Named Disease Stages¶
In the last section you learned how to use demographics with different
disease stages to model hospital and ICU admissions. While this worked,
the calculation of statistics from the simulation was slightly hacky,
as the disease stages were still labelled E, I and R, when
we really wanted to refer to them as H1, H2 etc.
Fortunately, metawards supports custom naming of disease stages.
You can do this by adding a stage field to the disease file.
Simple example¶
For example, here is a simple disease file that uses stages A,
B and C. Please create the file named.json and copy in the
below;
{
"stage" : [ "A", "B", "C" ],
"beta" : [ 0.0, 0.5, 0.0 ],
"progress" : [ 1.0, 1.0, 0.0 ],
"too_ill_to_move" : [ 0.0, 0.0, 0.0 ],
"contrib_foi" : [ 1.0, 1.0, 0.0 ],
"start_symptom" : 1
}
Note
Note that we’ve not included the name, author or other metadata
fields as these are not needed for this simple example. These are optional
fields. We recommend you include them when you want to publish a disease
file.
This file defines three disease stages, called A, B and C.
The first stage (A) is not infectious, as beta["A"] is 0.0.
The infectious stage is B, as beta["B"] is 0.5. The final
stage is C, which is not infectious, and is where the disease ends
(progress["C"] is 0.0).
Run metawards using this disease file via;
metawards -a ExtraSeedsLondon.dat -d named.json --nsteps 20
You should see output similar to;
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 0 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Loading additional seeds from /Users/chris/GitHub/MetaWardsData/extra_seeds/ExtraSeedsLondon.dat
(1, 255, 5, None)
S: 56082077 A: 0 B: 0 C: 0 IW: 0 POPULATION: 56082077
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 1 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
seeding play_infections[0][255] += 5
S: 56082072 A: 0 B: 5 C: 0 IW: 0 POPULATION: 56082077
Number of infections: 5
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 2 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082067 A: 5 B: 0 C: 5 IW: 2 POPULATION: 56082077
Number of infections: 10
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 3 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082067 A: 0 B: 5 C: 5 IW: 0 POPULATION: 56082077
Number of infections: 10
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 4 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082063 A: 4 B: 0 C: 10 IW: 3 POPULATION: 56082077
Number of infections: 14
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 5 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082063 A: 0 B: 4 C: 10 IW: 0 POPULATION: 56082077
Number of infections: 14
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 6 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082062 A: 1 B: 0 C: 14 IW: 1 POPULATION: 56082077
Number of infections: 15
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 7 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082062 A: 0 B: 1 C: 14 IW: 0 POPULATION: 56082077
Number of infections: 15
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 8 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082062 A: 0 B: 0 C: 15 IW: 0 POPULATION: 56082077
Number of infections: 15
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 9 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082062 A: 0 B: 0 C: 15 IW: 0 POPULATION: 56082077
Number of infections: 15
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 10 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082062 A: 0 B: 0 C: 15 IW: 0 POPULATION: 56082077
Number of infections: 15
Note
Note that the simulation gets stuck in the C state. This is because
any individual who is not in S or R is counted as an infection,
and so the 15 individuals in C are counted as infecteds. To prevent
the model running forever we set the maximum number of days to
20 via --nsteps 20.
As you can see, the output now records movement from S to A, B
and then C. This data is also recorded in the output files, e.g.
>> import pandas as pd
>> df = pd.read_csv("output/results.csv.bz2")
>> df.head()
fingerprint repeat day date S E I A B C R IW UV
0 REPEAT 1 0 2020-06-23 56082077 0 0 0 0 0 0 0 1.0
1 REPEAT 1 1 2020-06-24 56082072 0 0 0 5 0 0 0 1.0
2 REPEAT 1 2 2020-06-25 56082067 0 0 5 0 5 0 2 1.0
3 REPEAT 1 3 2020-06-26 56082067 0 0 0 5 5 0 0 1.0
4 REPEAT 1 4 2020-06-27 56082063 0 0 4 0 10 0 3 1.0
>> df = pd.read_csv("output/trajectory.csv.bz2")
>> df.head()
day date demographic S E I A B C R IW
0 0 2020-06-23 overall 56082077 0 0 0 0 0 0 0
1 1 2020-06-24 overall 56082072 0 0 0 5 0 0 0
2 2 2020-06-25 overall 56082067 0 0 5 0 5 0 2
3 3 2020-06-26 overall 56082067 0 0 0 5 5 0 0
4 4 2020-06-27 overall 56082063 0 0 4 0 10 0 3
Additional columns have been added to the tables in these files for the
A, B and C states.
Sub-stages example¶
You can have multiple named sub-stages of each stage, e.g. instead of
having a single infectious B stage, you can have B1, B2 and
B3. The totals reported for a the B stage will be the sum of
the number of individuals in each sub-stage. For example, edit
named.json to read;
{
"stage" : [ "A", "B1", "B2", "B3", "C" ],
"beta" : [ 0.0, 0.2, 0.8, 0.1, 0.0 ],
"progress" : [ 1.0, 1.0, 1.0, 1.0, 0.0 ],
"too_ill_to_move" : [ 0.0, 0.0, 0.2, 0.8, 0.0 ],
"contrib_foi" : [ 1.0, 1.0, 1.0, 1.0, 0.0 ],
"start_symptom" : 1
}
Here we’ve expanded the B stage into three infectious sub-stages
(B1, B2 and B3), similar to the three stages of the lurgy.
