Getting Started in Python¶
Prerequisites¶
First, you need to start an interactive Python session using a Python
interpreter with which MetaWards has been installed. To make this easier,
MetaWards comes with two applications; metawards-python and
metawards-jupyter, that will start an interative python or jupyter
session using the python interpreter used by MetaWards.
To start this, e.g. running a jupyter notebook, type;
metawards-jupyter notebook
This should open a Jupyter notebook session in your browser. In here, click “New” to start a new Python3 notebook, and then type the commands for MetaWards below in the Jupyter cells.
You will also need to import pandas, as we will use this for analysing and plotting the results.
>>> import pandas as pd
Importing metawards¶
First we need to import the metawards Python module. To do this
we just need to type;
>>> import metawards as mw
The module comes with lots of help documentation, so feel free to use that and tab-completion to explore the module.
Creating the disease¶
You should now be in a Jupyter notebook (or ipython session) and have
imported metawards.
To run a simulation you need to define the Disease
that you want to model. MetaWards implements a SEIR-style model, but
you have complete control to define as many (or few) stages as you wish.
First, we will create a disease, which we will call lurgy, that
will consist of four stages: S, E, I and R. To do this, let’s create
the disease;
>>> lurgy = mw.Disease(name="lurgy")
Next, we will add each stage. You don’t define the “S” stage, as the model starts with a set of susceptible individuals by default. Instead, we need to add in the E, I and R stages.
First, lets add the latent (“E”) stage. Latent individuals are not
infectious, and so we will set beta (the infectivity parameter) to 0.0.
Individuals will progress quickly through this stage, so we will set
progress to 0.5, meaning that 50% of individuals move to
the next stage each day.
>>> lurgy.add("E", beta=0.0, progress=0.5)
Next we will add the infectious (“I”) stage. This will have a high beta
value (0.8), but a lower progress (0.25) as we will model this as a
disease with a long symptomatic period.
>>> lurgy.add("I", beta=0.8, progress=0.25)
Finally, we need to add the recovered (“R”) stage. We don’t need to set the
beta or progress values, as MetaWards will automatically recognise
this as the recovered state, and will set beta to 0 and progress
to 0 automatically.
>>> lurgy.add("R")
You can should print this disease to the screen to confirm that everything has been correctly set.
>>> print(lurgy)
* Disease: lurgy
* stage: ['E', 'I', 'R']
* mapping: ['E', 'I', 'R']
* beta: [0, 0.8, 0]
* progress: [0.5, 0.25, 0]
* too_ill_to_move: [0, 0, 0]
* start_symptom: 2
Note
You can save this disease to a file using
lurgy.to_json("lurgy.json.bz2"), and then load it back
using lurgy = metawards.Disease.from_json("lurgy.json.bz2")
Creating the wards (network)¶
Next, you need to define the wards (network) that will contain the individuals who will experience the model outbreak.
We will first start with a single ward, called home.
>>> home = mw.Ward(name="home")
MetaWards works by assigning individuals as either workers or players. The difference is that workers make fixed (predictable) movements between different wards each day, while players make random movements. Since we have just a single ward, we will start by populating it with 10,000 players.
>>> home.set_num_players(10000)
>>> print(home)
Ward( info=home, num_workers=0, num_players=10000 )
Note
You can save this Ward to a file using
home.to_json("home.json.bz2"), and then load it back
using home = metawards.Ward.from_json("home.json.bz2")
Running the model¶
Now we have a disease and a network, we can now model an outbreak. To do this,
we will use the metawards.run() function.
>>> results = metawards.run(model=home, disease=lurgy)
This will print a lot to the screen. The key lines are these;
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 0 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 10000 E: 0 I: 0 R: 0 IW: 0 POPULATION: 10000
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 1 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 10000 E: 0 I: 0 R: 0 IW: 0 POPULATION: 10000
Number of infections: 0
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 2 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 10000 E: 0 I: 0 R: 0 IW: 0 POPULATION: 10000
Number of infections: 0
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 3 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 10000 E: 0 I: 0 R: 0 IW: 0 POPULATION: 10000
Number of infections: 0
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 4 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 10000 E: 0 I: 0 R: 0 IW: 0 POPULATION: 10000
Number of infections: 0
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 5 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 10000 E: 0 I: 0 R: 0 IW: 0 POPULATION: 10000
Number of infections: 0
Ending on day 5
This shows the number of people in the different stages of the outbreak. In this case, there was no infection seeded, and so the number of infections remained zero.
Seeding the outbreak¶
We need to seed the outbreak with some additional seeds. We do this using
the additional option. This can be very powerful (e.g. adding seeds
at different days, different wards etc.), but at its simplest, it is
just the number of initial infections on the first day in the first
ward. We will start with 100 initial infections;
>>> results = metawards.run(model=home, disease=lurgy, additional=100)
Now you get a lot more output, e.g. for me the outbreak runs for 75 days.
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 70 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 423 E: 0 I: 1 R: 9576 IW: 0 POPULATION: 10000
Number of infections: 1
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 71 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 423 E: 0 I: 1 R: 9576 IW: 0 POPULATION: 10000
Number of infections: 1
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 72 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 423 E: 0 I: 1 R: 9576 IW: 0 POPULATION: 10000
Number of infections: 1
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 73 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 423 E: 0 I: 1 R: 9576 IW: 0 POPULATION: 10000
Number of infections: 1
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 74 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 423 E: 0 I: 1 R: 9576 IW: 0 POPULATION: 10000
Number of infections: 1
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 75 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 423 E: 0 I: 0 R: 9577 IW: 0 POPULATION: 10000
Number of infections: 0
Ending on day 75
Visualising the results¶
The output results contains the filename of a csv file that contains
the S, E, I and R data (amongst other things). You can load and plot this
using standard R commands, e.g.
>>> df = pd.read_csv(results)
>>> print(df)
fingerprint repeat day date S E I R IW SCALE_UV
0 REPEAT 1 0 2020-07-21 10000 0 0 0 0 1.0
1 REPEAT 1 1 2020-07-22 9900 76 24 0 1 1.0
2 REPEAT 1 2 2020-07-23 9878 79 39 4 1 1.0
3 REPEAT 1 3 2020-07-24 9840 95 49 16 1 1.0
4 REPEAT 1 4 2020-07-25 9800 111 59 30 1 1.0
.. ... ... ... ... ... ... .. ... .. ...
103 REPEAT 1 103 2020-11-01 511 0 1 9488 0 1.0
104 REPEAT 1 104 2020-11-02 511 0 1 9488 0 1.0
105 REPEAT 1 105 2020-11-03 511 0 1 9488 0 1.0
106 REPEAT 1 106 2020-11-04 511 0 1 9488 0 1.0
107 REPEAT 1 107 2020-11-05 511 0 0 9489 0 1.0
[108 rows x 10 columns]
We can visualise the data using;
>>> df.plot.line(x="day", y=["S","E","I","R"])
The result should look something like this;
Complete code¶
The complete Python code for this part of the getting started guide is re-copied below;
# import the required modules
import pandas as pd
import metawards as mw
# create the disease
lurgy = mw.Disease(name="lurgy")
lurgy.add("E", beta=0.0, progress=0.25)
lurgy.add("I", beta=0.8, progress=0.25)
lurgy.add("R")
# create the wards network
home = mw.Ward(name="home")
home.set_num_players(10000)
# run the model
results = metawards.run(model=home, disease=lurgy, additional=100)
# load and graph the results
df = pd.read_csv(results)
df.plot.line(x="day", y=["S","E","I","R"])