ecological-agent-skills 3.1.0

package/skills/SKILL_INDEX.json

@@ -0,0 +1,1020 @@
+{
+  "skills": [
+    {
+      "skill_id": "biostatistics-workbench",
+      "display_name": "Biostatistics Workbench",
+      "version": "1.0.0",
+      "domain": [
+        "statistics",
+        "GLM",
+        "GLMM",
+        "hypothesis testing",
+        "model selection"
+      ],
+      "trigger_keywords": [
+        "statistical test",
+        "GLM",
+        "GLMM",
+        "mixed model",
+        "linear model",
+        "effect size",
+        "confidence interval",
+        "AIC",
+        "model selection",
+        "normality test",
+        "assumption check",
+        "regression",
+        "ANOVA",
+        "p-value",
+        "overdispersion",
+        "residual diagnostics"
+      ],
+      "min_inputs": {
+        "response_variable": "required",
+        "predictor_variables": "required",
+        "random_effects_structure": "conditional",
+        "study_design_description": "recommended"
+      },
+      "primary_outputs": [
+        "model_summary.txt",
+        "model_selection_table.csv",
+        "assumption_diagnostics/",
+        "effect_sizes.csv",
+        "stats_report.md"
+      ],
+      "depends_on_skills": [
+        "ecological-data-foundation"
+      ],
+      "called_by_workflows": [
+        "assess-ecological-impact",
+        "analyze-community-structure",
+        "run-occupancy-analysis"
+      ],
+      "decision_points": {
+        "n_min_glm": 20,
+        "n_recommended_glm": 50,
+        "action_if_overdispersion": "switch to negative binomial or quasi family",
+        "action_if_residuals_fail": "transform response or use non-parametric alternative"
+      },
+      "skill_md_path": "skills/biostatistics-workbench/SKILL.md"
+    },
+    {
+      "skill_id": "community-ecology-ordination",
+      "display_name": "Community Ecology Ordination",
+      "version": "1.0.0",
+      "domain": [
+        "community ecology",
+        "ordination",
+        "multivariate",
+        "diversity",
+        "beta diversity"
+      ],
+      "trigger_keywords": [
+        "species composition",
+        "community structure",
+        "NMDS",
+        "PCA ordination",
+        "PERMANOVA",
+        "beta diversity",
+        "alpha diversity",
+        "species richness",
+        "Bray-Curtis",
+        "assemblage",
+        "species matrix",
+        "diversity index",
+        "indicator species",
+        "cluster analysis",
+        "dissimilarity"
+      ],
+      "min_inputs": {
+        "species_site_matrix_csv": "required",
+        "site_environmental_metadata_csv": "recommended",
+        "grouping_variable": "recommended"
+      },
+      "primary_outputs": [
+        "ordination_plot.png",
+        "diversity_metrics.csv",
+        "beta_diversity_matrix.csv",
+        "permanova_results.txt",
+        "cluster_dendrogram.png",
+        "community_report.md"
+      ],
+      "depends_on_skills": [
+        "ecological-data-foundation"
+      ],
+      "called_by_workflows": [
+        "analyze-community-structure"
+      ],
+      "decision_points": {
+        "n_sites_min": 5,
+        "n_sites_recommended": 10,
+        "nmds_stress_max_acceptable": 0.2,
+        "action_if_stress_above_threshold": "increase NMDS dimensions to 3 or reduce species set",
+        "action_if_permanova_r2_low": "report effect size and discuss ecological significance"
+      },
+      "skill_md_path": "skills/community-ecology-ordination/SKILL.md"
+    },
+    {
+      "skill_id": "ecological-data-foundation",
+      "display_name": "Ecological Data Foundation",
+      "version": "1.0.0",
+      "domain": [
+        "data cleaning",
+        "occurrence records",
+        "data validation",
+        "QA",
+        "Darwin Core"
+      ],
+      "trigger_keywords": [
