Occurrence Calibration Data¶
To run the data generation for the incidence/prevalence calibration:
cd LEAP
python3 leap/data_generation/occurrence_calibration_data.py
This will update the file leap/processed_data/asthma_occurrence_correction.csv. This file contains the incidence / prevalence correction parameters and is formatted as follows:
| Column | Type | Description |
|---|---|---|
year |
int
|
format XXXX, e.g 2000, range [2000, 2026]
|
age |
int
|
The age in years, a value in [3, 63]
|
sex |
str
|
"F" = Female,
"M" = Male
|
correction |
float
|
The correction term for the asthma incidence / prevalence equation |
type |
str
|
One of "incidence"
"prevalence"
|
If you want to rerun the optimization for the \(\beta\) parameters, add the flag
--retrain-beta:
cd LEAP
python3 leap/data_generation/occurrence_calibration_data.py --retrain-beta
This will update the file leap/processed_data/asthma_occurrence_correction.csv as described above, and will also update leap/processed_data/occurrence_calibration_parameters.json:
{
"β_fhx_age": 0.6445257,
"β_abx_age": -0.2968535
}
Warning
Rerunning the beta parameters optimization is slow - could take up to 24 hours.