ecological-agent-skills 3.2.0 → 3.2.1

package/skills/ecological-impact-assessment/scripts/power_analysis_baci.py

@@ -0,0 +1,284 @@
+#!/usr/bin/env python3
+# ecological-agent-skills / Copyright (C) 2026 Francisco Diego Barros Barata
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""
+power_analysis_baci.py
+Compute statistical power for BACI designs and recommend minimum sample sizes.
+Usage: python power_analysis_baci.py <output_dir> [effect_size] [n_sites] [n_surveys] [alpha] [variance_estimate]
+Outputs: power_curves.png, power_summary.csv, minimum_n_recommendation.md
+Requires: numpy, scipy, matplotlib
+"""
+import logging
+import math
+import sys
+from datetime import datetime
+from pathlib import Path
+
+SKILL_NAME = "ecological-impact-assessment"
+_LOG_DIR   = Path("logs")
+_LOG_DIR.mkdir(parents=True, exist_ok=True)
+_log_file  = _LOG_DIR / f"skill_{SKILL_NAME}_{datetime.now().strftime('%Y%m%d_%H%M%S')}.log"
+logging.basicConfig(
+    level=logging.INFO,
+    format="[%(asctime)s] [%(levelname)s] [" + SKILL_NAME + "] %(message)s",
+    datefmt="%Y-%m-%d %H:%M:%S",
+    handlers=[
+        logging.StreamHandler(sys.stdout),
+        logging.FileHandler(_log_file, encoding="utf-8"),
+    ],
+)
+logger = logging.getLogger(SKILL_NAME)
+
+
+def log_step(n: int, desc: str) -> None:
+    logger.info("-- STEP %d: %s", n, desc)
+
+
+def log_decision(var: str, val, why: str) -> None:
+    logger.info("DECISION | %s = %s | %s", var, val, why)
+
+
+import numpy as np
+from scipy import stats
+import matplotlib
+matplotlib.use("Agg")
+import matplotlib.pyplot as plt
+
+
+# ── Helper: BACI power ──────────────────────────────────────────────────────
+# BACI interaction term is tested as a two-sample t-test on the
+# difference-in-differences. Effective n per group = n_sites * n_surveys.
+# Cohen's d adjusted for variance: d = effect_size / sqrt(variance_estimate)
+
+def baci_power(n_s: int, n_sv: int, eff: float, var_est: float, a: float) -> float:
+    """Compute power for a BACI design using non-central t distribution."""
+    try:
+        d_adj = eff / math.sqrt(var_est)
+        n_eff = n_s * n_sv  # effective replication per group
+        df = 2 * n_eff - 2  # degrees of freedom for two-sample t-test
+        if df < 1:
+            return float("nan")
+        # Non-centrality parameter
+        ncp = d_adj * math.sqrt(n_eff / 2.0)
+        t_crit = stats.t.ppf(1.0 - a / 2.0, df)
+        # Power = P(|T_ncp| > t_crit) = 1 - P(-t_crit < T_ncp < t_crit)
+        power = 1.0 - (stats.nct.cdf(t_crit, df, ncp) - stats.nct.cdf(-t_crit, df, ncp))
+        return power
+    except Exception:
+        return float("nan")
+
+
+def find_min_n(target_power: float, vary: str, fixed_n: int, eff: float,
+               var_est: float, a: float, n_sv_or_ns: int) -> int | None:
+    """Find minimum n_sites or n_surveys to reach target_power."""
+    upper = 200 if vary == "sites" else 100
+    for n in range(2 if vary == "sites" else 1, upper + 1):
+        if vary == "sites":
+            p = baci_power(n, n_sv_or_ns, eff, var_est, a)
+        else:
+            p = baci_power(n_sv_or_ns, n, eff, var_est, a)
+        if not math.isnan(p) and p >= target_power:
+            return n
+    return None
+
+
+def main():
+    # ── Arguments ────────────────────────────────────────────────────────────
+    args = sys.argv[1:]
+    output_dir        = args[0] if len(args) >= 1 else "outputs/power_analysis"
+    effect_size       = float(args[1]) if len(args) >= 2 else 0.5
+    n_sites           = int(args[2])   if len(args) >= 3 else 10
+    n_surveys         = int(args[3])   if len(args) >= 4 else 4
+    alpha             = float(args[4]) if len(args) >= 5 else 0.05
+    variance_estimate = float(args[5]) if len(args) >= 6 else 1.0
+
+    log_decision("effect_size", effect_size,
+                 "Cohen's d: 0.2=small, 0.5=medium, 0.8=large. Use 0.5 if no pilot data available.")
+    log_decision("n_sites", n_sites,
+                 "Number of control + impact sites each side. Minimum recommended: 5 per group.")
+    log_decision("n_surveys", n_surveys,
+                 "Survey occasions before + after. Minimum recommended: 3 pre + 3 post = 6 total.")
+    log_decision("alpha", alpha,
+                 "Type I error rate. Standard: 0.05. Use 0.10 for preliminary screening.")
+    log_decision("variance_estimate", variance_estimate,
+                 "Within-group variance from pilot data or literature. Affects Cohen's d calculation.")
