Script File Formats¶
The PoPy script formats are shown in Table 67:-
| 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}