+        "clean data",
+        "validate records",
+        "occurrence data",
+        "duplicate removal",
+        "coordinate cleaning",
+        "outlier detection",
+        "data preparation",
+        "data ingestion",
+        "merge datasets",
+        "standardise fields",
+        "GBIF download",
+        "Darwin Core",
+        "data quality",
+        "flagged records",
+        "taxonomic harmonisation",
+        "data foundation",
+        "iNaturalist",
+        "eBird",
+        "OBIS",
+        "IUCN Red List",
+        "occurrence download",
+        "biodiversity data",
+        "marine occurrence",
+        "conservation status"
+      ],
+      "min_inputs": {
+        "raw_occurrence_or_survey_data": "required",
+        "data_dictionary_or_protocol": "recommended",
+        "environmental_layers": "optional",
+        "existing_metadata_record": "optional"
+      },
+      "primary_outputs": [
+        "data_clean.csv",
+        "qa_report.md",
+        "schema.yaml",
+        "metadata.xml",
+        "flagged_records.csv",
+        "occurrences_raw_GBIF_{species}_{date}.csv",
+        "occurrences_raw_iNat_{species}_{date}.csv",
+        "occurrences_raw_eBird_{species}_{date}.csv",
+        "occurrences_raw_OBIS_{species}_{date}.csv",
+        "iucn_status_{species}.csv",
+        "iucn_habitats_{species}.csv",
+        "download_metadata_{source}_{species}.txt"
+      ],
+      "depends_on_skills": [],
+      "called_by_workflows": [
+        "run-sdm-study",
+        "run-occupancy-analysis",
+        "assess-ecological-impact",
+        "analyze-community-structure",
+        "analyze-environmental-change",
+        "assess-ecosystem-services",
+        "run-multispecies-screening"
+      ],
+      "decision_points": {
+        "n_records_min_for_sdm": 30,
+        "action_if_duplicates_exceed_20pct": "investigate source bias before proceeding",
+        "action_if_coordinates_fail_cleaning": "flag and exclude; document in qa_report.md"
+      },
+      "skill_md_path": "skills/ecological-data-foundation/SKILL.md"
+    },
+    {
+      "skill_id": "ecological-impact-assessment",
+      "display_name": "Ecological Impact Assessment",
+      "version": "1.0.0",
+      "domain": [
+        "BACI",
+        "impact assessment",
+        "fragmentation",
+        "landscape ecology",
+        "pressure index"
+      ],
+      "trigger_keywords": [
+        "BACI",
+        "before after control impact",
+        "impact assessment",
+        "disturbance effect",
+        "land use change",
+        "fragmentation",
+        "landscape metrics",
+        "pressure index",
+        "threat index",
+        "intervention effect",
+        "management effectiveness",
+        "before after comparison",
+        "control impact"
+      ],
+      "min_inputs": {
+        "indicator_time_series_csv": "required",
+        "disturbance_event_date": "required",
+        "land_cover_maps": "conditional",
+        "pressure_layers": "optional"
+      },
+      "primary_outputs": [
+        "baci_results.csv",
+        "fragmentation_metrics.csv",
+        "pressure_index.tif",
+        "impact_synthesis.md",
+        "impact_plots/"
+      ],
+      "depends_on_skills": [
+        "ecological-data-foundation",
+        "geoprocessing-for-ecology"
+      ],
+      "called_by_workflows": [
+        "assess-ecological-impact"
+      ],
+      "decision_points": {
+        "n_sites_min_per_group": 5,
+        "n_time_periods_min": 3,
+        "action_if_baci_ns": "compute post-hoc power; report effect size with CI",
+        "action_if_permdisp_significant": "report PERMDISP alongside PERMANOVA; discuss heterogeneity"
+      },
+      "skill_md_path": "skills/ecological-impact-assessment/SKILL.md"
+    },
+    {
+      "skill_id": "ecosystem-services-assessment",
