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Script File Formats

The PoPy script formats are shown in Table 62:-

Table 62 Script Format
Name Purpose Child Scripts
fit Fit a model to data grph/sim/msim/fitsum
gen Generate data from a model grph/sim/gensum
sim Simulate PK/PD curves grph
tut Gen data and fit + compare grph/fit/comp/tutsum
comp Compare gen and fit results none
mfit Fit a model to multiple data sets none
mgen Generate multiple data from a model none
msim Simulate multiple PK/PD curves vpc
mtut Gen multiple data and fit + compare mgen/mfit/mcomp
mcomp Compare mgen and mfit results none
grph Plot graphs none
vpc Plot VPCs none
fitsum HTML summary of fit results none
gensum HTML summary of gen results none
tutsum HTML summary of tut results none
n2pdat converts Nonmem to PoPy data none
p2ndat converts PoPy to Nonmem data none

A PoPy script file is a text file that defines how PoPy works with a PK/PD model. Each configuration file typically has a ‘.pyml’ file extension. The file suffix .pyml stands for PoPy YAML format.

To run a PoPy command on a particular script, Open a PoPy Command Prompt in the directory containing the script file and type:-

$ popy_XXXX YYYY.pyml

Where XXXX is one of the Command Line Tools, such as ‘run’, ‘create’, ‘check’ or ‘format’. And YYYY.pyml is the file name of the script itself. For example:-

$ popy_run my_fit_file.pyml

for running a script to fit PK/PD parameters to a pre-existing data set, or:-

$ popy_create gen my_gen_file.pyml

for creating a new script file that will generate synthetic PK/PD data.

PoPy will first parse the script to check it is in the correct format. If so, PoPy will then process the script.

A PoPy script file can be one of multiple formats, as specified at the start of each script, in METHOD_OPTIONS. For example a Fit Script starts with:-

METHOD_OPTIONS: {py_module: fit}

And a Gen Script starts with:-

METHOD_OPTIONS: {py_module: gen}
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