Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update model-configuration-input.md #4617

Merged
merged 2 commits into from
Aug 30, 2024
Merged

Update model-configuration-input.md #4617

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
12b530f
Update model-configuration-input.md
blanchco Aug 29, 2024
a9fce9c
Update model-configuration-input.md
blanchco Aug 29, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
71 changes: 43 additions & 28 deletions testing/manual/model-configuration-input.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,40 +11,55 @@ Report any issues into GitHub: [open an issue](https://github.com/DARPA-ASKEM/te
2. Create, or open, project named `QA [Your Name]`
3. Upload model [SIR.json](https://drive.google.com/file/d/1eXlvpBfMmhrfC0xUXfuz0s_19gi-Rird/view?usp=drive_link) to project

### 2. Configure a Model**
1. Add the SIR model to your workflow canvas. Add a `Configure Model` operator and connect this to your SIR model. Open the configuration editor.
2. Make sure the initial condition (e.g. SIR) and parameter (e.g. beta,gamma) tables appear as expected with data.
### 2. Configure a Model
1. Add the SIR model to your workflow canvas. Add a `Configure Model` operator and connect it to your SIR model. Open the configuration editor.
2. Verify that the initial condition (e.g., SIR) and parameter (e.g., β, γ) tables are populated with data.
3. Update the configuration name and add a description.
4. Pick an initial condition and update it (e.g., change S to 1000; I to 2; R to 0).
5. Pick an initial condition and add a source (e.g., NY Times data).
6. Pick a parameter and update it (e.g. change beta from uniform to constant and set to .9).
7. Pick an initial condition and add a source (e.g., https://www.mdpi.com/1099-4300/23/1/59 )
8. Save your configuration and make sure the changes you have made persist.
4. Modify an initial condition (e.g., change S to 1000; I to 2; R to 0).
5. Update a parameter (e.g., change β from uniform to constant and set it to 0.9).
6. Add a source to an initial condition or parameter (e.g., NY Times data).
7. Attempt to save the configuration:
- Verify that the **Save** button is disabled and the **Save As** button is enabled since values have been modified.
8. Use the **Save As** button to create a new configuration. Confirm that the changes persist.

### 3. Add Uncertainty to Parameter**
1. Update the configuration name and add a description (e.g., SIR with uncertainty).
2. In the parameter table click `add uncertainty.`Apply this to beta. Make sure that this has been updated from `constant` to `uniform.` and has values set to +/- 10% of the intial constant.
3. Save as a new configuration and make sure the changes you've made persist.
### 3. Update Metadata Only
1. Open an existing model configuration in the configuration editor.
2. Modify the configuration name, description, or initial/parameter sources without changing any values.
3. Attempt to save the configuration:
- Verify that the **Save** button is enabled and that the configuration can be saved without creating a new one.
4. Confirm that the changes persist after saving.

### 4. Add Uncertainty to a Parameter
1. Open an existing model configuration in the configuration editor.
2. Add uncertainty to a parameter (e.g., apply uncertainty to β, changing it from constant to uniform with values set to +/- 10% of the initial constant). Note: uncertainties can **only** be applied to **constant** parameter types
3. Attempt to save the configuration:
- Verify that the **Save** button is disabled and the **Save As** button is enabled due to the modification of the parameter values.
4. Use the **Save As** button to create a new configuration. Confirm that the changes persist.

### 4. Configure a Stratified Model**
1. Add the SIR model to your workflow canvas. Add a `Stratify Model` operator and connect this to your SIR Model. Open the stratification editor.
2. In the stratification editor create a new strata for `age` with two levels: old, young. Stratify for the initial conditions SIR and parameter gamma. Uncheck create new transition between strata (we are assuming people stay in their age category). Run stratification and save as a new model. Name this `Stratified SIR`
3. Return to your workflow canvas and add the `Stratifed SIR ` to your canvas. Add the `Configure Model` operator and connect this to your stratified model.
4. Make sure the initial conditions (SIR) and parameter tables appear as expected with data. Note that the initial condition R should have two levels: old and young. 5
### 5. Configure a Stratified Model
1. Add the SIR model to your workflow canvas. Add a `Stratify Model` operator and connect it to your SIR model. Open the stratification editor.
2. Create a new strata for `age` with two levels: old, young. Stratify the initial conditions (SIR) and parameter (γ). Uncheck `Create New Transition Between Strata` (assuming people remain in their age category). Run the stratification and save it as a new model named `Stratified SIR`.
3. Return to the workflow canvas and add the `Stratified SIR` to the canvas. Add the `Configure Model` operator and connect it to the stratified model. Open the configuration editor.
4. Verify that the initial condition (SIR) and parameter tables are correctly stratified with data. For example, ensure that the initial condition R has two levels: old and young.
5. Update the configuration name and add a description.
6. Ensure you have matrices for young and old for SIR, and gamma. Update the configuration values to the following:
6. Update stratified values as follows:
1. S_young: 1000
2. S_old: 500
3. I_young: 1
4. I_old: 2
5. R_young:0
6. R_old:0
7. Gamma_young: 14
8. Gamma_old: 21
7. Add a source to one of the initial conditions or parameters: e.g., NY Times data
8. Change beta to constant: .9
9. Save as a new configuration and make sure that your changes persisted.
10. Create a new configuration name and new description.
11. Add uncertainty to beta: In the parameter table click `add uncertainty.`Apply this to beta. Make sure that this has been updated from `constant` to `uniform.` and has values set to +/- 10% of the initial constant (should be min .81 and max 99).
12. Save as a new configuration and make sure the changes you've made persist.
5. R_young: 0
6. R_old: 0
7. γ_young: 14
8. γ_old: 21
7. Add a source to an initial condition or parameter (e.g., NY Times data).
8. Modify a parameter (e.g., change β to constant: 0.9).
9. Attempt to save the configuration:
- Verify that the **Save** button is disabled and the **Save As** button is enabled due to changes in values.
10. Use the **Save As** button to create a new configuration. Confirm that the changes persist.
11. Add uncertainty to a parameter (e.g., apply uncertainty to β, setting it from constant to uniform with min 0.81 and max 0.99).
12. Use the **Save As** button to create a new configuration. Confirm that the changes persist.

### 6. Reset Changes
1. For any configuration where changes have been made but not saved, click the **Reset** button.
2. Verify that all unsaved changes are discarded and the configuration reverts to its original state before any modifications were made.