ziggie 0.1.1
Infectious disease modelling package
Requires Python: >=3.5

# Ziggie macro modelling

Ziggie is a Python package for infectious disease modelling.

The macro module facilitates compartmental modelling using difference equations,
or macro models.

## Quick start

Ziggie requires Python 3.5 or later.

First install it:

```bash
pip install ziggie
```

Here's Python code to create and run a simple SIR model

```Python
from ziggie import macro

# Simple SIR model with susceptible population of 1 million and
# one infection. Effective contact rate per day is 0.6 and the
# infection duration is ten days.

simple = {
    'name': 'Simple model',
    'compartments': {
        'S': 1000000, # Susceptible
        'I': 1,       # Infectious
        'R': 0        # Recovered
    },
    'transitions': {
        # (sometimes called beta in the literature)
        'S_I': 0.6, # Effective contact rate
        'I_R': 0.1  # Recovery rate per day
    },
}

# Make a list of outputs with the results
# which by default are printed out every 50 days and
# at the beginning and end of the simulation.
# Each entry in the results table is an updated model
# For a particular day.
results = macro.simulate([simple])
print("Final day's results")
print(results[-1])

# Flatten the final day's results into a table
table = macro.modelList_to_table(results[-1])
print("Time series table")
print(table)

# Put all the results into a CSV file
macro.series_to_csv(results, "my_csv_file.csv")

# Run model and create CSV in one step
macro.series_to_csv(macro.simulate([simple]), "my_csv_file.csv")

```

The output is:

```Python
Final day's results
[{'name': 'Simple model', 'compartments': {'S': 65525.67886409458, 'I': 1.5383929100326267e-07, 'R': 56934475.32113576}, 'transitions': {'S_I': 0.6, 'I_R': 0.1}, 'parameters': {'from': 0, 'to': 365, 'record_frequency': 50, 'reduce_infectivity': 1.0, 'asymptomatic_infectiousness': 1.0, 'treatment_infectiousness': 1.0, 'noise': 0.0, 'discrete': False, 'record_first': True, 'record_last': True, 'transition_funcs': {'S_I': <function delta_S_I at 0x7fa842cdb8b0>, 'S_E': <function delta_S_I at 0x7fa842cdb8b0>, 'S_I1': <function delta_S_I1 at 0x7fa84651e5e0>, 'S_E1': <function delta_S_I1 at 0x7fa84651e5e0>, 'B_S': <function delta_birth_X at 0x7fa84651e3a0>, 'default': <function delta_X_Y at 0x7fa846519310>}, 'before_funcs': [], 'after_funcs': []}, 'iteration': 365}]
Time series table
[['iter', 'name_0', 'S', 'I', 'R'], [0, 'Simple model', 57000000, 1, 0], [50, 'Simple model', 2200495.449318898, 28345727.9672264, 26453777.583454713], [100, 'Simple model', 66701.56917131442, 167716.11455651774, 56765583.316272154], [150, 'Simple model', 65531.91780545574, 898.2457754223102, 56933570.83641911], [200, 'Simple model', 65525.71227208052, 4.810125157065176, 56934470.477602795], [250, 'Simple model', 65525.67904299378, 0.025758303410947692, 56934475.29519872], [300, 'Simple model', 65525.67886505151, 0.00013793615973905623, 56934475.32099703], [350, 'Simple model', 65525.67886409864, 7.38650518227673e-07, 56934475.32113517], [365, 'Simple model', 65525.67886409458, 1.5383929100326267e-07, 56934475.32113576]]
```

You can also open one of the generated CSV files in your favourite spreadsheet program.

It's also easy to use with numpy. In the above example the table variable
consists of string and floats. Numpy arrays really only make sense if they're
numbers, so we'll chop off the strings before conversion.. Here's a continuation
of the above example:

```Python
import numpy

table_float = [t[2:] for t in table[1:]]
print(numpy.array(table_float))

```

The output should be:

```Python
array([[5.70000000e+07, 1.00000000e+00, 0.00000000e+00],
       [2.20049545e+06, 2.83457280e+07, 2.64537776e+07],
       [6.67015692e+04, 1.67716115e+05, 5.67655833e+07],
       [6.55319178e+04, 8.98245775e+02, 5.69335708e+07],
       [6.55257123e+04, 4.81012516e+00, 5.69344705e+07],
       [6.55256790e+04, 2.57583034e-02, 5.69344753e+07],
       [6.55256789e+04, 1.37936160e-04, 5.69344753e+07],
       [6.55256789e+04, 7.38650518e-07, 5.69344753e+07],
       [6.55256789e+04, 1.53839291e-07, 5.69344753e+07]])
```

## Transitions

A transition name consists of two compartment names separated by an
underscore. There are default transition functions, depending on the
compartments involved, which you can override by including a 'parameters'
dictionary in your model, and then overriding entries in its 'transition_funcs' sub-dictionary.

This is what the default *transition_funcs* dictionary looks like:

```Python
    'transition_funcs': {
        'S_I': delta_S_I,
        'S_E': delta_S_I,
        'S_I1': delta_S_I1,
        'S_E1': delta_S_I1,
        'B_S': delta_birth_X,
        'default': delta_X_Y
    }
```

The transition function to execute is looked up in this dictionary. If it's not
found the function specified by 'default' is executed.