+      "display_name": "Ecosystem Services Assessment",
+      "version": "1.0.0",
+      "domain": [
+        "ecosystem services",
+        "InVEST",
+        "trade-offs",
+        "land cover",
+        "PES"
+      ],
+      "trigger_keywords": [
+        "ecosystem services",
+        "ES assessment",
+        "InVEST",
+        "carbon stock",
+        "water yield",
+        "soil erosion",
+        "biodiversity service",
+        "trade-off analysis",
+        "PES",
+        "payments for ecosystem services",
+        "ES mapping",
+        "ES valuation",
+        "natural capital",
+        "RUSLE",
+        "habitat quality",
+        "pollination service"
+      ],
+      "min_inputs": {
+        "land_cover_map": "required",
+        "biophysical_data": "required",
+        "study_area_polygon": "required",
+        "socioeconomic_data": "optional"
+      },
+      "primary_outputs": [
+        "es_indicator_maps/",
+        "es_summary_table.csv",
+        "tradeoff_matrix.csv",
+        "tradeoff_plot.png",
+        "es_report.md"
+      ],
+      "depends_on_skills": [
+        "ecological-data-foundation",
+        "geoprocessing-for-ecology"
+      ],
+      "called_by_workflows": [
+        "assess-ecosystem-services"
+      ],
+      "decision_points": {
+        "land_cover_accuracy_min": 85,
+        "action_if_accuracy_below": "perform uncertainty analysis; include classification error in ES estimates",
+        "action_if_invest_nodata_exceeds_30pct": "check CRS and extent alignment before rerunning"
+      },
+      "skill_md_path": "skills/ecosystem-services-assessment/SKILL.md"
+    },
+    {
+      "skill_id": "environmental-time-series",
+      "display_name": "Environmental Time Series Analysis",
+      "version": "1.0.0",
+      "domain": [
+        "time series",
+        "trend detection",
+        "BFAST",
+        "remote sensing",
+        "anomaly detection"
+      ],
+      "trigger_keywords": [
+        "time series",
+        "trend analysis",
+        "NDVI trend",
+        "EVI",
+        "LST",
+        "Mann-Kendall",
+        "BFAST",
+        "breakpoint",
+        "structural change",
+        "anomaly detection",
+        "seasonal decomposition",
+        "recovery trajectory",
+        "regime shift",
+        "temporal trend",
+        "pixel-wise trend",
+        "Sen slope",
+        "STL decomposition"
+      ],
+      "min_inputs": {
+        "time_indexed_variable": "required",
+        "time_series_frequency": "required",
+        "disturbance_event_date": "conditional",
+        "baseline_period": "recommended"
+      },
+      "primary_outputs": [
+        "trend_results.csv",
+        "seasonal_decomposition.png",
+        "breakpoints.csv",
+        "anomaly_series.csv",
+        "recovery_metrics.csv",
+        "timeseries_report.md"
+      ],
+      "depends_on_skills": [
+        "ecological-data-foundation",
+        "geoprocessing-for-ecology"
+      ],
+      "called_by_workflows": [
+        "analyze-environmental-change",
+        "build-fire-risk-map"
+      ],
+      "decision_points": {
+        "n_time_steps_min": 10,
+        "action_if_autocorrelation_detected": "apply pre-whitening before Mann-Kendall test",
+        "action_if_bfast_breakpoints_exceed_5": "increase h parameter; check for artefacts"
+      },
+      "skill_md_path": "skills/environmental-time-series/SKILL.md"
+    },
+    {
+      "skill_id": "geoprocessing-for-ecology",
+      "display_name": "Geoprocessing for Ecology",
+      "version": "1.0.0",
+      "domain": [
+        "geoprocessing",
+        "CRS",
+        "raster",
+        "vector",
+        "spatial extraction",
+        "remote sensing"
+      ],
+      "trigger_keywords": [
+        "reproject",
+        "CRS",
+        "coordinate reference system",
+        "clip raster",