+
+    out_path = Path(output_dir)
+    out_path.mkdir(parents=True, exist_ok=True)
+
+    # ── Step 1: Power x n_sites ──────────────────────────────────────────────
+    log_step(1, "Computing power x n_sites curve")
+    sites_range = np.arange(2, 31)
+    pow_vs_sites = np.array([baci_power(int(ns), n_surveys, effect_size, variance_estimate, alpha)
+                             for ns in sites_range])
+    current_power = baci_power(n_sites, n_surveys, effect_size, variance_estimate, alpha)
+    logger.info("Power at n_sites=%d (n_surveys=%d fixed): %.3f", n_sites, n_surveys, current_power)
+
+    # ── Step 2: Power x n_surveys ────────────────────────────────────────────
+    log_step(2, "Computing power x n_surveys curve")
+    surveys_range = np.arange(1, 21)
+    pow_vs_surveys = np.array([baci_power(n_sites, int(nv), effect_size, variance_estimate, alpha)
+                               for nv in surveys_range])
+
+    # ── Step 3: Power x effect_size ──────────────────────────────────────────
+    log_step(3, "Computing power x effect_size curve")
+    eff_range = np.arange(0.1, 1.55, 0.05)
+    pow_vs_eff = np.array([baci_power(n_sites, n_surveys, float(e), variance_estimate, alpha)
+                           for e in eff_range])
+
+    # ── Step 4: Minimum n calculations ───────────────────────────────────────
+    log_step(4, "Calculating minimum n for power = 0.80 and 0.90")
+
+    min_sites_80  = find_min_n(0.80, "sites", n_sites, effect_size, variance_estimate, alpha, n_surveys)
+    min_sites_90  = find_min_n(0.90, "sites", n_sites, effect_size, variance_estimate, alpha, n_surveys)
+    min_surveys_80 = find_min_n(0.80, "surveys", n_surveys, effect_size, variance_estimate, alpha, n_sites)
+    min_surveys_90 = find_min_n(0.90, "surveys", n_surveys, effect_size, variance_estimate, alpha, n_sites)
+
+    logger.info("Min sites for power=0.80: %s | power=0.90: %s (surveys=%d fixed)",
+                min_sites_80, min_sites_90, n_surveys)
+    logger.info("Min surveys for power=0.80: %s | power=0.90: %s (sites=%d fixed)",
+                min_surveys_80, min_surveys_90, n_sites)
+
+    if min_sites_80 is None:
+        logger.warning("Power 0.80 not achievable with sites<=200. Increase effect_size or reduce variance_estimate.")
+
+    # ── Step 5: Power curves plot ────────────────────────────────────────────
+    log_step(5, "Generating power curves plot")
+    try:
+        fig, axes = plt.subplots(3, 1, figsize=(8, 12))
+
+        # Panel 1: power vs sites
+        ax = axes[0]
+        ax.plot(sites_range, pow_vs_sites, color="#2471a3", linewidth=2)
+        ax.axhline(0.80, linestyle="--", color="#e74c3c", linewidth=0.8)
+        ax.axhline(0.90, linestyle="--", color="#27ae60", linewidth=0.8)
+        if min_sites_80 is not None:
+            ax.axvline(min_sites_80, linestyle=":", color="#e74c3c", linewidth=0.8)
+            ax.annotate(f"n={min_sites_80}\n(80%)", xy=(min_sites_80 + 0.5, 0.05),
+                        fontsize=8, color="#e74c3c")
+        if min_sites_90 is not None:
+            ax.axvline(min_sites_90, linestyle=":", color="#27ae60", linewidth=0.8)
+            ax.annotate(f"n={min_sites_90}\n(90%)", xy=(min_sites_90 + 0.5, 0.05),
+                        fontsize=8, color="#27ae60")
+        ax.set_ylim(0, 1)
+        ax.set_ylabel("Statistical Power")
+        ax.set_xlabel("Number of sites per group")
+        ax.set_title(f"BACI Power vs. Sites (n_surveys={n_surveys} fixed)")
+
+        # Panel 2: power vs surveys
+        ax = axes[1]
+        ax.plot(surveys_range, pow_vs_surveys, color="#8e44ad", linewidth=2)
+        ax.axhline(0.80, linestyle="--", color="#e74c3c", linewidth=0.8)
+        ax.axhline(0.90, linestyle="--", color="#27ae60", linewidth=0.8)
+        ax.set_ylim(0, 1)
+        ax.set_ylabel("Statistical Power")
+        ax.set_xlabel("Survey occasions (before + after)")
+        ax.set_title(f"BACI Power vs. Surveys (n_sites={n_sites} fixed)")
+
+        # Panel 3: power vs effect size
+        ax = axes[2]
+        ax.plot(eff_range, pow_vs_eff, color="#e67e22", linewidth=2)
+        ax.axhline(0.80, linestyle="--", color="#e74c3c", linewidth=0.8)
+        ax.axhline(0.90, linestyle="--", color="#27ae60", linewidth=0.8)
+        ax.axvline(effect_size, linestyle=":", color="grey", linewidth=0.8)
+        ax.set_ylim(0, 1)
+        ax.set_ylabel("Statistical Power")
+        ax.set_xlabel("Effect size (Cohen's d)")
