ecological-agent-skills 3.1.1 → 3.2.0

package/AGENT_CONTEXT.md

@@ -47,10 +47,17 @@ Each workflow lives at `workflows/<workflow-id>/WORKFLOW.md`.
 | **Environmental time series** | ecological-data-foundation | environmental-time-series | biostatistics-workbench | reproducible-ecology-pipeline | — |
 | **Ecosystem services** | ecological-data-foundation | geoprocessing-for-ecology | ecosystem-services-assessment | model-validation-and-uncertainty | reproducible-ecology-pipeline |
 | **Multispecies screening** | ecological-data-foundation | geoprocessing-for-ecology | species-distribution-modeling (loop) | model-validation-and-uncertainty | reproducible-ecology-pipeline |
+| **Acoustic monitoring** | ecological-data-foundation | acoustic-monitoring | biostatistics-workbench | model-validation-and-uncertainty | reproducible-ecology-pipeline |
+| **Camera trap occupancy** | ecological-data-foundation | camera-trap-processing | occupancy-and-detection | model-validation-and-uncertainty | reproducible-ecology-pipeline |
+| **Landscape connectivity** | ecological-data-foundation | geoprocessing-for-ecology | landscape-connectivity | model-validation-and-uncertainty | reproducible-ecology-pipeline |
+| **Population viability** | ecological-data-foundation | biostatistics-workbench | population-viability-analysis | model-validation-and-uncertainty | reproducible-ecology-pipeline |
+| **Conservation prioritization** | ecological-data-foundation | geoprocessing-for-ecology | species-distribution-modeling | spatial-prioritization | reproducible-ecology-pipeline |
 
 For multispecies projects always read `workflows/run-multispecies-screening/WORKFLOW.md`
 before starting. It contains the priority classification logic.
 
+Available workflows (14): `run-sdm-study`, `run-multispecies-screening`, `run-occupancy-analysis`, `run-camera-trap-occupancy`, `run-acoustic-monitoring`, `run-population-viability`, `run-conservation-prioritization`, `assess-ecological-impact`, `assess-ecosystem-services`, `assess-landscape-connectivity`, `analyze-community-structure`, `analyze-environmental-change`, `build-fire-risk-map`, `produce-technical-report`.
+
 ---
 
 ## 3. Disambiguation Rules for Overlapping Skills
@@ -153,7 +160,53 @@ Apply the appropriate routing based on project complexity:
 
 ---
 
-## 7. File Conventions of This Repository
+## 7. Environmental Data Sources
+
+### Default source: CHELSA v2.1
+
+The default environmental predictor source for all SDM and geoprocessing workflows is **CHELSA v2.1**
+(Climatologies at High resolution for the Earth's Land Surface Areas).
+
+- Resolution: ~1 km (30 arcsec)
+- Variables: BIO1-BIO19 (1981-2010 climatology)
+- Download URL pattern: `https://os.zhdk.cloud.switch.ch/chelsav2/GLOBAL/climatologies/1981-2010/bio/CHELSA_bio{N}_1981-2010_V.2.1.tif`
+- No authentication required
+- License: CC BY 4.0
+
+**WorldClim v2.1** is the automatic fallback if CHELSA downloads fail.
+The `download_predictors.py` script handles this transparently — no user action required.
+
+Do not default to WorldClim unless the user explicitly requests it or CHELSA is unavailable.
+
+### Python version compatibility
+
+| Python | Status for this repository |
+|--------|---------------------------|
+| 3.11 | Recommended — all packages build correctly |
+| 3.12 | Supported — most packages available |
+| 3.13 | Untested |
+| 3.14 | Not recommended — `elapid` (MaxEnt) fails to build; `pygbif` has API bugs |
+
+If `elapid` is unavailable (Python 3.12+), `sdm_pipeline.py` automatically falls back to an
+RF + BRT ensemble without MaxEnt. This is logged as a DECISION entry.
+
+If `pygbif` raises a `TypeError` on `Session.request()` (Python 3.14), `download_from_gbif.py`
+automatically falls back to direct HTTP calls to the GBIF REST API.
+
+### Spatial thinning
+
+`clean_occurrences.py` accepts an optional third argument `thin_deg` (decimal degrees).
+When provided, one record is retained per `thin_deg × thin_deg` grid cell to reduce
+spatial autocorrelation before SDM fitting. Recommended values: 0.1 (~11 km) to 0.5 (~55 km).
+
+Example:
+```bash
+python clean_occurrences.py data/raw/occurrences.csv data/processed 0.1
+```
+
+---
+
+## 8. File Conventions of This Repository
 
 ### Where to put input data
 - Place raw input files in `data/raw/` (create if absent).

package/CATALOG.md

@@ -152,7 +152,7 @@ A quick-reference index for all 17 skills. Each row summarises the skill's domai
 **When to use:** When processing audio recordings from AudioMoth, SM4, or similar recorders to compute soundscape indices or detect species via BirdNET or similar classifiers.
 **Inputs:** Audio directory (WAV/FLAC), recording metadata, species list (optional), location coordinates
 **Outputs:** Acoustic indices time series (CSV), detection list with confidence scores, species accumulation curve, soundscape heatmap
-**Used by workflows:** (standalone; pairs with environmental-time-series)
+**Used by workflows:** run-acoustic-monitoring; pairs with environmental-time-series
 
