Testbranch1beta_RS

[RashmiG5]

first pull request.

Summary by Sourcery

Add an extended parameter set for interventions and disease dynamics, update the plotting output path and tune key transmission parameters

New Features:

• Introduce data/parameters3.yaml with intervention parameters, contact/mixing rates, and disease progression probabilities

Enhancements:

• Update default plot_results save path and docstring
• Adjust base model transmission parameters (beta and sigma) in data/parameters.yaml

[sourcery-ai]

Reviewer's Guide

Updated visualization method path and docstring, adjusted core transmission parameters, and introduced a new extended parameters file with intervention and contact settings.

Entity relationship diagram for updated and new parameters files

erDiagram
    PARAMETERS_YAML {
        beta float
        sigma float
        gamma float
        mu float
    }
    PARAMETERS3_YAML {
        beta float
        sigma float
        gamma float
        mu float
        treatment_rate float
        vaccine_efficacy float
        contact_rate int
        prob_fast_progression float
        prob_reactivation float
    }
    PARAMETERS_YAML ||--|| PARAMETERS3_YAML : "extends"

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Class diagram for updated plot_results method in tb_model.py

classDiagram
    class TBModel {
        +run_simulation(years)
        +plot_results(save_path)
        results
    }
    TBModel : plot_results(save_path)
    TBModel : results

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File-Level Changes

Change	Details	Files
Updated plot_results default path and documentation	Changed default save_path to './results/tb_model_output.png' Extended docstring with usage note and save path Inserted a stray 'save.path' line	src/tb_model.py
Adjusted baseline transmission parameters	Increased beta from 0.05 to 0.125 Decreased sigma from 0.0002 to 0.0001	data/parameters.yaml
Added a new parameters file with intervention and contact settings	Created parameters3.yaml with model_parameters section Defined treatment_rate, vaccine_efficacy, contact_rate, and progression probabilities	data/parameters3.yaml

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[sourcery-ai]

Hey there - I've reviewed your changes - here's some feedback:

• Clean up the plot_results docstring to remove the stray "save.path" line and clearly document the save_path parameter.
• If you’re adding parameters3.yaml, either integrate it into your config‐loading logic or remove it to avoid shipping an unused file.
• Avoid hardcoding './results/' in plot_results; consider using pathlib or passing a configurable output directory instead.

Prompt for AI Agents

Please address the comments from this code review:

## Overall Comments
- Clean up the plot_results docstring to remove the stray "save.path" line and clearly document the save_path parameter.
- If you’re adding parameters3.yaml, either integrate it into your config‐loading logic or remove it to avoid shipping an unused file.
- Avoid hardcoding './results/' in plot_results; consider using pathlib or passing a configurable output directory instead.

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