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Update model-configuration-extracting-variables.md #5711

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Update model-configuration-extracting-variables.md #5711

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83 changes: 73 additions & 10 deletions testing/manual/model-configuration-extracting-variables.md
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Expand Up @@ -12,16 +12,18 @@ Report any issues into GitHub: [open an issue](https://github.com/DARPA-ASKEM/te

### 2. Upload assets
1. From the manual testing [data folder](https://drive.google.com/drive/folders/14z6WAldQky0xgOAM69f6hakXhyHobYMe), add these resources to your project by clicking the `Upload` button and dragging these downloaded files onto the popup:
a. [SIR Document 1](https://drive.google.com/file/d/1ZQXSGhesif_G0bjQiB9nx0B_BJ1xV1Wx/view?usp=sharing)
b. [SIR Document 2](https://drive.google.com/file/d/1U1h5YCBxom9k475QSOzkiIwyi5V159dV/view?usp=sharing)
c. [SIR Model](https://drive.google.com/file/d/1F9UWuvwJPZY_XAGflsOIYy4Qrl56KS91/view?usp=sharing)
d. [Stratified SIR model](https://drive.google.com/file/d/1r-zfKmHrOub7QT9BfdQEZabfZqveLhIq/view?usp=sharing)
e. [SIDARTHE model](https://drive.google.com/drive/folders/14z6WAldQky0xgOAM69f6hakXhyHobYMe)
f. [SIDARTHE paper](https://drive.google.com/file/d/1pOb1MuarNEyrDf6I6z96Pdf_hQ9Q3_v0/view?usp=drive_link)
g. [SIR timeseries Dataset 1](https://drive.google.com/file/d/1QM2TL6XrBHIlFOVSavugKAQErls7XtY8/view?usp=sharing)
h. [SIR timeseries Dataset 2](https://drive.google.com/file/d/1zKySIpyPN_aa-icxy1e8NHmVtkZs51Fn/view?usp=sharing)
i. [SIR contact matrix dataset](https://drive.google.com/file/d/17TByirv-LwunB0gDq46-Ww-SyJZYaHKD/view?usp=sharing)
2. Wait a minute or two for the Document Intelligence service to finish extracting artifacts from the uploaded document.
1. [SIR Document 1](https://drive.google.com/file/d/1ZQXSGhesif_G0bjQiB9nx0B_BJ1xV1Wx/view?usp=sharing)
2. [SIR Document 2](https://drive.google.com/file/d/1U1h5YCBxom9k475QSOzkiIwyi5V159dV/view?usp=sharing)
3. [SIR Model](https://drive.google.com/file/d/1F9UWuvwJPZY_XAGflsOIYy4Qrl56KS91/view?usp=sharing)
4. [Stratified SIR model](https://drive.google.com/file/d/1r-zfKmHrOub7QT9BfdQEZabfZqveLhIq/view?usp=sharing)
5. [SIDARTHE model](https://drive.google.com/drive/folders/14z6WAldQky0xgOAM69f6hakXhyHobYMe)
6. [SIDARTHE paper](https://drive.google.com/file/d/1pOb1MuarNEyrDf6I6z96Pdf_hQ9Q3_v0/view?usp=drive_link)
7. [SIR timeseries Dataset 1](https://drive.google.com/file/d/1QM2TL6XrBHIlFOVSavugKAQErls7XtY8/view?usp=sharing)
8. [SIR timeseries Dataset 2](https://drive.google.com/file/d/1zKySIpyPN_aa-icxy1e8NHmVtkZs51Fn/view?usp=sharing)
9. [SIR contact matrix dataset](https://drive.google.com/file/d/17TByirv-LwunB0gDq46-Ww-SyJZYaHKD/view?usp=sharing)
10. [Prob 5 Model C](https://drive.google.com/file/d/1CF-n8OUroRaaNCaRTwvOgrPuASrktj1P/view?usp=drive_link)
11. [Rosenblatt 2024](https://drive.google.com/file/d/1mGU2HwXG5ZWjgo24DNaNkq2oS5ipL6_V/view?usp=drive_link)
3. Wait a minute or two for the Document Intelligence service to finish extracting artifacts from the uploaded document.

