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.

Table 68 Common Script Sections
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

Documentation