 ---
 
@@ -192,14 +192,15 @@ A quick-reference index for all 17 skills. Each row summarises the skill's domai
 | analyze-community-structure | ✓ | | ✓ | | ✓ | | | ✓ | | | | ✓ | | | | | |
 | build-fire-risk-map | ✓ | ✓ | | ✓ | ✓ | | | | ✓ | ✓ | | | | | | | |
 | run-occupancy-analysis | ✓ | | ✓ | | ✓ | | ✓ | | | | | ✓ | | | | | |
-| analyze-environmental-change | ✓ | ✓ | | | | | | | ✓ | ✓ | | ✓ | | ✓ | | | |
+| analyze-environmental-change | ✓ | ✓ | | | | | | | ✓ | ✓ | | ✓ | | | | | |
 | assess-ecosystem-services | ✓ | ✓ | ✓ | | | | | | | | ✓ | ✓ | | | | | |
-| produce-technical-report | | | | | | | | | | | | ✓ | | | | | |
+| produce-technical-report | | | ✓ | | | | | | | | | ✓ | | | | | |
 | run-multispecies-screening | ✓ | ✓ | | ✓ | ✓ | ✓ | | | | | | | | | | | |
 | run-camera-trap-occupancy | ✓ | | | | ✓ | | ✓ | | | | | ✓ | ✓ | | | | |
 | assess-landscape-connectivity | ✓ | ✓ | | | ✓ | | | | | | | ✓ | | | ✓ | | |
 | run-population-viability | ✓ | | ✓ | | ✓ | | | | | | | ✓ | | | | ✓ | |
 | run-conservation-prioritization | ✓ | ✓ | | | | ✓ | | | | | | ✓ | | | | | ✓ |
+| run-acoustic-monitoring | ✓ | | ✓ | | ✓ | | | | | | | ✓ | | ✓ | | | |
 
 ---
 

package/README.md

@@ -8,7 +8,7 @@ Teach your AI agent to do rigorous ecology.
 
 Works with Claude Code, Gemini CLI, Cursor, GitHub Copilot, and any agent that reads Markdown.
 
-**17 modular skills** | **13 multi-step workflows** | **58 R/Python scripts** | **14 worked examples across 6 continents**
+**17 modular skills** | **14 multi-step workflows** | **58 R/Python scripts** | **14 worked examples across 6 continents**
 
 ---
 
@@ -18,7 +18,7 @@ Works with Claude Code, Gemini CLI, Cursor, GitHub Copilot, and any agent that r
 - [Installation](#installation)
 - [Core Concepts](#core-concepts)
 - [Skills (17)](#skills-17)
-- [Workflows (13)](#workflows-13)
+- [Workflows (14)](#workflows-14)
 - [How to Use Skills](#how-to-use-skills)
 - [For AI Agents](#for-ai-agents)
 - [Examples (14)](#examples-14)
@@ -194,7 +194,7 @@ See [CATALOG.md](CATALOG.md) for full metadata, inputs, outputs, and workflow li
 
 ---
 
-## Workflows (13)
+## Workflows (14)
 
 | Workflow | Skills Used | Purpose |
 |----------|-------------|---------|
@@ -211,6 +211,7 @@ See [CATALOG.md](CATALOG.md) for full metadata, inputs, outputs, and workflow li
 | `assess-landscape-connectivity` | 1 → 2 → 15 → 5 → 12 | Corridor and patch importance |
 | `run-population-viability` | 1 → 3 → 16 → 5 → 12 | PVA and extinction risk |
 | `run-conservation-prioritization` | 1 → 2 → 6 → 17 → 12 | Reserve network design |
+| `run-acoustic-monitoring` | 1 → 14 → 3 → 5 → 12 | Soundscape indices and species detection |
 
 ---
 
@@ -309,7 +310,7 @@ ecological-agent-skills/
 │       ├── resources/            ← checklists, glossaries, templates
 │       ├── examples/             ← usage prompt examples
 │       └── scripts/              ← R/Python helpers
-├── workflows/                    ← 13 multi-step playbooks
+├── workflows/                    ← 14 multi-step playbooks
 │   └── <workflow-name>/
 │       └── WORKFLOW.md
 ├── templates/                    ← reusable prompts, reports, checklists

