Structure of OUTPUT_SCRIPTS¶

The OUTPUT_SCRIPTS in all Script File Formats share a common format, as follows:-

OUTPUT_SCRIPTS:
    <child_script1>: {output_mode: run}
    <child_script2>: {output_mode: create}
    <child_script3>: {output_mode: none}

The OUTPUT_SCRIPTS section is a dict record. i.e it is a Python dictionary with child script names as keys.

All child script sections share the ‘output_mode’ field, which can take the following values:-

• run - create the child script and run it
• create - create the child script, but do not run it
• none - do not create the child script

Generally if a child script is not mentioned in the parent script the ‘output_mode’ defaults to ‘none’.

The available child scripts are dependent on the parent script type. Also there maybe additional options for each child script, see examples below for more concrete details.

Example OUTPUT_SCRIPTS for tut_script¶

The example below is used in Generate data and Fit using a Two Compartment Model.

OUTPUT_SCRIPTS:
    GEN: {output_mode: run, sim_time_step: 1.0}
    FIT: {output_mode: run, sim_time_step: 1.0}
    COMP: {output_mode: run}
    TUTSUM: {output_mode: run}

This specifies that a child Gen Script, Fit Script, Comp Script and TutSum Script are all run.

Note it’s possible to miss out the OUTPUT_SCRIPTS section from a Tut Script, then the default settings are run, which is equivalent to:-

OUTPUT_SCRIPTS:
    GEN: {output_mode: run, sim_time_step: -1.0, grph_list: ["OBS_vs_TIME"]}
    FIT: {output_mode: run, sim_time_step: -1.0, grph_list: ["OBS_vs_TIME"]}
    COMP: {output_mode: none}
    TUTSUM: {output_mode: run}

This results in more limited tutorial outputs compared to the previous example.

Example OUTPUT_SCRIPTS for gen_script¶

The example below is used in Generate a Two Compartment PopPK Data Set.

OUTPUT_SCRIPTS:
    SIM: {output_mode: run, sim_time_step: 1.0}
    GENSUM: {output_mode: run}

This specifies that a child Sim Script and GenSum Script are run.

Note it’s possible to miss out the OUTPUT_SCRIPTS section from a Gen Script, then the default settings are run, which is equivalent to:-

OUTPUT_SCRIPTS:
    GRPH: {output_mode: none, grph_list: ["OBS_vs_TIME"]}
    SIM: {output_mode: none, grph_list: ["OBS_vs_TIME"], sim_time_step: -1.0}
    GENSUM: {output_mode: none}

i.e. if you miss out the OUTPUT_SCRIPTS then you just get the Gen Script output and no further processing, as you might expect.

Example OUTPUT_SCRIPTS for fit_script¶

The example below is used in Fitting a Two Compartment PopPK Model.

OUTPUT_SCRIPTS:
    SIM: {output_mode: run, sim_time_step: 1.0}
    MSIM: {output_mode: create}
    FITSUM: {output_mode: run}

This specifies that a child Sim Script and FitSum Script are run and a MSim Script is created on disk but not run automatically.

Note it’s possible to miss out the OUTPUT_SCRIPTS section from a Fit Script, then the default settings are run, which is equivalent to:-

OUTPUT_SCRIPTS:
    GRPH: {output_mode: none, grph_list: ["OBS_vs_TIME"]}
    SIM: {output_mode: none, grph_list: ["OBS_vs_TIME"], sim_time_step: 1.0}
    MSIM: {output_mode: none, vpc_list: ["OBS_vs_TIME_VPC"]}
    FITSUM: {output_mode: none}

i.e. if you miss out the OUTPUT_SCRIPTS then you just get the Fit Script output and no further processing, as you might expect.

Example OUTPUT_SCRIPTS for sim_script¶

The example below is from a Sim Script generated by a Fit Script in Fitting a Two Compartment PopPK Model.

OUTPUT_SCRIPTS: {GRPH: {}}

The single ‘GRPH’ child script above, is used to plot the results of the Sim Script simulated PK curves.

You can edit the ‘GRPH’ options to control the graphical output.

Example OUTPUT_SCRIPTS for msim_script¶

The example below is from a MSim Script generated by a Fit Script in Fitting a Two Compartment PopPK Model.

OUTPUT_SCRIPTS:
    VPC:
        output_mode: run
        vpc_list: ["COMB_QUANT_SIM_VPC"]

The single ‘VPC’ child script above, is used to plot a VPC using the results of the MSim Script multi population simulated PK curves.

You can edit the ‘VPC’ options to control the graphical output.

Example OUTPUT_SCRIPTS for mtut_script¶

The example below is used in Generate multiple data sets and Fit using a Two Compartment Model.

OUTPUT_SCRIPTS:
    MGEN: {output_mode: run}
    MFIT: {output_mode: run}
    MCOMP: {output_mode: run, dot_size: 12}

This MTut Script outputs and runs a MGen Script, MFit Script and MComp Script.

Notice you can optionally alter the size of the dots on the MComp Script scatter plots using the ‘dot_size’ field.