Script File Sections¶
A PoPy script file is hierarchical and based on YAML.
The file is indented with the main sections defined at the start of a line. Subsections are indented within the main sections.
In Table 68 we list the main sections that are common to many Script File Formats.
| Section | Purpose |
|---|---|
| METHOD_OPTIONS | Script type and run options |
| PARALLEL | Speed up processing by running in parallel |
| DESCRIPTION | Title and summary of model |
| FILE_PATHS | Paths to load and output data |
| DATA_FIELDS | Define type/id/time fields for data |
| PREPROCESS | Filter or expand the input data |
| EFFECTS | Define population f[X] and r[X] variable structure |
| MODEL_PARAMS | Define m[X] for each data row, given f[X], r[X] and c[X] |
| STATES | Define initial value s[X], given m[X] and c[X] |
| DERIVATIVES | Define d[X] wrt time, given m[X], c[X] and s[X] |
| PREDICTIONS | Define p[X] for each data row, given m[X], c[X] and s[X] |
| POSTPROCESS | Filter or expand the generated data |
| ODE_SOLVER | Define ordinary differential equation method and parameters |
| FIT_METHODS | Define fit methods and parameters |
| COVARIANCE | Define a method for computing standard errors |
| OUTPUT_SCRIPTS | Declare child scripts for post processing |
| OUTPUT_OPTIONS | Miscellaneous output parameters |