+        ax.set_title(f"BACI Power vs. Effect Size (n={n_sites} sites, {n_surveys} surveys)")
+
+        fig.tight_layout()
+        plot_file = out_path / "power_curves.png"
+        fig.savefig(plot_file, dpi=150)
+        plt.close(fig)
+        logger.info("Power curves plot saved: %s", plot_file)
+    except Exception as exc:
+        logger.error(
+            "Failed to generate power plot: %s\n"
+            "Probable cause: matplotlib not installed.\n"
+            "Check: pip install matplotlib",
+            exc,
+        )
+        sys.exit(1)
+
+    # ── Step 6: Power summary CSV ────────────────────────────────────────────
+    log_step(6, "Saving power summary CSV")
+    import pandas as pd
+
+    summary_df = pd.DataFrame({
+        "parameter": [
+            "effect_size", "n_sites", "n_surveys", "alpha", "variance_estimate",
+            "power_current", "min_sites_power80", "min_sites_power90",
+            "min_surveys_power80", "min_surveys_power90",
+        ],
+        "value": [
+            effect_size, n_sites, n_surveys, alpha, variance_estimate,
+            round(current_power, 4),
+            min_sites_80 if min_sites_80 is not None else "NA",
+            min_sites_90 if min_sites_90 is not None else "NA",
+            min_surveys_80 if min_surveys_80 is not None else "NA",
+            min_surveys_90 if min_surveys_90 is not None else "NA",
+        ],
+    })
+    csv_file = out_path / "power_summary.csv"
+    summary_df.to_csv(csv_file, index=False)
+    logger.info("Power summary saved: %s", csv_file)
+
+    # ── Step 7: Recommendation markdown ──────────────────────────────────────
+    log_step(7, "Writing minimum-n recommendation report")
+    adequacy = "ADEQUATE" if (not math.isnan(current_power) and current_power >= 0.80) else "INSUFFICIENT"
+
+    def _fmt(val):
+        return str(val) if val is not None else "not achievable"
+
+    rec_lines = f"""# BACI Power Analysis -- Field Protocol Recommendation
+
+Generated: {datetime.now().strftime('%Y-%m-%d %H:%M:%S')}
+
+## Input Parameters
+- **Effect size (Cohen's d):** {effect_size}
+- **Number of sites (per group):** {n_sites}
+- **Survey occasions (before + after):** {n_surveys}
+- **Significance level (alpha):** {alpha}
+- **Variance estimate:** {variance_estimate}
+
+## Current Design Power
+**Statistical power = {round(current_power * 100, 1)}%** ({adequacy})
+
+{"WARNING: The current design has insufficient power to detect the target effect." if adequacy == "INSUFFICIENT" else "The current design has adequate power to detect the target effect."}
+
+## Minimum Sample Size Recommendations
+
+### To achieve power = 80% (alpha = {alpha})
+- **Sites per group:** >= {_fmt(min_sites_80)} (with {n_surveys} survey occasions)
+- **Survey occasions:** >= {_fmt(min_surveys_80)} (with {n_sites} sites)
+
+### To achieve power = 90% (alpha = {alpha})
+- **Sites per group:** >= {_fmt(min_sites_90)} (with {n_surveys} survey occasions)
+- **Survey occasions:** >= {_fmt(min_surveys_90)} (with {n_sites} sites)
+
+## Interpretation
+- A Cohen's d of **{effect_size}** corresponds to detecting a {round(effect_size * math.sqrt(variance_estimate), 3)} unit difference between impact and control sites, adjusting for var = {variance_estimate}.
+- **Rule of thumb:** BACI studies should have >=5 control and >=5 impact sites, with >=3 survey occasions before and >=3 after the impact.
+- If power is insufficient, prioritise adding **sites** (stronger than adding surveys) because spatial replication reduces pseudo-replication bias.
+
+## How to Obtain Variance Estimate
+1. **From pilot data:** compute SD of the response variable across sites, then var = SD^2.
+2. **From literature:** use SD values reported for the same metric and habitat type.
+3. **Conservative default:** use variance_estimate = 1.0 (corresponds to Cohen's d units).
+
+## References
+- Cohen, J. (1988). *Statistical Power Analysis for the Behavioral Sciences* (2nd ed.).
+- Underwood, A.J. (1994). On beyond BACI. *Ecological Applications*, 4(1), 3-15.
+- Stewart-Oaten, A. & Bence, J.R. (2001). Temporal and spatial variation in environmental impact assessment. *Ecological Monographs*, 71(2), 305-339.
+"""
+
+    md_file = out_path / "minimum_n_recommendation.md"
+    md_file.write_text(rec_lines, encoding="utf-8")
+    logger.info("Recommendation report saved: %s", md_file)
+
+    log_step(8, "Done -- power analysis outputs in: %s" % output_dir)
+
+
+if __name__ == "__main__":
+    main()

