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# Infectious-Disease-Modeling
A project to model infectious diseases with the SIR model and variations.
## Usage
For SARS in Hong Kong use
`./solver2.py --country=Hong_Kong --popcountry=20000 --initial=1000 --disease=SARS --start=4/10/03 --mode={SIR,Linear,ESIR,SEIR}`
For COVID-19 in the US use
`./solver2.py --popcountry=3000000 --initial=100 --mode={SIR,Linear,ESIR,SEIR}`
General usage:
```
usage: solver2.py [-h] [--mode {SIR,Linear,ESIR,SEIR}]
[--data [{Actual,S,I,R,E} [{Actual,S,I,R,E} ...]]]
[--folder FOLDER] [--disease DISEASE] [--out OUT]
[--start START] [--end END] [--incubation INCUBATION_PERIOD]
[--predict PREDICTION_RANGE] [--country COUNTRY]
[--popcountry POPCOUNTRY] [--popmodel POPMODEL]
[--initial INITIAL]
optional arguments:
-h, --help show this help message and exit
--mode {SIR,Linear,ESIR,SEIR}, -m {SIR,Linear,ESIR,SEIR}
change the mode of the model (SIR, Linear, ESIR,
SEIR); default: SIR
--data [{Actual,S,I,R,E} [{Actual,S,I,R,E} ...]], -d [{Actual,S,I,R,E} [{Actual,S,I,R,E} ...]]
change the type of data to present in the graph
(Actual, S, I, R, E); default: Actual S I R
--folder FOLDER, -f FOLDER
the folder in which to find the data files; defaults
to looking in the data folder
--disease DISEASE, -D DISEASE
the disease to model; defaults to COVID-19
--out OUT, -o OUT the name of the graph and csv files; defaults to the
name of the disease
--start START, -s START
the date where the data starts (defaults to the start
date of COVID-19 (1/22/20))
--end END, -e END the date where the data stops (defaults to whereever
the input data ends)
--incubation INCUBATION_PERIOD, -i INCUBATION_PERIOD
the incubation period of the disease (only applicable
if using SIRE model; ignored otherwise); none by
default
--predict PREDICTION_RANGE, -p PREDICTION_RANGE
the number of days to predict the course of the
disease (defaults to None, meaning the model will not
predict beyond the given data)
--country COUNTRY, -c COUNTRY
the country that is being modeled (defaults to US)
--popcountry POPCOUNTRY, -pc POPCOUNTRY
the population of the country (defaults to US
population)
--popmodel POPMODEL, -pm POPMODEL
the population of the model (defaults to 10000)
--initial INITIAL, -I INITIAL
initial infected people (defaults to 1)
```
## Credits
Original code by [JasonXu314](https://github.com/JasonXu314/covid-19-project/) and [Lewuathe](https://github.com/Lewuathe/COVID19-SIR)
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