ecological-agent-skills

Performs multivariate community ecology analyses including ordination, diversity metrics, and assemblage comparisons. Use this skill when the user mentions species composition, NMDS, PCA ordination, PERMANOVA, beta diversity, alpha diversity, species richness, Bray-Curtis dissimilarity, indicator species analysis, cluster analysis, species-by-site matrices, diversity indices, or assemblage structure comparisons.

Guides predictor selection, collinearity checks, cross-validation strategy, and hyperparameter tuning for ecological predictive models. Use this skill when the user mentions VIF, collinearity, feature selection, spatial cross-validation, block CV, hyperparameter tuning, overfitting prevention, data leakage auditing, background point selection, pseudo-absence generation, ENMeval tuning, regularization, or spatial autocorrelation correction.

Quantifies ecological impacts using BACI designs, landscape fragmentation metrics, and pressure indices. Use this skill when the user mentions BACI analysis, before-after-control-impact, impact assessment, disturbance effects, land use change impacts, fragmentation metrics, landscape metrics, pressure or threat indices, intervention effectiveness, management outcome evaluation, or control-impact comparisons.

Maps and quantifies ecosystem services including carbon stocks, water yield, soil erosion, and habitat quality with trade-off analysis. Use this skill when the user mentions ecosystem services, InVEST models, ES mapping, carbon sequestration, water yield estimation, RUSLE erosion modeling, habitat quality, pollination services, trade-off analysis, PES (payments for ecosystem services), natural capital, or ES valuation.

Validates predictive models and quantifies uncertainty including AUC/TSS metrics, calibration, extrapolation risk (MOP/MESS/ExDet), and ensemble uncertainty maps. Use this skill when the user needs model performance evaluation, ROC curves, cross-validation results, calibration curves, overfitting diagnostics, prediction intervals, bootstrap uncertainty, sensitivity/specificity assessment, or extrapolation risk analysis.

Runs frequentist statistical analyses including GLMs, GLMMs, model selection, and assumption diagnostics for ecological data. Use this skill when the user needs statistical tests, linear or mixed models, ANOVA, effect sizes, confidence intervals, AIC-based model selection, residual diagnostics, overdispersion checks, regression analysis, p-value interpretation, normality tests, or hypothesis testing on ecological datasets.

Detects trends, breakpoints, and recovery trajectories in environmental time series data from remote sensing or field measurements. Use this skill when the user mentions time series analysis, NDVI/EVI/LST trends, Mann-Kendall tests, Sen slope, BFAST breakpoints, structural change detection, seasonal decomposition (STL), anomaly detection, recovery trajectories, regime shifts, or pixel-wise trend analysis.

Fits single-season and dynamic occupancy models that account for imperfect detection in wildlife survey data. Use this skill when the user mentions occupancy estimation, detection probability, imperfect detection, detection histories, repeated visits, MacKenzie models, psi estimation, dynamic occupancy (colonization/extinction), goodness-of-fit testing (c-hat), site occupancy, or unmarked package analyses.

Ensures full reproducibility of ecological analyses through provenance tracking, decision logging, parameter manifests, and environment documentation. Use this skill when the user mentions reproducibility, audit trails, data provenance, decision logs, file manifests, session info, renv, targets, DVC, MLflow, parameter versioning, checksums, or pipeline documentation and project initialization.

Runs the complete species distribution modeling (SDM/ENM) pipeline: occurrence preparation, model fitting (MaxEnt, ensemble), thresholding, projection under climate scenarios, and interpretation. Use this skill when the user mentions habitat suitability, niche modeling, MaxEnt, biomod2, potential distribution, range maps, suitable area mapping, climate projections, invasion risk, range shift analysis, suitability mapping, ENM, ecological niche model, or calibration area definition.

Cleans, validates, and standardizes ecological occurrence records and downloads biodiversity data from global repositories. Use this skill when the user needs data cleaning, coordinate validation, duplicate removal, outlier detection, taxonomic harmonization, or downloads from GBIF, iNaturalist, eBird, OBIS, or IUCN Red List. Also triggers for Darwin Core formatting, data quality reports, flagged records, and biodiversity data preparation.

Handles spatial data operations: reprojection, raster stacking, clipping, extraction, and environmental predictor downloads for ecological analyses. Use this skill when the user needs CRS reprojection, raster masking or cropping, spatial extraction, buffer creation, raster resampling, spatial joins, GeoTIFF processing, shapefile operations, WorldClim/CHELSA/ERA5 predictor downloads, GDAL operations, or predictor stack preparation.

Processes passive acoustic monitoring (PAM) data to compute soundscape indices and detect species from audio recordings. Use this skill when the user mentions acoustic monitoring, bioacoustics, soundscape ecology, acoustic indices (ACI, NDSI, ADI), BirdNET, AudioMoth, bat detectors, dawn chorus analysis, passive acoustic recorders, species detection from audio, or sound diversity metrics.

Processes camera trap image records into structured detection data, activity patterns, and trap effort summaries. Use this skill when the user mentions camera traps, wildlife cameras, trap nights, detection events, diel activity patterns, camtrapR, temporal overlap indices (Dhat), RAI (relative abundance index), camera station data, detection history generation, or independence thresholds for photo events.

Analyzes landscape connectivity using graph theory, resistance surfaces, and corridor identification for conservation planning. Use this skill when the user mentions habitat connectivity, wildlife corridors, Circuitscape, least-cost paths, resistance surfaces, IIC/dPC connectivity metrics, stepping stones, patch importance ranking, betweenness centrality, fragmentation analysis, landscape graphs, or pinchpoint identification.

Builds matrix population models (Leslie/Lefkovitch) and runs stochastic PVA simulations to assess extinction risk and IUCN criteria. Use this skill when the user mentions PVA, population viability, lambda growth rate, Leslie or Lefkovitch matrices, quasi-extinction thresholds, elasticity or sensitivity analysis, stochastic population projections, minimum viable population (MVP), or IUCN Criterion E assessment.

Solves systematic conservation planning problems using integer linear programming (prioritizr), Marxan, or Zonation for protected area design. Use this skill when the user mentions conservation planning, 30x30 targets, Marxan, Zonation, prioritizr, irreplaceability, boundary length modifier (BLM), minimum set problems, representation targets, systematic conservation, or protected area network design.