+        "mask raster",
+        "spatial extraction",
+        "extract values",
+        "buffer",
+        "raster stack",
+        "resample",
+        "spatial join",
+        "overlay",
+        "geoprocessing",
+        "GeoTIFF",
+        "shapefile",
+        "GDAL",
+        "study area mask",
+        "crop raster",
+        "align rasters"
+      ],
+      "min_inputs": {
+        "occurrence_or_sample_points": "required",
+        "study_area_polygon": "required",
+        "environmental_rasters": "required",
+        "land_cover_layer": "optional"
+      },
+      "primary_outputs": [
+        "layers_reprojected/",
+        "predictors_stack.tif",
+        "points_with_env.csv",
+        "study_area_buffered.gpkg",
+        "spatial_qa_report.md",
+        "worldclim/wc2.1_{res}m_bio_{1..19}.tif",
+        "chelsa/CHELSA_bio{1..19}.tif",
+        "era5/era5_land_temp_precip_monthly.nc",
+        "predictor_metadata.csv"
+      ],
+      "depends_on_skills": [
+        "ecological-data-foundation"
+      ],
+      "called_by_workflows": [
+        "run-sdm-study",
+        "assess-ecological-impact",
+        "assess-ecosystem-services",
+        "build-fire-risk-map",
+        "run-multispecies-screening"
+      ],
+      "decision_points": {
+        "action_if_crs_mismatch": "reproject all layers to common CRS before any spatial operation",
+        "action_if_resolution_mismatch": "resample to coarsest resolution; document choice in decision_log.md",
+        "action_if_extent_mismatch": "clip all layers to study area extent"
+      },
+      "skill_md_path": "skills/geoprocessing-for-ecology/SKILL.md"
+    },
+    {
+      "skill_id": "model-validation-and-uncertainty",
+      "display_name": "Model Validation and Uncertainty",
+      "version": "1.0.0",
+      "domain": [
+        "model validation",
+        "AUC",
+        "calibration",
+        "uncertainty",
+        "extrapolation risk",
+        "MOP"
+      ],
+      "trigger_keywords": [
+        "model performance",
+        "AUC",
+        "ROC curve",
+        "model validation",
+        "calibration curve",
+        "uncertainty",
+        "extrapolation risk",
+        "MOP analysis",
+        "MESS",
+        "ExDet",
+        "overfitting",
+        "cross-validation performance",
+        "TSS",
+        "sensitivity",
+        "specificity",
+        "ensemble uncertainty",
+        "prediction interval",
+        "bootstrap uncertainty"
+      ],
+      "min_inputs": {
+        "fitted_model_object": "required",
+        "validation_dataset": "required",
+        "training_cv_predictions": "required",
+        "prediction_surface": "conditional"
+      },
+      "primary_outputs": [
+        "performance_metrics.csv",
+        "calibration_plot.png",
+        "roc_curve.png",
+        "sensitivity_report.md",
+        "uncertainty_map.tif",
+        "validation_report.md"
+      ],
+      "depends_on_skills": [
+        "predictive-modeling-best-practices"
+      ],
+      "called_by_workflows": [
+        "run-sdm-study",
+        "run-multispecies-screening",
+        "assess-ecosystem-services"
+      ],
+      "decision_points": {
+        "auc_min_acceptable": 0.7,
+        "tss_min_acceptable": 0.4,
+        "mop_zero_pct_warning_threshold": 30,
+        "action_if_auc_below": "revise predictors; expand calibration grid; report as unreliable",
+        "action_if_mop_zero_exceeds_threshold": "restrict projection extent; add explicit caveats"
+      },
+      "skill_md_path": "skills/model-validation-and-uncertainty/SKILL.md"
+    },
+    {
+      "skill_id": "occupancy-and-detection",
+      "display_name": "Occupancy and Detection Modeling",
+      "version": "1.0.0",
+      "domain": [
+        "occupancy",
+        "detection probability",
+        "unmarked",
+        "monitoring",
