To run the preprocessing pipeline:
python preprocess.py ../configs/T01/SP/preprocess_T01_SP.cfg
Config file must encode:
| Parameter | Description |
|---|---|
PARAM_SOURCEPATH |
directory where the raw datafile is stored, as a list |
PARAM_TARGETPATH |
directory where results will be stored, as a list |
PARAM_DATAFILE |
the name of the raw datafile |
PARAM_DATAFIELDS |
list with the fields that correspond to region, state, city, date, #newCases, and #newDeaths, using the strings in the header of PARAM_DATAFILE |
PARAM_TERRITORY |
list of areas that compose the territory under analysis (i.e., territorial units) |
PARAM_POPSIZES |
dictionary of population sizes per territorial unit |
PARAM_OUTCOMES |
list of (p, mu, rsd) tuples, with p as the share of cases with some outcome category (e.g., cases with mild to moderate progression), mu is the mean recovery time of cases (in days), and rsd is the relative standard deviation of recovery time |
PARAM_MA_WINDOW |
the number of days to consider in the moving average of new cases and deaths |
PARAM_CORE_MODEL |
Peddireddy of IB-forward. See comments in ./code/sharedDefs.py/createBoL(...) |
PARAM_MASK_ERRORS |
If True, adjustments in the R(t) estimator to avoid negative values will be performed |
Several UTF-8, flat files with tab-separated fields are created:
| File | Description |
|---|---|
daily_changes.csv |
File with daily changes of the variables of interest, namely ∆S(t), ∆C(t), ∆I(t), ∆R(t), and ∆D(t) |
surveillance.csv |
File with daily status of the variables of interest, namely S(t), C(t), I(t), R(t), and D(t) |
violations.csv |
File listing the violations of quality criteria for the generated data. See criteria in ./code/sharedDefs.py/playBoL(...) |
roulette.csv |
File describing the roulette employed to assign the recovery time to an arbitrary case |
The resulting data can be visualised with Excel; a template is available at ./assets/Helper_SP.xlsx