comod package

Submodules

comod.base module

class comod.base.FunctionModel(states=None, parameters=None, rules=None, sum_state='N', nihil_state='!')[source]

Bases: comod.base._Model

A compartment model with transition rules defined by callables

class comod.base.Model(states=None, parameters=None, rules=None, sum_state='N', nihil_state='!')[source]

Bases: comod.base._Model

A compartment model with transition rules defined by strings

solve_time(initial, parameters, t, **kwargs)[source]

Solve the model numerically for parameters given as functions of time.

The solution is found using scipy.integrate.solve_ivp, which uses by default an Explicit Runge-Kutta method of order 5(4).

Parameters

  • initial (list of float) – Initial population for each of the states.

  • parameters (list of callable) – Functions of time defining the parameters.

  • t (list of float) – Mesh of time values for which the solution is found.

  • kwargs – Additional arguments passed to solve_ivp.

Returns

Values of each component (first coordinate) at the t mesh (second).

Return type

numpy.ndarray

comod.base.add_natural(model, birth_param='nu', death_param='mu', birth_state=None)[source]

Add some “natural” birth and death dynamics to a model

Births are described by an absolute rate, while deaths are relative to the population.

Parameters

  • model (Model) – Base model which will be extended.

  • birth_param (str) – Name of the birth rate parameter.

  • death_param (str) – Name of the death rate parameter.

  • birth_state (str) – State were births take place. Defaults to the first state of model.

Returns

A new model with the extended dynamics.

Return type

Model

comod.community module

class comod.community.CommunityModel(base_model, communities, topology=None, exchange_term='m', equal_parameters=False, symmetric_matrix=False, labels=None)[source]

Bases: comod.base.Model

comod.data module

comod.data.fetch_JHU_daily(date_start, date_end, countries=None, columns=None, progress=True)[source]

Fetch a Dataframe with data from JHU CSSE COVID-19 Data.

The full repository name is COVID-19 Data Repository by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University.

Cf. https://github.com/CSSEGISandData/COVID-19 for license and terms of use.

Parameters

  • date_start (str) – Start date in ISO format (e.g., 2021-01-31).

  • date_end (str) – End date in ISO format.

  • countries (None, str or list of str) – If provided, list of countries to keep.

  • columns (None or list of str) – If provided, lists of columns to use.

  • progress (bool) – Whether to diplay a progress bar.

Returns

A dataframe with the information.

Return type

pd.DataFrame

comod.data.get_population_data()[source]

Get a series mapping countries to their population

comod.data.get_spain_population_data()[source]

Get a series mapping Spanish Autonomous communities to their population

comod.data.iter_JHU_daily(date_start, date_end, countries=None, columns=None)[source]
comod.data.tqdm(arg, *args, **kwargs)[source]

comod.models module

Module contents

comod - Compartment model Python package