### 3. Extracting configurations from multiple documents and timeseries datasets
1. Create a new workflow
Expand Down Expand Up @@ -85,3 +87,64 @@ Report any issues into GitHub: [open an issue](https://github.com/DARPA-ASKEM/te
- `Restrictive NPIs Scenario`
- Initial expressions for S, I, D, A, R, T, H, and E should be extracted for all configurations
- Parameter values for alpha, beta, delta, epsilon, eta, gamma, kappa, lambda, mu, nu, rho, theta, xi, zeta, tau, and sigma should be extracted for all configurations

### 6. Extracting configuration from a table with probability distributions (Not supported yet)

This is difficult test case since it involves extracting values from a table _and_ some of the parameters are probability distributions.

1. Add `Prob 5 Model C` model and `Rosenblatt 2024` document to the workflow
2. Create a new "Configure model" operator
3. Connect the model and document to this operator
4. Open the operator and click "Extract configuration from inputs"
5. There should be only one model configuration that is extracted
6. Confirm the values

| Parameters | Type | Distribution Parameter(s) |
| --- | --- | --- |
| α | LogNormal1 | meanLog = 4.72, stdevLog = 0.63 |
| AER | Constant | 4 |
| Aw | Constant | 100 |
| Ci | Constant | 0.0014 |
| Nw | Constant | 1000 |
| S | Constant | 0.24 |
| Vair | Constant | 7.03 |
| Vdrop | Constant | 0.01 |
| e | Constant | 2.71828 |
| kappa | Constant | 11.35 |
| lambda | Constant | 0.63 |
| q | Constant | 0.34 |
| rhoA | LogNormal1 | meanLog = 3.47, stdevLog = 0.23 |
| theta | LogNormal1 | meanLog = 0.28, stdevLog = 0.27 |
| epsilonD | LogitNormal1 | location = -1.46, scale = 0.71 |
| k | Constant | 410 |
| y | Constant | 0.1666 |
| IR_W_W | Constant | 0.85 |
| IR_W_C | Constant | 0.85 |
| IR_W_H | Constant | 0.85 |
| IR_C_W | Constant | 0.85 |
| IR_C_C | Constant | 0.85 |
| IR_C_H | Constant | 0.85 |
| IR_H_W | Constant | 0.53 |
| IR_H_C | Constant | 0.53 |
| IR_H_H | Constant | 0.53 |
| omega_W_C | Constant | 0.00072 |
| omega_C_W | Constant | 0.00072 |
| omega_C_C | LogNormal1 | meanLog = 3.47, stdevLog = 0.91 |
| omega_H_W | LogNormal1 | meanLog = -1.59, stdevLog = 1.70 |
| omega_W_H | LogNormal1 | meanLog = -1.59, stdevLog = 1.70 |
| omega_H_C | LogNormal1 | meanLog = 2.52, stdevLog = 1.13 |
| omega_C_H | LogNormal1 | meanLog = 2.52, stdevLog = 1.13 |
| tContact_W_W | LogNormal1 | meanLog = 1.55, stdevLog = 1.27 |
| tContact_W_C | LogNormal1 | meanLog = 1.55, stdevLog = 1.27 |
| tContact_C_W | LogNormal1 | meanLog = 1.55, stdevLog = 1.27 |
| tContact_C_C | LogNormal1 | meanLog = 1.55, stdevLog = 1.27 |
| tContact_C_H | LogNormal1 | meanLog = 1.79, stdevLog = 1.15 |
| tContact_W_H | LogNormal1 | meanLog = -0.36, stdevLog = 0.98 |
| Cvs | LogNormal1 | meanLog = 0.22, stdevLog = 0.34 |
| Cv_C_C | LogNormal1 | meanLog = 0.22, stdevLog = 0.34 |
| Cv_C_W | LogNormal1 | meanLog = 0.22, stdevLog = 0.34 |
| Cv_W_C | LogNormal1 | meanLog = 0.22, stdevLog = 0.34 |
| Cv_C_H | LogNormal1 | meanLog = 5.6 * log(10), stdevLog = 1.2 * log(10) |

| Cv_W_H | LogNormal1 | meanLog = 5.6 * log(10), stdevLog = 1.2 * log(10) |
| Vsputum | Constant | 100 |