package/skills/ecosystem-services-assessment/scripts/tradeoff_analysis.py

@@ -0,0 +1,245 @@
+#!/usr/bin/env python3
+# ecological-agent-skills / Copyright (C) 2026 Francisco Diego Barros Barata
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+"""
+tradeoff_analysis.py
+ES trade-off and synergy analysis across pixels or land cover units.
+Usage: python tradeoff_analysis.py <es_summary_csv> <output_dir>
+Requires: pandas, numpy, scipy, matplotlib, seaborn
+"""
+import logging
+import sys
+from datetime import datetime
+from pathlib import Path
+from itertools import combinations
+
+SKILL_NAME = "ecosystem-services-assessment"
+_LOG_DIR   = Path("logs")
+_LOG_DIR.mkdir(parents=True, exist_ok=True)
+_log_file  = _LOG_DIR / f"skill_{SKILL_NAME}_{datetime.now().strftime('%Y%m%d_%H%M%S')}.log"
+logging.basicConfig(
+    level=logging.INFO,
+    format="[%(asctime)s] [%(levelname)s] [" + SKILL_NAME + "] %(message)s",
+    datefmt="%Y-%m-%d %H:%M:%S",
+    handlers=[
+        logging.StreamHandler(sys.stdout),
+        logging.FileHandler(_log_file, encoding="utf-8"),
+    ],
+)
+logger = logging.getLogger(SKILL_NAME)
+
+
+def log_step(n: int, desc: str) -> None:
+    logger.info("-- STEP %d: %s", n, desc)
+
+
+def log_decision(var: str, val, why: str) -> None:
+    logger.info("DECISION | %s = %s | %s", var, val, why)
+
+
+import numpy as np
+import pandas as pd
+from scipy.stats import spearmanr
+import matplotlib
+matplotlib.use("Agg")
+import matplotlib.pyplot as plt
+import seaborn as sns
+
+
+def main():
+    # ── Arguments ────────────────────────────────────────────────────────────
+    es_file    = sys.argv[1] if len(sys.argv) >= 2 else "outputs/ecosystem_services/es_summary_table.csv"
+    output_dir = sys.argv[2] if len(sys.argv) >= 3 else "outputs/ecosystem_services"
+
+    out_path = Path(output_dir)
+    out_path.mkdir(parents=True, exist_ok=True)
+
+    logger.info("Skill: %s | es_file=%s | output_dir=%s", SKILL_NAME, es_file, output_dir)
+
+    # ── Input precondition check ─────────────────────────────────────────────
+    if not Path(es_file).exists():
+        logger.error(
+            "Input not found: %s\n"
+            "Probable cause: o script de quantificacao de servicos ecossistemicos nao foi executado ou o caminho esta errado.\n"
+            "Check: execute primeiro o script de mapeamento/quantificacao de ES.\n"
+            "Previous skill: ecosystem-services-assessment (quantification step).",
+            es_file,
+        )
+        sys.exit(1)
+
+    # ── Step 1: Load ─────────────────────────────────────────────────────────
+    log_step(1, "Load ecosystem services table")
+    try:
+        es = pd.read_csv(es_file)
+    except Exception as exc:
+        logger.error(
+            "Failed to read CSV de servicos ecossistemicos: %s\n"
+            "Probable cause: corrupted file ou com separador incorreto.\n"
+            "Check: abra o arquivo em editor de texto e confira o formato.\n"
+            "Previous skill: ecosystem-services-assessment (quantification step).",
+            exc,
+        )
+        sys.exit(1)
+
+    logger.info("ES table loaded: %d land use classes", len(es))
+
+    n_na_total = int(es.isna().sum().sum())
+    if n_na_total > 0:
+        logger.warning(
+            "ES table contains %d NA values total — correlations will be computed with complete observations.",
+            n_na_total,
+        )
+