For most transitions, a proportion of the "from" compartment is moved
to the "to" compartment. The delta_X_Y function takes care of this.

But for new infections you almost always want a standard SIR-like equation such
as this:

delta = susceptibles * number of contacts per iteration *
                       risk of infection per contact *
                       total number of infectious individuals /
                       total population

susceptibles -= delta
infectious (or exposed) individuals += delta

Two functions are provided to deal with this: the very simple delta_S_I
and the more sophisticated (but slower) delta_S_I1.

The delta_SI1 calculates the total number of infectious individuals by adding
all the compartments starting with an *I* as well as all compartments starting
with an *A* (asymptomatic individuals) and *T* (treated individuals). Moreover
the infectiousness of the asymptomatic individuals is multiplied by the
parameter *asymptomatic_infectiousness* and the infectiousness of treated
individuals by *treatment_infectiousness* (both default to 1).

## Compartment names which have meaning

Some of the compartment name prefixes are meaningful, in that the code might
make assumptions about the compartment. A compartment name generally starts with
one of these meaningful prefixes and then a unique identifier. E.g. I1, I2, I3
or I4 for various stages of infectiousness.

- S - Susceptible  (See delta_S_I and delta_S_I1)
- E - Exposed  (See delta_S_I and delta_S_I1)
- I - Infectious (See delta_S_I and delta_S_I1)
- A - Asymptomatic (See delta_S_I1 and asymptomatic_infectiousness)
- T - On treatment (See delta_S_I1 and treatment_infectiousness)
- N - Population size. Strictly reserved. Do not prefix any compartment N.
- D - Dead (not included in totalling N)
- B - Birth (not included in totalling N)
- R - Recovered
- M - Maternal immunity
- V - Vaccinated

You can also prefix a compartment name with any other letter.

## Noise

You can also add noise to your model so that it is stochastic. We add a
'parameters' key to our model, and within the parameters, we add a 'noise'
key. Like so:

```Python
 {
    'name': 'Simple model',
    'compartments': {
        'S': 57000000,
        'I': 1,
        'R': 0
    },
    'transitions': {
        'S_I': 0.6,
        'I_R': 0.1
    },
    'parameters': {
        'noise': 0.05
    }
}
```

Now every transition calculation is multipled by a uniform random number in the
range [1-0.05, 1+0.05].

## Parameters

Besides 'noise' there are many other parameters that can be modified
directly. These are the default parameters:

```Python
{
    # The model is executed from iteration 'from' to iteration 'to' - 1.
    'from': 0,
    'to': 365,
    # The results are recorded every 'record_frequency' iterations. Set
    # to 1 if you want to record the output of every iteration.
    'record_frequency': 50,  # Write results every X iterations
    # Multiply S_E or S_I by X every iteration if reduce_infectivity
    # function executed. This is useful for modelling heterogeneity, i.e. the
    # fact that usually the most susceptible people get infected earliest in an
    # epidemic
    'reduce_infectivity': 1.0,
    # If you have multiple infectiousness compartments including
    # asymptomatic and treatment compartments, you can
    'asymptomatic_infectiousness': 1.0,
    'treatment_infectiousness': 1.0,
    # Add stochastic noise to transitions
    'noise': 0.0,
    # Round all transition calculations to round numbers (not tested yet)
    'discrete': False,
    # Include the initial state of the model in the results
    'record_first': True,
    # Include the final state of the model in the results.
    # If record_frequency is 1 or divides into the "to" parameter,
    # you probably want to set this to False.
    'record_last': True,
    # The transition functions
    'transition_funcs': {
        'S_I': delta_S_I,
        'S_E': delta_S_I,
        'S_I1': delta_S_I1,
        'S_E1': delta_S_I1,
        'B_S': delta_birth_X,
        'default': delta_X_Y
    },
    # Any functions specified here are executed for each model before
    # each iteration
    'before_funcs': [],
    # Any functions specified here are executed for each model after
    # each iteration
    'after_funcs': [],
}
```

## More sophisticated example

Let's say we want to model the Covid-19 epidemic in South Africa.

Our model world might like this:

- We have three distinct geographies: (1) urban areas with formal housing (2)
  urban areas with informal housing and (3) rural areas.
- Each area has three distinct age groups: (1) 0-24 years old, (2) 25-54, and
  (3) 55 and older.
- People start off (S)usceptible. Upon being infected they are (E)xposed. They
  transition from (E)xposed to either (A)symptomatic or infectious with mild
  symptoms(Im). Asymptomatic people transition to (R)ecovered. Infectious with
  mild symptoms transition to infectious with critical symptoms (Ic) and then
  either to (R)ecovered or (D)eath.
- After each iteration, there is a bit of migration between the three
  geographies.