package/docs/DECISION_TREE.md

@@ -0,0 +1,218 @@
+# Skill Selection Decision Tree
+
+Use this guide to identify which skill (or sequence of skills) to invoke based on your data type and analytical goal. Start at the top and follow the branches that match your situation.
+
+---
+
+## Quick Reference Table
+
+| If your data is... | And your goal is... | Start with skill |
+|--------------------|---------------------|------------------|
+| Occurrence records (species coordinates) | Download, clean, validate | ecological-data-foundation |
+| Occurrence records + environmental layers | Model species distribution | ecological-data-foundation → geoprocessing-for-ecology → predictive-modeling-best-practices → species-distribution-modeling |
+| Raster / vector layers only | Reproject, clip, stack, extract values | geoprocessing-for-ecology |
+| Tabular ecological data (1 response, N predictors) | Statistical test or regression | biostatistics-workbench |
+| Species × site matrix | Community composition / ordination | ecological-data-foundation → community-ecology-ordination |
+| Replicated detection/non-detection surveys | Occupancy and detection probability | ecological-data-foundation → occupancy-and-detection |
+| Before/after, control/impact data | Quantify disturbance effect (BACI) | ecological-data-foundation → ecological-impact-assessment |
+| Time-indexed environmental variable | Trend, breakpoint, anomaly | ecological-data-foundation → environmental-time-series |
+| Land cover + biophysical layers | Ecosystem services mapping | ecological-data-foundation → geoprocessing-for-ecology → ecosystem-services-assessment |
+| Camera trap image records | Detection events, diel activity | camera-trap-processing (→ occupancy-and-detection) |
+| Audio recordings (WAV/FLAC) | Soundscape indices, species detection | acoustic-monitoring (→ environmental-time-series) |
+| Habitat patches + land cover raster | Landscape connectivity, corridors | geoprocessing-for-ecology → landscape-connectivity |
+| Vital rates (survival, fecundity by stage) | Population viability, IUCN Criterion E | biostatistics-workbench → population-viability-analysis |
+| Suitability maps + planning units | Reserve design, prioritization | species-distribution-modeling → spatial-prioritization |
+| Any fitted model | Evaluate performance, quantify uncertainty | model-validation-and-uncertainty |
+| Any completed analysis | Audit trail, reproducibility checklist | reproducible-ecology-pipeline |
+
+---
+
+## Decision Tree — Detailed
+
+### Step 1: What type of data do you have?
+
+```
+Root
+ ├── A. Occurrence records (species lat/lon)        → go to Branch A
+ ├── B. Spatial rasters or vectors only             → go to Branch B
+ ├── C. Tabular survey data (sites × variables)     → go to Branch C
+ ├── D. Time series data                            → go to Branch D
+ ├── E. Multimedia data (images / audio)            → go to Branch E
+ └── F. Model outputs (predictions, suitability)   → go to Branch F
+```
+
+---
+
+### Branch A — Occurrence Records
+
+```
+A. Occurrence records
+ ├── A1. Raw / uncleaned records?
+ │    └── ALWAYS start with: ecological-data-foundation
+ │         (cleaning, QA, deduplication, coordinate flags)
+ │
+ ├── A2. Goal: map species distribution / suitability?
+ │    └── ecological-data-foundation
+ │         → geoprocessing-for-ecology       (extract env. values)
+ │         → predictive-modeling-best-practices  (predictor selection, CV design)
+ │         → species-distribution-modeling   (MaxEnt / RF / BRT / ensemble)
+ │         → model-validation-and-uncertainty (AUC, TSS, uncertainty maps)
+ │         → reproducible-ecology-pipeline
+ │
+ ├── A3. Goal: occupancy and detection probability?
+ │    → Replicated visit data required (detection history matrix)
+ │    └── ecological-data-foundation
+ │         → occupancy-and-detection
+ │         → biostatistics-workbench
+ │         → reproducible-ecology-pipeline
+ │
+ └── A4. Multiple species simultaneously?
+      └── Follow workflow: run-multispecies-screening
+           (ecological-data-foundation → geoprocessing-for-ecology
+            → species-distribution-modeling (loop) → model-validation-and-uncertainty)
+```
+
+---
+
+### Branch B — Spatial Rasters or Vectors
+
+```
+B. Spatial rasters or vectors
+ ├── B1. Need to reproject, clip, resample, stack layers?
+ │    └── geoprocessing-for-ecology (standalone)
+ │
+ ├── B2. Need to extract environmental values at occurrence points?
+ │    └── geoprocessing-for-ecology (stack_and_extract.py)
+ │         → then continue with predictive-modeling-best-practices
+ │
+ ├── B3. Land cover raster + biophysical data → ecosystem services?
+ │    └── ecological-data-foundation → geoprocessing-for-ecology
+ │         → ecosystem-services-assessment → reproducible-ecology-pipeline
+ │
+ └── B4. Habitat patches + dispersal distance → connectivity?
+      └── geoprocessing-for-ecology → landscape-connectivity