+    # ── Step 2: Identify numeric ES columns ──────────────────────────────────
+    log_step(2, "Identify ES indicator columns and normalise 0-1")
+    exclude_cols = {"lulc_code", "n_pixels"}
+    es_cols = [c for c in es.select_dtypes(include=[np.number]).columns if c not in exclude_cols]
+    logger.info("ES indicators: %s", ", ".join(es_cols))
+    log_decision(
+        "es_cols", ", ".join(es_cols),
+        "colunas numericas excluindo lulc_code e n_pixels sao tratadas como indicadores de ES",
+    )
+
+    if len(es_cols) < 2:
+        logger.warning(
+            "Fewer than 2 ES indicators found — trade-off analysis not possible with only %d column(s).",
+            len(es_cols),
+        )
+        logger.info("Exiting without error. Add more indicators to the input CSV.")
+        sys.exit(0)
+
+    # ── Normalise to 0-1 ─────────────────────────────────────────────────────
+    try:
+        es_norm = es.copy()
+        eps = 1e-10
+        for col in es_cols:
+            cmin = es_norm[col].min()
+            cmax = es_norm[col].max()
+            es_norm[col] = (es_norm[col] - cmin) / (cmax - cmin + eps)
+    except Exception as exc:
+        logger.error(
+            "Failed to normalise indicators 0-1: %s\n"
+            "Probable cause: non-numeric columns incorrectly identified as indicators.\n"
+            "Check: column types in the input CSV.\n"
+            "Previous skill: ecosystem-services-assessment (quantification step).",
+            exc,
+        )
+        sys.exit(1)
+
+    log_decision(
+        "normalization", "min-max [0,1] with epsilon 1e-10",
+        "evita divisao por zero quando todos os valores de um indicador sao iguais",
+    )
+
+    # ── Step 3: Correlation matrix (Spearman) ────────────────────────────────
+    log_step(3, "Compute Spearman correlation matrix among ES indicators")
+    try:
+        subset = es_norm[es_cols].dropna()
+        rho, _ = spearmanr(subset)
+        if len(es_cols) == 2:
+            # spearmanr returns scalar for 2 variables — reshape to matrix
+            cor_mat = np.array([[1.0, rho], [rho, 1.0]])
+        else:
+            cor_mat = rho
+        cor_df = pd.DataFrame(cor_mat, index=es_cols, columns=es_cols)
+    except Exception as exc:
+        logger.error(
+            "Failed to compute correlation matrix: %s\n"
+            "Probable cause: all values in some column are NA after normalisation.\n"
+            "Check: presence of variation in ES indicators.\n"
+            "Previous skill: ecosystem-services-assessment (quantification step).",
+            exc,
+        )
+        sys.exit(1)
+
+    log_decision(
+        "correlation_method", "Spearman",
+        "metodo nao-parametrico robusto a distribuicoes assimetricas comuns em dados de ES",
+    )
+
+    try:
+        csv_path = out_path / "tradeoff_matrix.csv"
+        cor_df.to_csv(csv_path)
+        logger.info("tradeoff_matrix.csv saved in: %s", output_dir)
+    except Exception as exc:
+        logger.error(
+            "Failed to salvar tradeoff_matrix.csv: %s\n"
+            "Probable cause: permissao negada ou disco cheio.\n"
+            "Check: permissoes do output directory.\n"
+            "Previous skill: [none].",
+            exc,
+        )
+        sys.exit(1)
+
+    # ── Step 4: Correlation heatmap ──────────────────────────────────────────
+    log_step(4, "Generate trade-off heatmap")
+    try:
+        fig, ax = plt.subplots(figsize=(8, 7))