The source code file ziggie/samples.py contains a class called MacroModels
which contains a method called corona that implements this. Here it is:

```Python
from copy import deepcopy
from ziggie import macro

def corona(self):
    parameters = {
        'to': 365,
        'record_frequency': 1,
        'record_last': False,
        'noise': 0.1,
        'asymptomatic_infectiousness': 0.75,
        'reduce_infectivity': 0.999,
        'after_funcs': [macro.reduce_infectivity, ],
        'transition_funcs': {
            'S_E': macro.delta_S_I1,
        }
    }

    parameters_rural = deepcopy(parameters)
    parameters_rural['after_funcs'] = [macro.reduce_infectivity,
                                       mix_models, ]
    return [
        {
            'name': 'Urban informal',
            'parameters': parameters,
            'transitions': {
                'S_E': 0.4,
                'E_A': 0.125,
                'E_Im': 0.125,
                'Im_Ic': 0.2,
                'Ic_R': 0.2,
                'A_R': 0.2
            },
            'groups': [
                {
                    'name': '0-24',
                    'transitions': {
                        'E_A': 0.25,
                        'E_Im': 0.01,
                        'Ic_D': 0.002
                    },
                    'compartments': {
                        'S': 2100000,
                        'E': 10,
                        'Im': 0,
                        'Ic': 0,
                        'A': 0,
                        'R': 0,
                        'D': 0
                    }
                },
                {
                    'name': '25-54',
                    'transitions': {
                        'Ic_D': 0.0032
                    },
                    'compartments': {
                        'S': 2100000,
                        'E': 0,
                        'Im': 0,
                        'Ic': 0,
                        'A': 0,
                        'R': 0,
                        'D': 0
                    }
                },
                {
                    'name': '55-',
                    'transitions': {
                        'Ic_D': 0.032
                    },
                    'compartments': {
                        'S': 600000,
                        'E': 0,
                        'Im': 0,
                        'Ic': 0,
                        'A': 0,
                        'R': 0,
                        'D': 0
                    }
                }
            ]
        },
        {
            'name': 'Urban formal',
            'parameters': parameters,
            'transitions': {
                'S_E': 0.3,
                'E_A': 0.125,
                'E_Im': 0.125,
                'Im_Ic': 0.2,
                'Ic_R': 0.2,
                'A_R': 0.2
            },
            'groups': [
                {
                    'name': '0-24',
                    'transitions': {
                        'E_A': 0.25,
                        'E_Im': 0.01,
                        'Ic_D': 0.002
                    },
                    'compartments': {
                        'S': 16940000,
                        'E': 10,
                        'Im': 0,
                        'Ic': 0,
                        'A': 0,
                        'R': 0,
                        'D': 0
                    }
                },
                {
                    'name': '25-54',
                    'transitions': {
                        'Ic_D': 0.003
                    },
                    'compartments': {
                        'S': 16940000,
                        'E': 0,
                        'Im': 0,
                        'Ic': 0,
                        'A': 0,
                        'R': 0,
                        'D': 0
                    }
                },
                {
                    'name': '55-',
                    'transitions': {
                        'Ic_D': 0.03
                    },
                    'compartments': {
                        'S': 4620000,
                        'E': 0,
                        'Im': 0,
                        'Ic': 0,
                        'A': 0,
                        'R': 0,
                        'D': 0
                    }
                }
            ]
        },
        {
            'name': 'Rural',
            'parameters': parameters_rural,
            'transitions': {
                'S_E': 0.27,
                'E_A': 0.125,
                'E_Im': 0.125,
                'Im_Ic': 0.2,
                'Ic_R': 0.2,
                'A_R': 0.2
            },
            'groups': [
                {
                    'name': '0-24',
                    'transitions': {
                        'E_A': 0.25,
                        'E_Im': 0.01,
                        'Ic_D': 0.002
                    },
                    'compartments': {
                        'S': 7260000,
                        'E': 10,
                        'Im': 0,
                        'Ic': 0,
                        'A': 0,
                        'R': 0,
                        'D': 0
                    }
                },
                {
                    'name': '25-54',
                    'transitions': {
                        'Ic_D': 0.0035
                    },
                    'compartments': {
                        'S': 7260000,
                        'E': 0,
                        'Im': 0,
                        'Ic': 0,
                        'A': 0,
                        'R': 0,
                        'D': 0
                    }
                },
                {
                    'name': '55-',
                    'transitions': {
                        'Ic_D': 0.035
                    },
                    'compartments': {
                        'S': 2000000,
                        'E': 0,
                        'Im': 0,
                        'Ic': 0,
                        'A': 0,
                        'R': 0,
                        'D': 0
                    }
                }

            ]
        }
    ]

m = corona()
results = macro.simulate(m)
print("Number of results:", len(results)) # Outputs 366
print("Number of models:", len(results[-1])) # Outputs 3
totals = [macro.calc_totals(results[-1][i])
          for i in range(len(results[-1]))
print(macro.sum_totals(totals))
```

The output is something like this:

```
Number of results: 366
Number of models: 3
{'N': 59685873.7194506, 'S': 47387513.37539025, 'E': 283059.79850507394, 'Im': 108802.85166144818, 'Ic': 106605.46023480814, 'A': 264806.9195997677, 'R': 11535085.314059254, 'D': 134156.28054939664}
```