+```
+
+---
+
+### Branch C — Tabular Survey Data
+
+```
+C. Tabular survey data
+ ├── C1. Single response variable (abundance, richness, biomass)?
+ │    └── ecological-data-foundation → biostatistics-workbench
+ │         (GLM/GLMM, hypothesis testing, model selection)
+ │
+ ├── C2. Species × site matrix (multiple species, multiple sites)?
+ │    └── ecological-data-foundation → community-ecology-ordination
+ │         (NMDS, PCA, PCoA, diversity indices, PERMANOVA)
+ │
+ ├── C3. Before/after, control/impact sites (BACI)?
+ │    └── ecological-data-foundation → ecological-impact-assessment
+ │         → biostatistics-workbench → model-validation-and-uncertainty
+ │
+ ├── C4. Vital rates by age/stage class?
+ │    └── biostatistics-workbench → population-viability-analysis
+ │         (lambda, elasticity, stochastic PVA, IUCN Criterion E)
+ │
+ └── C5. Planning units + species features?
+      └── species-distribution-modeling → spatial-prioritization
+           (prioritizr/Marxan, representation targets, reserve design)
+```
+
+---
+
+### Branch D — Time Series Data
+
+```
+D. Time series data
+ ├── D1. Environmental signal (NDVI, temperature, rainfall)?
+ │    └── ecological-data-foundation → environmental-time-series
+ │         (Mann-Kendall trend, BFAST breakpoint, anomaly detection)
+ │
+ ├── D2. Biodiversity metric over time (species index, acoustic)?
+ │    └── ecological-data-foundation → environmental-time-series
+ │         → biostatistics-workbench (if inferential comparison needed)
+ │
+ └── D3. Fire risk or land cover change?
+      └── Follow workflow: build-fire-risk-map or analyze-environmental-change
+           (ecological-data-foundation → geoprocessing-for-ecology
+            → ecological-impact-assessment → environmental-time-series)
+```
+
+---
+
+### Branch E — Multimedia Data
+
+```
+E. Multimedia data
+ ├── E1. Camera trap images?
+ │    └── camera-trap-processing
+ │         (detection events, diel activity, trap effort table)
+ │         → occupancy-and-detection  (if occupancy estimation needed)
+ │
+ └── E2. Audio recordings (WAV/FLAC)?
+      └── acoustic-monitoring
+           (ACI/NDSI/ADI soundscape indices, BirdNET species detection)
+           → environmental-time-series  (if temporal trend analysis needed)
+```
+
+---
+
+### Branch F — Model Outputs
+
+```
+F. Model outputs
+ ├── F1. Model fitted; need performance metrics?
+ │    └── model-validation-and-uncertainty
+ │         (AUC, TSS, RMSE, calibration, sensitivity, uncertainty maps)
+ │
+ ├── F2. Suitability maps; need conservation priorities?
+ │    └── spatial-prioritization
+ │         (planning units, targets, BLM, prioritizr/Marxan)
+ │
+ └── F3. Any outputs; need reproducibility checklist?
+      └── reproducible-ecology-pipeline
+           (parameter manifest, decision log, audit trail)
+```
+
+---
+
+## Disambiguation Rules
+
+Apply exactly one rule when two skills seem applicable.
+
+### ecological-data-foundation vs. geoprocessing-for-ecology
+- **ecological-data-foundation**: cleaning, deduplication, column validation, coordinate QA.
+- **geoprocessing-for-ecology**: spatial operations on rasters/vectors (reproject, mask, stack, extract).
+- If the task involves occurrence records AND spatial operations, run **ecological-data-foundation first**.
+
+### predictive-modeling-best-practices vs. model-validation-and-uncertainty
+- **predictive-modeling-best-practices**: BEFORE fitting — predictor selection, collinearity, CV design.
+- **model-validation-and-uncertainty**: AFTER fitting — metrics, calibration, uncertainty quantification.
+- Never reverse this order.
+
+### species-distribution-modeling vs. occupancy-and-detection
+- **species-distribution-modeling**: suitability surface from presence/absence + environmental predictors.
+- **occupancy-and-detection**: occupancy probability (psi) + detection (p) from replicated visit data.
+
+### ecological-impact-assessment vs. biostatistics-workbench
+- **ecological-impact-assessment**: data with explicit before/after + control/impact structure (BACI), or landscape fragmentation metrics.
+- **biostatistics-workbench**: statistical comparisons without BACI design.
+
+### biostatistics-workbench vs. community-ecology-ordination
+- **biostatistics-workbench**: one response variable, one or more predictors.
+- **community-ecology-ordination**: species × site matrix as primary input (multivariate assemblage data).
+
+---
+
+## Minimum Records Quick Reference
+
+| Analysis | Do NOT proceed below | Recommended |
+|----------|----------------------|-------------|
+| SDM (any algorithm) | 10 occurrences | >= 30 |
+| Occupancy model | 15 sites | >= 30 sites, >= 3 visits |
+| BACI mixed model | 5 control + 5 impact sites | >= 10 per group |
+| Community ordination | 5 sites | >= 10 sites |
+| GLM (single predictor) | 20 observations | >= 50 |
+| Stochastic PVA | 5 years of count data | >= 10 years |