+        "imperfect detection"
+      ],
+      "trigger_keywords": [
+        "occupancy model",
+        "detection probability",
+        "imperfect detection",
+        "occupancy estimation",
+        "unmarked",
+        "MacKenzie",
+        "psi",
+        "detection history",
+        "repeated visits",
+        "site occupancy",
+        "dynamic occupancy",
+        "colonisation",
+        "extinction probability",
+        "goodness of fit",
+        "MacKenzie-Bailey",
+        "c-hat"
+      ],
+      "min_inputs": {
+        "detection_history_matrix": "required",
+        "site_covariates_csv": "recommended",
+        "observation_covariates_csv": "recommended",
+        "n_seasons": "conditional"
+      },
+      "primary_outputs": [
+        "occupancy_estimates.csv",
+        "detection_estimates.csv",
+        "model_selection_table.csv",
+        "covariate_effects.csv",
+        "gof_report.md",
+        "occupancy_map.tif"
+      ],
+      "depends_on_skills": [
+        "ecological-data-foundation"
+      ],
+      "called_by_workflows": [
+        "run-occupancy-analysis"
+      ],
+      "decision_points": {
+        "n_sites_min": 15,
+        "n_sites_recommended": 30,
+        "n_visits_min": 3,
+        "c_hat_threshold": 1.5,
+        "action_if_gof_fails": "add detection covariate or relax closure assumption",
+        "action_if_c_hat_above_threshold": "use QAICc for model selection; report overdispersion"
+      },
+      "skill_md_path": "skills/occupancy-and-detection/SKILL.md"
+    },
+    {
+      "skill_id": "predictive-modeling-best-practices",
+      "display_name": "Predictive Modeling Best Practices",
+      "version": "1.0.0",
+      "domain": [
+        "predictive modeling",
+        "collinearity",
+        "cross-validation",
+        "hyperparameter tuning",
+        "data leakage"
+      ],
+      "trigger_keywords": [
+        "collinearity",
+        "VIF",
+        "predictor selection",
+        "feature selection",
+        "cross-validation strategy",
+        "spatial CV",
+        "block CV",
+        "hyperparameter tuning",
+        "overfitting",
+        "data leakage",
+        "sampling bias",
+        "background points",
+        "pseudo-absence",
+        "model design",
+        "predictor reduction",
+        "ENMeval tuning",
+        "regularisation",
+        "spatial autocorrelation"
+      ],
+      "min_inputs": {
+        "feature_matrix_csv": "required",
+        "target_variable": "required",
+        "spatial_coordinates": "recommended",
+        "candidate_model_list": "optional"
+      },
+      "primary_outputs": [
+        "cv_strategy.md",
+        "collinearity_report.csv",
+        "selected_predictors.txt",
+        "tuning_results.csv",
+        "leakage_audit.md",
+        "modeling_plan.md"
+      ],
+      "depends_on_skills": [
+        "ecological-data-foundation",
+        "geoprocessing-for-ecology"
+      ],
+      "called_by_workflows": [
+        "run-sdm-study",
+        "run-multispecies-screening"
+      ],
+      "decision_points": {
+        "vif_max_acceptable": 10,
+        "pearson_correlation_max": 0.7,
+        "action_if_vif_above_threshold": "remove predictor with highest VIF iteratively until all below threshold",
+        "action_if_spatial_autocorrelation": "use spatial block CV instead of random CV"
+      },
+      "skill_md_path": "skills/predictive-modeling-best-practices/SKILL.md"
+    },
+    {
+      "skill_id": "reproducible-ecology-pipeline",
+      "display_name": "Reproducible Ecology Pipeline",
+      "version": "1.0.0",
+      "domain": [
+        "reproducibility",
+        "provenance",
+        "audit trail",
+        "renv",
+        "targets",
+        "DVC"
+      ],
+      "trigger_keywords": [
+        "reproducibility",
+        "audit trail",
+        "data provenance",