Run metawards using this disease file via;
metawards -a ExtraSeedsLondon.dat -d named.json --nsteps 20
You should see in the output that the population of A, B and C
are summarised, e.g.
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 0 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Loading additional seeds from /Users/chris/GitHub/MetaWardsData/extra_seeds/ExtraSeedsLondon.dat
(1, 255, 5, None)
S: 56082077 A: 0 B: 0 C: 0 IW: 0 POPULATION: 56082077
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 1 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
seeding play_infections[0][255] += 5
S: 56082072 A: 0 B: 5 C: 0 IW: 0 POPULATION: 56082077
Number of infections: 5
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 2 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082071 A: 1 B: 5 C: 0 IW: 1 POPULATION: 56082077
Number of infections: 6
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 3 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082067 A: 4 B: 6 C: 0 IW: 4 POPULATION: 56082077
Number of infections: 10
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 4 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082066 A: 1 B: 5 C: 5 IW: 1 POPULATION: 56082077
Number of infections: 11
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 5 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082064 A: 2 B: 6 C: 5 IW: 2 POPULATION: 56082077
Number of infections: 13
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 6 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082060 A: 4 B: 7 C: 6 IW: 4 POPULATION: 56082077
Number of infections: 17
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 7 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082058 A: 2 B: 7 C: 10 IW: 2 POPULATION: 56082077
Number of infections: 19
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 8 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082053 A: 5 B: 8 C: 11 IW: 4 POPULATION: 56082077
Number of infections: 24
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 9 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082053 A: 0 B: 11 C: 13 IW: 0 POPULATION: 56082077
Number of infections: 24
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 10 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082049 A: 4 B: 7 C: 17 IW: 4 POPULATION: 56082077
Number of infections: 28
These are also summarised in the output/results.csv.bz2 and
output/trajectory.csv.bz2 files.
However, the actual populations in each individual stage are given in the
play_infections.csv.bz2 (play infections), work_infections.csv.bz2
(work infections) and number_infected_wards.csv.bz2 (number of infected
wards) files, e.g.
>>> import pandas as pd
>>> df = pd.read_csv("output/total_infections.csv.bz2")
>>> df.head()
day A B1 B2 B3 C
0 1 0 5 0 0 0
1 2 1 0 5 0 0
2 3 4 1 0 5 0
3 4 1 4 1 0 5
4 5 2 1 4 1 5
>>> df = pd.read_csv("output/number_infected_wards.csv.bz2")
>>> df.head()
day A B1 B2 B3 C
0 1 0 1 0 0 0
1 2 1 0 1 0 0
2 3 4 1 0 1 0
3 4 1 4 1 0 1
4 5 2 1 4 1 1
These files are very useful if you want to see, e.g. how many workers
are infected at each different stage on each day, or how many wards
have a population infected in the B1 state on each day.
Scanning named stage parameters¶
You can also use the name of a stage when scanning disease parameters.
For example, create a file called scan.dat and copy in the below;
beta["B1"] beta["B2"]
0.2 0.7
0.3 0.8
Hopefully you can see that this will adjust the beta parameters for
the B1 and B2 stages. You can run this file using;
metawards -a ExtraSeedsLondon.dat -d named.json --nsteps 20 -i scan.dat
and should see that the specified variables are indeed scanned, e.g.
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Adjustable parameters to scan ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
• (beta["B1"]=0.2, beta["B2"]=0.7)[repeat 1]
• (beta["B1"]=0.3, beta["B2"]=0.8)[repeat 1]
[...]
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ MULTIPROCESSING ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Computing model run ✔
┌────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
│ │
│ Completed job 1 of 2 │
│ (beta["B1"]=0.2, beta["B2"]=0.7)[repeat 1] │
│ 2020-07-13: DAY: 20 S: 56081987 A: 6 B: 21 C: 63 IW: 6 UV: 1.0 TOTAL POPULATION 56082077 │
│ │
└────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
Computing model run ✔
┌────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
│ │
│ Completed job 2 of 2 │
│ (beta["B1"]=0.3, beta["B2"]=0.8)[repeat 1] │
│ 2020-07-13: DAY: 20 S: 56081794 A: 47 B: 93 C: 143 IW: 43 UV: 1.0 TOTAL POPULATION 56082077 │
│ │
└────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
Mapping stages to summaries¶
By default, the population of a disease sub-stage is summed into a summary
value that has the same name (but missing the sub-stage number). So B1,
B2 and B3 sub-stages will accumulate into the B stage.
You can control this mapping via the mapping value in the disease file.
You can set a disease stage to map to any individual stage (e.g. you could
map B1 to be B1 only), to any grouped stage (e.g. you could map
C to map to the grouped B stage), or to any of the standard mapped
stages (E, I, R or *).