package/docs/GBIF_SETUP.md

@@ -0,0 +1,88 @@
+# GBIF Credentials Setup
+
+GBIF credentials are **optional** but enable async downloads with a citable DOI,
+which is required for reproducible publications and for datasets > 100,000 records.
+
+Without credentials, `download_from_gbif.py` falls back to `occ.search`
+(no DOI, max ~100,000 records, still functional for most studies).
+
+---
+
+## Step 1 — Create a free GBIF account
+
+1. Go to https://www.gbif.org
+2. Click **Login** > **Register**
+3. Fill in username, email, and password
+4. Confirm your email address
+
+---
+
+## Step 2 — Set environment variables
+
+Set these three variables in your shell before running any skill:
+
+```bash
+# Linux / macOS — add to ~/.bashrc or ~/.zshrc
+export GBIF_USER="your_gbif_username"
+export GBIF_PWD="your_gbif_password"
+export GBIF_EMAIL="your_email@example.com"
+```
+
+```powershell
+# Windows — PowerShell (current session only)
+$env:GBIF_USER  = "your_gbif_username"
+$env:GBIF_PWD   = "your_gbif_password"
+$env:GBIF_EMAIL = "your_email@example.com"
+```
+
+```powershell
+# Windows — PowerShell (permanent, per user)
+[System.Environment]::SetEnvironmentVariable("GBIF_USER",  "your_gbif_username", "User")
+[System.Environment]::SetEnvironmentVariable("GBIF_PWD",   "your_gbif_password", "User")
+[System.Environment]::SetEnvironmentVariable("GBIF_EMAIL", "your_email@example.com", "User")
+```
+
+If using conda, you can also add them to `environment.yaml` under `variables:`
+(not recommended for shared/committed files — use a `.env` file instead).
+
+---
+
+## Step 3 — Verify
+
+```bash
+python -c "import os; print(os.getenv('GBIF_USER'))"
+```
+
+Should print your GBIF username.
+
+---
+
+## When credentials are used vs. not used
+
+| Scenario | Method used | DOI | Max records |
+|----------|-------------|-----|-------------|
+| Credentials set + dataset > 100k records | Async download | Yes | Unlimited |
+| Credentials set + dataset <= 100k records | `occ.search` | No | ~100k |
+| No credentials | `occ.search` fallback | No | ~100k |
+
+---
+
+## Citing GBIF downloads
+
+When credentials are set and an async download completes, the script saves a
+`download_metadata_*.txt` file containing the DOI. Cite it in publications as:
+
+> GBIF.org (YYYY) GBIF Occurrence Download https://doi.org/10.15468/dl.XXXXXX
+
+---
+
+## Troubleshooting
+
+**"GBIF async download requires env vars"** — credentials not set; see Step 2 above.
+
+**"occ.count returned 400"** — `hasCoordinate` is not supported by the count endpoint;
+this is a known GBIF API limitation. The script handles this silently.
+
+**pygbif TypeError on Python 3.14** — `pygbif` has an API incompatibility with
+Python 3.14's `requests` session. The script automatically falls back to direct
+HTTP calls to the GBIF REST API. No action needed.

