Graphically create a peripheral elimination model

This example shows how to turn a standard two-compartment model into a model with non-standard elimination by using the graphical editor.

Note:The completed project (Periph_Elim.phxproj) is available for reference in …\Exam­ples\NLME.

Set up the Phoenix Model object

  1. Create a new project called Periph Elim.

  2. Import the dataset …\Examples\NLME\Supporting files\peripheral elim.dat.

  3. Click Finish in the File Import Wizard dialog.

  4. Right-click the worksheet and select Send To > Phoenix Modeling > Phoenix Model.

  5. In the Structure tab of the Phoenix model, select Micro from the Parameterization menu.

  6. In the Num Compartments menu, select 2.

  7. Change C (continuous observation) to a multiplicative error model by selecting Multiplicative in the C error menu.

  8. The Stdev field should read 0.1.

examples_graphical_setup_tab.png 

Map the model variables

  1. Select the option buttons in the Main Mappings panel to map the data types as follows:
    id to the ID context.
    time to the Time context.
    dv to the CObs context.
    amt to the A1 context.
    Leave rate mapped to None.

examples_graphical_mapping.png 

Edit the graphical model

  1. Click Edit as Graphical.

  2. In the confirmation dialog, click Yes.

  3. In a second confirmation dialog about not using the closed-form, click Yes.

  4. If needed, click Model in the Phoenix Model object Setup tab list to display the Model diagram panel.

    5. Periph_Elim_graphical_model.png 

  5. Delete the PK flow between the Central compartment C and the Elimination compartment A0 by selecting the square labeled Ke, then right-clicking and selecting Delete.

  6. Confirm the deletion by clicking Yes in the dialog.

    The graphical model now looks like this:

    7. PK_flow_deleted_between_C_and_A0.png 

  7. Add a PK flow between the Peripheral compartment A2 and the Elimination compartment A0.

    A PK flow can be added in one of two ways:
    Click Add_PK_Flow_button_1.png in the Phoenix Model object toolbox.
    Or
    Right-click anywhere in the Model diagram panel and select Insert > Flow.

    When the PK flow is inserted, the first and second compartments of the flow must be selected.
    Left-click the first compartment of the flow, the Peripheral compartment A2.
    Left-click the second compartment of the flow, the Elimination compartment A0.

    The PK flow is inserted between the two-compartments.

    8. PK_flow_added_between_A2_and_A0.png 

  8. Select the PK flow named K_A2_A0, if it is not already selected, and type KePe in the Structure tab field Kfwd.

    KePe stands for the rate of elimination between the peripheral compartment and the elimination compartment.

    9. Edit_PK_flow_name.png 

  9. Select the Parameters > Fixed Effects sub-tab.

  10. In the Initial column, type the following initial estimates for each of the parameters:

    11. Parameter

    Initial Value

    tvV

    1

    tvK12

    .01

    tvK21

    .01

    tvKePe

    .01

     

    examples_graphical_initial_values.png 

  11. Select the Run Options tab.

  12. In the Algorithm menu select Naive pooled.

    13. Periph_Elim_final_graphical_model.png 

  13. Click execute_button_72.png to execute the object.

    The first model execution is used to find better initial estimates for the fixed effects.

  14. Select the Parameters > Fixed Effects sub-tab.

  15. Click Accept All Fixed+Random to copy the new estimates to the Initial estimates field for each parameter.

  16. Select the Run Options tab.

  17. In the Algorithm menu select FOCE L-B.

  18. Click execute_button_73.png to execute the object.

Save and close the project

  1. Select File > Save Project.

  2. Click Save.

  3. Select File > Close Project.

The project is saved and closed and Phoenix can be safely exited.

This concludes the peripheral elimination model example.

 

Last modified date:6/26/19
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