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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 63 we list the main sections that are common to many Script File Formats.

Table 63 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
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