package/docs/glossary.md

@@ -0,0 +1,197 @@
+# Glossary — Quantitative Ecology
+
+Trilingual reference (English / Portuguese / Spanish) for terms used across all 17 skills.
+Entries are grouped by theme. Definitions are written for the analytical context of this repository.
+
+---
+
+## How to Use
+
+Each entry lists:
+- **Term** — canonical English term used in scripts and documentation
+- **PT** — Portuguese equivalent (Brazilian usage)
+- **ES** — Spanish equivalent
+- **Definition** — brief definition in the analytical context of this repository
+- **Skill** — the skill where this term most commonly appears
+
+---
+
+## 1. Occurrence Data & Data Quality
+
+| Term | PT | ES | Definition | Skill |
+|------|----|----|------------|-------|
+| **occurrence record** | registro de ocorrência | registro de ocurrencia | A documented observation of a species at a specific location and time | ecological-data-foundation |
+| **presence-only data** | dados de presença apenas | datos solo de presencia | Records where only species presence is documented, not confirmed absence | ecological-data-foundation |
+| **presence-absence data** | dados de presença-ausência | datos de presencia-ausencia | Records confirming both where a species was detected AND surveyed but not detected | ecological-data-foundation |
+| **background points** | pontos de background | puntos de fondo | Pseudo-absences randomly sampled from the study area for presence-background models | species-distribution-modeling |
+| **spatial thinning** | rarefação espacial | rarefacción espacial | Removing records that fall within the same grid cell to reduce spatial autocorrelation | ecological-data-foundation |
+| **spatial autocorrelation** | autocorrelação espacial | autocorrelación espacial | Statistical dependence between observations that decreases with geographic distance | predictive-modeling-best-practices |
+| **duplicate record** | registro duplicado | registro duplicado | Record sharing the same species, coordinates, and date as another record | ecological-data-foundation |
+| **coordinate uncertainty** | incerteza de coordenadas | incertidumbre de coordenadas | The radius (in metres) within which the true observation location may lie | ecological-data-foundation |
+| **georeferencing** | georreferenciamento | georreferenciación | The process of assigning geographic coordinates to a locality description | ecological-data-foundation |
+| **QA flag** | marcador de qualidade | bandera de calidad | A label applied to a record indicating a data quality issue (e.g. COORD_ZERO) | ecological-data-foundation |
+| **DOI (data citation)** | DOI de citação de dados | DOI de citación de datos | A persistent digital identifier for a GBIF dataset download, used in publications | ecological-data-foundation |
+
+---
+
+## 2. Species Distribution Modelling (SDM / ENM)
+
+| Term | PT | ES | Definition | Skill |
+|------|----|----|------------|-------|
+| **SDM** | MDE (modelo de distribuição de espécie) | MDE (modelo de distribución de especie) | Statistical model relating species occurrences to environmental predictors to produce a suitability map | species-distribution-modeling |
+| **ENM** | MEN (modelagem de nicho ecológico) | MNE (modelado de nicho ecológico) | Approach that models the ecological niche of a species from occurrence data and environmental layers | species-distribution-modeling |
+| **MaxEnt** | MaxEnt | MaxEnt | Maximum entropy algorithm for presence-background SDM; implemented in `maxnet` | species-distribution-modeling |
+| **BRT** | BRT (árvores de regressão por boosting) | BRT (árboles de regresión potenciados) | Gradient Boosting Trees; ensemble ML method for SDM (Elith et al. 2008) | species-distribution-modeling |
+| **ensemble model** | modelo ensemble | modelo ensamblado | Combination of predictions from multiple algorithms to reduce model uncertainty | species-distribution-modeling |
+| **suitability map** | mapa de adequabilidade | mapa de idoneidad | Raster where each pixel represents the predicted habitat suitability for a species | species-distribution-modeling |
+| **habitat suitability** | adequabilidade de habitat | idoneidad de hábitat | The degree to which a location's environmental conditions match species requirements | species-distribution-modeling |
+| **calibration area (M)** | área de calibração (M) | área de calibración (M) | The geographic region accessible to a species and used to define background for SDM calibration | species-distribution-modeling |
+| **regularisation multiplier (RM)** | multiplicador de regularização | multiplicador de regularización | MaxEnt parameter controlling model complexity; higher values produce smoother predictions | species-distribution-modeling |
+| **feature class (FC)** | classe de feature | clase de característica | MaxEnt parameter controlling the shape of response curves (L, Q, P, H, T) | species-distribution-modeling |
+| **variable importance** | importância de variável | importancia de variable | Relative contribution of each predictor to a model's predictions | predictive-modeling-best-practices |
+| **partial response curve** | curva de resposta parcial | curva de respuesta parcial | Plot showing the modelled relationship between a predictor and suitability, holding others constant | species-distribution-modeling |
+| **future projection** | projeção futura | proyección futura | Application of a calibrated SDM to future climate scenarios (SSP/RCP) | species-distribution-modeling |
+| **climate scenario** | cenário climático | escenario climático | A standardised future climate trajectory (e.g. SSP2-4.5, SSP5-8.5) from CMIP6 | species-distribution-modeling |
+
+---
+
+## 3. Environmental Predictors
+
+| Term | PT | ES | Definition | Skill |
+|------|----|----|------------|-------|
+| **bioclimatic variable** | variável bioclimática | variable bioclimática | Derived climate variable (e.g. BIO1–BIO19) capturing ecologically meaningful signals | geoprocessing-for-ecology |
+| **BIO1** | BIO1 — temperatura média anual | BIO1 — temperatura media anual | Mean Annual Temperature (deg C × 10 in raw WorldClim/CHELSA) | geoprocessing-for-ecology |
+| **BIO12** | BIO12 — precipitação anual | BIO12 — precipitación anual | Annual Precipitation (mm) | geoprocessing-for-ecology |
+| **predictor stack** | pilha de preditores | pila de predictores | Multi-layer raster containing all environmental variables aligned to the same grid | geoprocessing-for-ecology |
+| **collinearity** | colinearidade | colinealidad | Strong correlation between predictors that inflates uncertainty and reduces interpretability | predictive-modeling-best-practices |