+        "decision log",
+        "file manifest",
+        "session info",
+        "software environment",
+        "renv",
+        "targets",
+        "DVC",
+        "MLflow",
+        "parameter manifest",
+        "reproducible workflow",
+        "version control",
+        "project initialisation",
+        "checksums",
+        "pipeline logging"
+      ],
+      "min_inputs": {
+        "project_directory": "required",
+        "analysis_scripts": "recommended",
+        "model_parameter_files": "recommended",
+        "qa_reports_from_upstream_skills": "recommended"
+      },
+      "primary_outputs": [
+        "reproducibility_checklist.md",
+        "parameter_manifest.yaml",
+        "decision_log.md",
+        "software_environment.txt",
+        "data_provenance.md",
+        "file_manifest.md"
+      ],
+      "depends_on_skills": [],
+      "called_by_workflows": [
+        "run-sdm-study",
+        "run-occupancy-analysis",
+        "assess-ecological-impact",
+        "analyze-community-structure",
+        "analyze-environmental-change",
+        "assess-ecosystem-services",
+        "produce-technical-report"
+      ],
+      "decision_points": {
+        "action_if_not_reproducible_from_params": "complete parameter manifest before finalising any report",
+        "action_if_seed_sensitive_results": "document random seed explicitly in parameter_manifest.yaml"
+      },
+      "skill_md_path": "skills/reproducible-ecology-pipeline/SKILL.md"
+    },
+    {
+      "skill_id": "species-distribution-modeling",
+      "display_name": "Species Distribution Modeling",
+      "version": "1.0.0",
+      "domain": [
+        "SDM",
+        "ENM",
+        "niche modeling",
+        "MaxEnt",
+        "ensemble modeling"
+      ],
+      "trigger_keywords": [
+        "distribution model",
+        "habitat suitability",
+        "MaxEnt",
+        "niche model",
+        "potential distribution",
+        "range map",
+        "suitable area",
+        "ecological niche",
+        "ENM",
+        "biomod2",
+        "ensemble SDM",
+        "climate projection",
+        "invasion risk",
+        "range shift",
+        "suitability map",
+        "calibration area",
+        "occurrence modeling"
+      ],
+      "min_inputs": {
+        "occurrences_csv": "required",
+        "predictor_stack_tif": "required",
+        "study_area": "required",
+        "future_scenarios": "optional"
+      },
+      "primary_outputs": [
+        "suitability_current.tif",
+        "suitability_binary.tif",
+        "suitability_scenarios/",
+        "ensemble_sd.tif",
+        "variable_importance.csv",
+        "response_curves.png",
+        "sdm_report.md"
+      ],
+      "depends_on_skills": [
+        "ecological-data-foundation",
+        "geoprocessing-for-ecology",
+        "predictive-modeling-best-practices"
+      ],
+      "called_by_workflows": [
+        "run-sdm-study",
+        "run-multispecies-screening"
+      ],
+      "decision_points": {
+        "n_occurrences_min": 10,
+        "n_occurrences_recommended": 30,
+        "auc_min_acceptable": 0.7,
+        "action_if_n_below_min": "do not fit model; use literature-based range map with explicit caveat",
+        "action_if_auc_below": "revise predictors and expand calibration grid"
+      },
+      "skill_md_path": "skills/species-distribution-modeling/SKILL.md"
+    },
+    {
+      "skill_id": "camera-trap-processing",
+      "display_name": "Camera Trap Processing",
+      "version": "1.0.0",
+      "domain": [
+        "camera traps",
+        "wildlife monitoring",
+        "activity patterns",
+        "occupancy"
+      ],
+      "trigger_keywords": [
+        "camera trap",
+        "wildlife camera",
+        "detection event",
+        "trap night",
+        "activity pattern",
