from the fraction infectious in a group rather than from a particular person (by events, solver=ss.solvers.abm(step='events'), each contact is with a particular person, so these have a source and route too). For a disease with strains (ss.Strains), each entry also has the strain transmitted (strain; for seeds, the strains they start with). As agents only.

The log stays on the disease (sim.diseases.sir.infection_log) as well, so several analyzers can read it, during the run or after. To follow transmission as the sim runs, an analyzer reads the entries of each step with disease.infection_log.to_df(ti=self.ti) (see ss.diseases.InfectionLog.to_df()).

Note: CRN safe.

Examples

import starsim as ss
sim = ss.Sim(n_agents=1000, diseases='sir', networks='random', analyzers='infection_log')
sim.run()
sim.analyzers[0].plot()

Attributes

Name	Description
log	The infection log, if there is only one disease

Methods

Name	Description
animate	Animate the infection log – mostly for amusement!
finalize_results	Collect the infection logs from each of the diseases (the same logs, so several analyzers can share them)
plot	Plot all of the infection logs
to_df	Convert the infection log to a dataframe, if there is only one disease

animate

analyzers.infection_log.animate(
    key=0,
    framerate=10,
    clear=False,
    cmap='parula',
    **kwargs,
)

Animate the infection log – mostly for amusement!

Parameters

Name	Type	Description	Default
key	int / str	which disease to animate the infection log of	0
framerate	float	how many frames per second to display	10
clear	bool	whether to clear the frame on each step	False
cmap	str	the colormap to use	'parula'
kwargs	dict	passed to ss.plot_args()

finalize_results

analyzers.infection_log.finalize_results()

Collect the infection logs from each of the diseases (the same logs, so several analyzers can share them)

plot

analyzers.infection_log.plot(**kwargs)

Plot all of the infection logs

Parameters

Name	Type	Description	Default
kwargs	dict	passed to ss.plot_args(), for the figure and plot options

to_df

analyzers.infection_log.to_df()

Convert the infection log to a dataframe, if there is only one disease