+| **VIF** | VIF (fator de inflação da variância) | VIF (factor de inflación de varianza) | Variance Inflation Factor; values > 10 indicate problematic collinearity | predictive-modeling-best-practices |
+| **CHELSA** | CHELSA | CHELSA | Climatologies at High resolution for the Earth's Land Surface Areas; 1 km global climate dataset | geoprocessing-for-ecology |
+| **WorldClim** | WorldClim | WorldClim | Global climate data at 1 km resolution; widely used for SDM | geoprocessing-for-ecology |
+| **ERA5-Land** | ERA5-Land | ERA5-Land | ECMWF reanalysis product providing hourly climate data at ~9 km resolution via Copernicus CDS | geoprocessing-for-ecology |
+| **raster** | raster | raster | Grid of cells (pixels) covering a geographic area, each storing a value | geoprocessing-for-ecology |
+| **CRS** | SRC (sistema de referência de coordenadas) | SRC (sistema de referencia de coordenadas) | Coordinate Reference System defining how geographic coordinates are projected | geoprocessing-for-ecology |
+| **reprojection** | reprojeção | reproyección | Converting raster or vector data from one CRS to another | geoprocessing-for-ecology |
+| **spatial resolution** | resolução espacial | resolución espacial | The size of each pixel in a raster, typically expressed in metres or decimal degrees | geoprocessing-for-ecology |
+
+---
+
+## 4. Model Validation & Uncertainty
+
+| Term | PT | ES | Definition | Skill |
+|------|----|----|------------|-------|
+| **AUC** | AUC (área sob a curva ROC) | AUC (área bajo la curva ROC) | Area Under the ROC Curve; ranges 0.5 (random) to 1.0 (perfect discrimination) | model-validation-and-uncertainty |
+| **TSS** | TSS (true skill statistic) | TSS (estadístico de habilidad verdadera) | True Skill Statistic = sensitivity + specificity - 1; ranges -1 to 1, threshold-independent | model-validation-and-uncertainty |
+| **partial ROC** | ROC parcial | ROC parcial | ROC analysis restricted to ecologically relevant omission rates (OR10 < 0.1) | model-validation-and-uncertainty |
+| **omission rate** | taxa de omissão | tasa de omisión | Proportion of presence records incorrectly predicted as unsuitable; OR10 uses 10th percentile threshold | model-validation-and-uncertainty |
+| **calibration** | calibração | calibración | Assessment of whether predicted probabilities match observed occurrence rates | model-validation-and-uncertainty |
+| **cross-validation** | validação cruzada | validación cruzada | Model evaluation using multiple train/test splits to estimate generalisation performance | predictive-modeling-best-practices |
+| **spatial cross-validation** | validação cruzada espacial | validación cruzada espacial | Cross-validation where folds are spatially blocked to avoid overly optimistic AUC estimates | predictive-modeling-best-practices |
+| **k-fold** | k-fold | k-fold | Cross-validation strategy dividing data into k equally sized subsets | predictive-modeling-best-practices |
+| **uncertainty map** | mapa de incerteza | mapa de incertidumbre | Raster showing the standard deviation of ensemble model predictions across pixels | model-validation-and-uncertainty |
+| **MOP** | MOP (análise de mobilidade de preditores) | MOP (análisis de movilidad de predictores) | Multivariate Overlap Procedure; identifies where transfer conditions are outside training range | model-validation-and-uncertainty |
+| **extrapolation risk** | risco de extrapolação | riesgo de extrapolación | Uncertainty arising when a model is applied to conditions outside its calibration range | model-validation-and-uncertainty |
+
+---
+
+## 5. Statistical Methods
+
+| Term | PT | ES | Definition | Skill |
+|------|----|----|------------|-------|
+| **GLM** | GLM (modelo linear generalizado) | GLM (modelo lineal generalizado) | Generalised Linear Model; extends linear regression to non-normal response distributions | biostatistics-workbench |
+| **GLMM** | GLMM (modelo misto generalizado) | GLMM (modelo mixto generalizado) | GLM with random effects to account for grouped or repeated-measures data | biostatistics-workbench |
+| **AIC** | AIC (critério de informação de Akaike) | AIC (criterio de información de Akaike) | Model selection criterion balancing fit and complexity; lower is better | biostatistics-workbench |
+| **BACI** | BACI (antes-depois, controle-impacto) | BACI (antes-después, control-impacto) | Before-After Control-Impact design; standard framework for detecting ecological impacts | ecological-impact-assessment |
+| **PERMANOVA** | PERMANOVA | PERMANOVA | Permutational MANOVA; tests for differences in multivariate composition between groups | community-ecology-ordination |
+| **NMDS** | NMDS (escalonamento multidimensional não-métrico) | NMDS (escalamiento multidimensional no métrico) | Non-metric Multidimensional Scaling; ordination technique for community composition data | community-ecology-ordination |
+| **PCA** | PCA (análise de componentes principais) | PCA (análisis de componentes principales) | Principal Component Analysis; linear dimensionality reduction | biostatistics-workbench |
+| **beta diversity** | diversidade beta | diversidad beta | Variation in species composition between sites; complement to alpha diversity | community-ecology-ordination |
+| **Mann-Kendall** | Mann-Kendall | Mann-Kendall | Non-parametric test for monotonic trends in time series; robust to non-normality | environmental-time-series |
+| **BFAST** | BFAST | BFAST | Breaks For Additive Season and Trend; detects structural breakpoints in time series | environmental-time-series |
+
+---
+
+## 6. Occupancy & Detection
+
+| Term | PT | ES | Definition | Skill |
+|------|----|----|------------|-------|
+| **occupancy (psi)** | ocupância (psi) | ocupancia (psi) | Probability that a site is occupied by a species (ψ); estimated separately from detection | occupancy-and-detection |
+| **detection probability (p)** | probabilidade de detecção (p) | probabilidad de detección (p) | Probability that a species is detected given that it is present at a site | occupancy-and-detection |
+| **imperfect detection** | detecção imperfeita | detección imperfecta | The common situation where p < 1, meaning absences may be false negatives | occupancy-and-detection |
+| **detection history** | histórico de detecção | historial de detección | Matrix of 1/0/NA values encoding whether a species was detected on each visit to each site | occupancy-and-detection |
+| **naive occupancy** | ocupância ingênua | ocupancia ingenua | Simple proportion of sites where species was detected, ignoring imperfect detection | occupancy-and-detection |
+| **single-season model** | modelo de temporada única | modelo de temporada única | Occupancy model assuming sites are closed to colonisation/extinction within the survey season | occupancy-and-detection |