+        "diel activity",
+        "camtrapR",
+        "overlap index",
+        "RAI",
+        "relative activity index",
+        "detection history",
+        "camera station"
+      ],
+      "min_inputs": {
+        "image_directory": "required",
+        "camera_metadata": "required",
+        "species_list": "recommended",
+        "independence_threshold_min": "optional"
+      },
+      "primary_outputs": [
+        "record_table.csv",
+        "detection_history.csv",
+        "camera_operation.csv",
+        "trap_effort_summary.csv",
+        "activity_overlap.csv",
+        "activity_plot.png"
+      ],
+      "depends_on_skills": [
+        "ecological-data-foundation",
+        "occupancy-and-detection"
+      ],
+      "called_by_workflows": [],
+      "decision_points": {
+        "independence_threshold_default_min": 30,
+        "min_events_for_activity": 75,
+        "min_events_for_RAI": 10,
+        "min_trap_nights_per_station": 100
+      },
+      "skill_md_path": "skills/camera-trap-processing/SKILL.md"
+    },
+    {
+      "skill_id": "acoustic-monitoring",
+      "display_name": "Acoustic Monitoring",
+      "version": "1.0.0",
+      "domain": [
+        "bioacoustics",
+        "PAM",
+        "soundscape ecology",
+        "species detection"
+      ],
+      "trigger_keywords": [
+        "acoustic monitoring",
+        "soundscape",
+        "bioacoustics",
+        "acoustic index",
+        "ACI",
+        "NDSI",
+        "BirdNET",
+        "passive acoustic",
+        "AudioMoth",
+        "dawn chorus",
+        "species detection",
+        "bat detector",
+        "acoustic complexity"
+      ],
+      "min_inputs": {
+        "audio_directory": "required",
+        "recording_metadata": "recommended",
+        "species_list": "optional",
+        "location_coordinates": "recommended"
+      },
+      "primary_outputs": [
+        "acoustic_indices_timeseries.csv",
+        "indices_summary.csv",
+        "detections_filtered.csv",
+        "species_list.csv",
+        "soundscape_plot.png"
+      ],
+      "depends_on_skills": [
+        "ecological-data-foundation",
+        "environmental-time-series"
+      ],
+      "called_by_workflows": [],
+      "decision_points": {
+        "min_confidence_threshold": 0.7,
+        "min_recording_hours_for_richness": 48,
+        "ndsi_disturbance_threshold": -0.3,
+        "snr_exclusion_threshold_db": 10
+      },
+      "skill_md_path": "skills/acoustic-monitoring/SKILL.md"
+    },
+    {
+      "skill_id": "landscape-connectivity",
+      "display_name": "Landscape Connectivity",
+      "version": "1.0.0",
+      "domain": [
+        "landscape ecology",
+        "connectivity",
+        "corridors",
+        "Circuitscape",
+        "graph theory"
+      ],
+      "trigger_keywords": [
+        "habitat connectivity",
+        "wildlife corridor",
+        "Circuitscape",
+        "IIC",
+        "dPC",
+        "resistance surface",
+        "least-cost path",
+        "stepping stone",
+        "fragmentation",
+        "patch importance",
+        "betweenness centrality",
+        "landscape graph"
+      ],
+      "min_inputs": {
+        "habitat_patches": "required",
+        "dispersal_distance_m": "required",
+        "landcover_raster": "recommended",
+        "resistance_table": "recommended"
+      },
+      "primary_outputs": [
+        "patch_metrics.csv",
+        "landscape_summary.csv",
+        "resistance_combined.tif",
+        "connectivity_graph.png",
+        "pinchpoints.tif"
+      ],
+      "depends_on_skills": [
+        "geoprocessing-for-ecology",
+        "ecological-impact-assessment"
+      ],
+      "called_by_workflows": [],
+      "decision_points": {
+        "min_patches_for_graph": 3,
+        "sensitivity_dmax_values": [
+          500,
+          1000,
+          2000,