For example, you could output every stage to the summary via;
{
"stage" : [ "A", "B1", "B2", "B3", "C" ],
"mapping" : [ "A", "B1", "B2", "B3", "C" ],
"beta" : [ 0.0, 0.2, 0.8, 0.1, 0.0 ],
"progress" : [ 1.0, 1.0, 1.0, 1.0, 0.0 ],
"too_ill_to_move" : [ 0.0, 0.0, 0.2, 0.8, 0.0 ],
"contrib_foi" : [ 1.0, 1.0, 1.0, 1.0, 0.0 ],
"start_symptom" : 1
}
Running metawards using this file will tell it to output every stage,
e.g.
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 0 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Loading additional seeds from /Users/chris/GitHub/MetaWardsData/extra_seeds/ExtraSeedsLondon.dat
(1, 255, 5, None)
S: 56082077 A: 0 B1: 0 B2: 0 B3: 0 C: 0 IW: 0 POPULATION: 56082077
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 1 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
seeding play_infections[0][255] += 5
S: 56082072 A: 0 B1: 5 B2: 0 B3: 0 C: 0 IW: 0 POPULATION: 56082077
Number of infections: 5
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 2 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082068 A: 4 B1: 0 B2: 5 B3: 0 C: 0 IW: 4 POPULATION: 56082077
Number of infections: 9
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 3 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082064 A: 4 B1: 4 B2: 0 B3: 5 C: 0 IW: 3 POPULATION: 56082077
Number of infections: 13
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 4 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082061 A: 3 B1: 4 B2: 4 B3: 0 C: 5 IW: 3 POPULATION: 56082077
Number of infections: 16
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 5 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082056 A: 5 B1: 3 B2: 4 B3: 4 C: 5 IW: 4 POPULATION: 56082077
Number of infections: 21
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 6 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082046 A: 10 B1: 5 B2: 3 B3: 4 C: 9 IW: 9 POPULATION: 56082077
Number of infections: 31
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 7 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082044 A: 2 B1: 10 B2: 5 B3: 3 C: 13 IW: 2 POPULATION: 56082077
Number of infections: 33
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 8 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082036 A: 8 B1: 2 B2: 10 B3: 5 C: 16 IW: 8 POPULATION: 56082077
Number of infections: 41
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 9 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082018 A: 18 B1: 8 B2: 2 B3: 10 C: 21 IW: 14 POPULATION: 56082077
Number of infections: 59
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 10 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082010 A: 8 B1: 18 B2: 8 B3: 2 C: 31 IW: 8 POPULATION: 56082077
Number of infections: 67
Alternatively, you can map your named stages to standard named accumulators, e.g.
{
"stage" : [ "A", "B1", "B2", "B3", "C" ],
"mapping" : [ "E", "I", "I", "I", "R" ],
"beta" : [ 0.0, 0.2, 0.8, 0.1, 0.0 ],
"progress" : [ 1.0, 1.0, 1.0, 1.0, 0.0 ],
"too_ill_to_move" : [ 0.0, 0.0, 0.2, 0.8, 0.0 ],
"contrib_foi" : [ 1.0, 1.0, 1.0, 1.0, 0.0 ],
"start_symptom" : 1
}
would count A as a latent E stage, B1 to B3 would be
infected I stages, and C would be accumulated as a R stage.
Running with this file would give;
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 0 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Loading additional seeds from /Users/chris/GitHub/MetaWardsData/extra_seeds/ExtraSeedsLondon.dat
(1, 255, 5, None)
S: 56082077 E: 0 I: 0 R: 0 IW: 0 POPULATION: 56082077
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 1 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
seeding play_infections[0][255] += 5
S: 56082072 E: 0 I: 5 R: 0 IW: 0 POPULATION: 56082077
Number of infections: 5
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 2 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082072 E: 0 I: 5 R: 0 IW: 0 POPULATION: 56082077
Number of infections: 5
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 3 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082068 E: 4 I: 5 R: 0 IW: 4 POPULATION: 56082077
Number of infections: 9
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 4 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082068 E: 0 I: 4 R: 5 IW: 0 POPULATION: 56082077
Number of infections: 4
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 5 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082068 E: 0 I: 4 R: 5 IW: 0 POPULATION: 56082077
Number of infections: 4
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 6 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082064 E: 4 I: 4 R: 5 IW: 4 POPULATION: 56082077
Number of infections: 8
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 7 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082064 E: 0 I: 4 R: 9 IW: 0 POPULATION: 56082077
Number of infections: 4
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 8 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082064 E: 0 I: 4 R: 9 IW: 0 POPULATION: 56082077
Number of infections: 4
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 9 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082062 E: 2 I: 4 R: 9 IW: 2 POPULATION: 56082077
Number of infections: 6
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Day 10 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
S: 56082061 E: 1 I: 2 R: 13 IW: 1 POPULATION: 56082077
Number of infections: 3
while the original stage names are still accessible in the
output/total_infections.csv.bz2, output/number_wards_infected.csv.bz2
files etc.
One advantage of doing this is that now, C is correctly interpreted
as an R state, and so metawards will exit correctly once the
outbreak has died out and all individuals are left in S or C.