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Update README with generated transmission spectra outputs and analysis summary #1

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Copilot Mar 2, 2026
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docs: add generated transmission spectra and analysis summary to README
Copilot Mar 2, 2026
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Expand Up @@ -102,6 +102,19 @@ This will generate:
5. `star_comparison_trends.png`: Abundance trends (N2O, NH3, O3, CH4).
6. `stellar_spectra_comparison.png`: Input stellar spectra.

### Generated Transmission Spectra (POSEIDON)
Additional transmission spectra were generated from the exported atmospheric profiles in `transmission spectra/profiles/` using the notebooks in `transmission spectra/notebooks/`.

Main outputs:
1. `transmission spectra/notebooks/POSEIDON_output/Earth/plots/Earth_transmission_spectra.pdf`
2. `transmission spectra/notebooks/POSEIDON_output/Trappist/plots/Trappist_transmission_spectra.pdf`
3. `transmission spectra/notebooks/POSEIDON_output/TRAPPIST-1e/plots/TRAPPIST-1e_spectral_decomposition.pdf`

Analysis summary:
- The transmission spectra compare the four agricultural scenarios (A0, A1, A2, A3) for each stellar environment.
- The analysis focuses on how increasing agricultural nitrogen emissions (N2O and NH3) modifies spectral features and the total transit depth signal.
- For TRAPPIST-1e, the spectral decomposition output separates molecular contributions, helping identify which species drive the A0 vs A3 differences.

### View Result Tables
To view abundance tables in the terminal:
```bash
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