From e6e599376855189c10d23ece18a2f4ef07dc5b49 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 2 Mar 2026 02:22:40 +0000
Subject: [PATCH 1/2] Initial plan


From 3d2073e027d774182c7c54998dd07a06cd7fb936 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 2 Mar 2026 02:24:26 +0000
Subject: [PATCH 2/2] docs: add generated transmission spectra and analysis
 summary to README

Co-authored-by: D4san <114251096+D4san@users.noreply.github.com>
---
 README.md | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/README.md b/README.md
index 0da7396..c8dedda 100644
--- a/README.md
+++ b/README.md
@@ -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