+        mask = np.triu(np.ones_like(cor_df, dtype=bool), k=1)
+        sns.heatmap(
+            cor_df, mask=mask, annot=True, fmt=".2f", cmap="RdBu_r",
+            vmin=-1, vmax=1, center=0, square=True, linewidths=0.5, ax=ax,
+        )
+        ax.set_title("ES Trade-offs (Spearman r)")
+        fig.tight_layout()
+        fig.savefig(out_path / "tradeoff_heatmap.png", dpi=150)
+        plt.close(fig)
+        logger.info("tradeoff_heatmap.png saved in: %s", output_dir)
+    except Exception as exc:
+        logger.error(
+            "Failed to generate heatmap de trade-offs: %s\n"
+            "Probable cause: matplotlib/seaborn not installed ou matriz de correlacao invalida.\n"
+            "Check: se os pacotes matplotlib e seaborn estao disponiveis e a matriz tem pelo menos 2 variaveis.\n"
+            "Previous skill: [none].",
+            exc,
+        )
+        sys.exit(1)
+
+    # ── Step 5: Scatter plots for top pairs ──────────────────────────────────
+    log_step(5, "Generate scatter plots for ES indicator pairs")
+    pair_combos = list(combinations(es_cols, 2))
+    n_pairs = min(6, len(pair_combos))
+    logger.info("Generating %d scatter plots (of %d possible pairs)", n_pairs, len(pair_combos))
+    log_decision(
+        "max_scatter_plots", str(n_pairs),
+        "limitado a 6 pares para evitar geracao excessiva de arquivos",
+    )
+
+    label_col = "lulc_code" if "lulc_code" in es.columns else None
+
+    for v1, v2 in pair_combos[:n_pairs]:
+        try:
+            fig, ax = plt.subplots(figsize=(5, 4))
+            ax.scatter(es[v1], es[v2], s=30, color="#2166ac", edgecolors="white", linewidths=0.5)
+            if label_col is not None:
+                for idx, row in es.iterrows():
+                    ax.annotate(
+                        str(row[label_col]),
+                        (row[v1], row[v2]),
+                        fontsize=7, alpha=0.7,
+                        textcoords="offset points", xytext=(4, 4),
+                    )
+            ax.set_xlabel(v1)
+            ax.set_ylabel(v2)
+            ax.set_title(f"Trade-off: {v1} vs {v2}")
+            fig.tight_layout()
+            fname = f"scatter_{v1}_vs_{v2}.png"
+            fig.savefig(out_path / fname, dpi=150)
+            plt.close(fig)
+            logger.info("Saved: %s", fname)
+        except Exception as exc:
+            logger.error(
+                "Failed to generate scatter plot for pair %s vs %s: %s\n"
+                "Probable cause: column missing after filtering or annotation error.\n"
+                "Check: columns '%s' and '%s' exist and have valid data.\n"
+                "Previous skill: [none].",
+                v1, v2, exc, v1, v2,
+            )
+            sys.exit(1)
+
+    logger.info("Trade-off analysis completed. Outputs in: %s", output_dir)
+
+
+if __name__ == "__main__":
+    main()

package/skills/environmental-time-series/SKILL.md

@@ -91,7 +91,7 @@ Guides the agent through the analysis of environmental and ecological time serie
 
 ---
 
-## Key Decisions to Document
+## Decision Points
 
 - Baseline period definition
 - Gap interpolation method

package/skills/model-validation-and-uncertainty/SKILL.md

@@ -100,7 +100,7 @@ Guides the agent through rigorous evaluation of any fitted model: computing perf
 
 ---
 
-## Key Decisions to Document
+## Decision Points
 
 - Primary and secondary metrics chosen and rationale
 - Threshold selection method