+          5000
+        ],
+        "min_iic_pc_for_connectivity": 0.01,
+        "pinchpoint_percentile": 95
+      },
+      "skill_md_path": "skills/landscape-connectivity/SKILL.md"
+    },
+    {
+      "skill_id": "population-viability-analysis",
+      "display_name": "Population Viability Analysis",
+      "version": "1.0.0",
+      "domain": [
+        "PVA",
+        "population dynamics",
+        "matrix models",
+        "extinction risk",
+        "IUCN"
+      ],
+      "trigger_keywords": [
+        "PVA",
+        "population viability",
+        "Leslie matrix",
+        "Lefkovitch matrix",
+        "lambda",
+        "quasi-extinction",
+        "IUCN criterion",
+        "extinction probability",
+        "elasticity",
+        "sensitivity",
+        "stochastic PVA",
+        "MVP",
+        "minimum viable population"
+      ],
+      "min_inputs": {
+        "vital_rates_csv": "required",
+        "initial_population_size": "recommended",
+        "time_horizon_years": "optional",
+        "quasi_extinction_threshold": "optional"
+      },
+      "primary_outputs": [
+        "lambda_summary.csv",
+        "sensitivity_elasticity.csv",
+        "stochastic_pva_results.csv",
+        "extinction_curve.csv",
+        "iucn_criterion_e.csv",
+        "trajectory_plot.png"
+      ],
+      "depends_on_skills": [
+        "biostatistics-workbench",
+        "occupancy-and-detection"
+      ],
+      "called_by_workflows": [],
+      "decision_points": {
+        "min_years_vital_rates": 3,
+        "cv_threshold_stochastic_required": 0.3,
+        "lambda_rapid_decline": 0.95,
+        "default_quasi_ext_threshold": 50,
+        "default_t_max_years": 100
+      },
+      "skill_md_path": "skills/population-viability-analysis/SKILL.md"
+    },
+    {
+      "skill_id": "spatial-prioritization",
+      "display_name": "Spatial Prioritization",
+      "version": "1.0.0",
+      "domain": [
+        "conservation planning",
+        "prioritizr",
+        "Marxan",
+        "Zonation",
+        "ILP",
+        "protected areas"
+      ],
+      "trigger_keywords": [
+        "conservation planning",
+        "Marxan",
+        "Zonation",
+        "prioritizr",
+        "30x30",
+        "irreplaceability",
+        "BLM",
+        "boundary length modifier",
+        "protected area design",
+        "minimum set",
+        "systematic conservation",
+        "representation target"
+      ],
+      "min_inputs": {
+        "planning_unit_raster": "required",
+        "feature_rasters": "required",
+        "representation_targets": "required",
+        "cost_layer": "recommended",
+        "locked_in_areas": "optional",
+        "locked_out_areas": "optional"
+      },
+      "primary_outputs": [
+        "solution.tif",
+        "feature_representation.csv",
+        "cost_summary.csv",
+        "irreplaceability.tif",
+        "blm_calibration.csv",
+        "portfolio_frequency.tif",
+        "prioritization_map.png"
+      ],
+      "depends_on_skills": [
+        "species-distribution-modeling",
+        "ecosystem-services-assessment",
+        "landscape-connectivity"
+      ],
+      "called_by_workflows": [],
+      "decision_points": {
+        "default_target": 0.3,
+        "max_iterations_before_target_relax": 1000,
+        "pct_targets_met_for_acceptance": 80,
+        "irreplaceability_restoration_threshold": 0.8,
+        "blm_calibration_values": [
+          0,
+          0.001,
+          0.01,
+          0.05,
+          0.1,
+          0.5,
+          1.0
+        ]
+      },
+      "skill_md_path": "skills/spatial-prioritization/SKILL.md"
+    }
+  ],
+  "_metadata": {
+    "repository": "ecological-agent-skills",
+    "index_version": "1.0.0",
+    "last_updated": "2026-03-05",
+    "total_skills": 17,
+    "total_workflows": 13
+  }
+}