+| **RAI** | IAR (índice de atividade relativa) | IAI (índice de actividad relativa) | Relative Activity Index for camera traps: detections per 100 trap-nights | camera-trap-processing |
+| **independence threshold** | limiar de independência | umbral de independencia | Minimum time interval between events of the same species at the same station (default 30 min) | camera-trap-processing |
+
+---
+
+## 7. Acoustic Monitoring
+
+| Term | PT | ES | Definition | Skill |
+|------|----|----|------------|-------|
+| **ACI** | ACI (índice de complexidade acústica) | ACI (índice de complejidad acústica) | Acoustic Complexity Index; measures heterogeneity in amplitude changes within a recording | acoustic-monitoring |
+| **NDSI** | NDSI (índice de sonoridade diel normalizado) | NDSI (índice normalizado de sonoridad) | Normalised Difference Soundscape Index; ratio of biophony to anthrophony | acoustic-monitoring |
+| **ADI** | ADI (índice de diversidade acústica) | ADI (índice de diversidad acústica) | Acoustic Diversity Index; analogous to Shannon diversity computed over frequency bands | acoustic-monitoring |
+| **biophony** | biofonia | biofonía | Sounds produced by living organisms; one component of soundscape | acoustic-monitoring |
+| **anthrophony** | antropofonia | antropofonía | Human-generated noise; estimated at high-frequency bands in NDSI | acoustic-monitoring |
+| **soundscape** | paisagem sonora | paisaje sonoro | All the sounds within a defined area; characterised through acoustic indices | acoustic-monitoring |
+| **BirdNET** | BirdNET | BirdNET | Deep-learning classifier for bird species identification from audio recordings | acoustic-monitoring |
+
+---
+
+## 8. Landscape Ecology & Connectivity
+
+| Term | PT | ES | Definition | Skill |
+|------|----|----|------------|-------|
+| **habitat patch** | fragmento de habitat | parche de hábitat | Contiguous area of suitable habitat separated from other patches by a matrix | landscape-connectivity |
+| **resistance surface** | superfície de resistência | superficie de resistencia | Raster where pixel values represent the cost of movement through each land cover type | landscape-connectivity |
+| **corridor** | corredor | corredor | Strip of habitat facilitating animal movement between patches | landscape-connectivity |
+| **IIC** | IIC (índice de conectividade integral) | IIC (índice de conectividad integral) | Integral Index of Connectivity; graph-theoretic metric combining area and link importance | landscape-connectivity |
+| **dPC** | dPC | dPC | Node removal importance metric based on Probability of Connectivity (PC); used to rank patches | landscape-connectivity |
+| **Circuitscape** | Circuitscape | Circuitscape | Circuit theory-based tool for modelling landscape connectivity; identifies pinchpoints | landscape-connectivity |
+| **fragmentation** | fragmentação | fragmentación | Process by which a habitat is divided into smaller, more isolated patches | ecological-impact-assessment |
+| **MESH** | MESH (habitat efetivo de malha) | MESH (hábitat efectivo de malla) | Effective Mesh Size; fragmentation metric inversely proportional to isolation | ecological-impact-assessment |
+
+---
+
+## 9. Population Ecology
+
+| Term | PT | ES | Definition | Skill |
+|------|----|----|------------|-------|
+| **lambda (lambda)** | taxa de crescimento populacional (lambda) | tasa de crecimiento poblacional (lambda) | Finite rate of population increase; lambda > 1 = growing, < 1 = declining | population-viability-analysis |
+| **elasticity** | elasticidade | elasticidad | Proportional change in lambda resulting from a proportional change in a vital rate | population-viability-analysis |
+| **sensitivity** | sensibilidade | sensibilidad | Absolute change in lambda from an absolute change in a vital rate | population-viability-analysis |
+| **PVA** | AVP (análise de viabilidade populacional) | AVP (análisis de viabilidad poblacional) | Population Viability Analysis; simulation-based method to estimate extinction probability | population-viability-analysis |
+| **quasi-extinction threshold** | limiar de quase-extinção | umbral de cuasi-extinción | Population size below which a population is considered functionally extinct | population-viability-analysis |
+| **Leslie matrix** | matriz de Leslie | matriz de Leslie | Age-structured population projection matrix | population-viability-analysis |
+| **Lefkovitch matrix** | matriz de Lefkovitch | matriz de Lefkovitch | Stage-structured population projection matrix | population-viability-analysis |
+| **IUCN Criterion E** | Critério E da IUCN | Criterio E de la UICN | Quantitative extinction risk criterion using PVA; >= 20% probability of extinction in 20 yrs = EN | population-viability-analysis |
+
+---
+
+## 10. Conservation Planning
+
+| Term | PT | ES | Definition | Skill |
+|------|----|----|------------|-------|
+| **planning unit** | unidade de planejamento | unidad de planificación | Spatial unit (polygon or raster cell) that can be included or excluded in a reserve network | spatial-prioritization |
+| **representation target** | meta de representação | meta de representación | The proportion of a feature's distribution that should be captured within selected planning units | spatial-prioritization |
+| **BLM** | BLM (modificador de comprimento de borda) | BLM (modificador de longitud de límite) | Boundary Length Modifier; penalty for fragmented solutions in Marxan/prioritizr | spatial-prioritization |
+| **irreplaceability** | insubstituibilidade | irreemplazabilidad | Frequency with which a planning unit appears in all near-optimal solutions | spatial-prioritization |
+| **minimum set problem** | problema de conjunto mínimo | problema de conjunto mínimo | Conservation planning objective: meet all targets at minimum cost | spatial-prioritization |
+| **30x30** | 30x30 | 30x30 | Global biodiversity target to protect 30% of land and sea by 2030 (Kunming-Montreal GBF) | spatial-prioritization |
+| **locked-in area** | área bloqueada (inclusão) | área bloqueada (inclusión) | Planning unit forced into the solution regardless of cost (e.g. existing protected area) | spatial-prioritization |
+| **locked-out area** | área bloqueada (exclusão) | área bloqueada (exclusión) | Planning unit excluded from the solution regardless of cost (e.g. urban, legally unavailable) | spatial-prioritization |
+
+---
+
+## 11. Reproducibility & Provenance
+
+| Term | PT | ES | Definition | Skill |
+|------|----|----|------------|-------|
+| **decision log** | registro de decisões | registro de decisiones | File documenting analytical choices, rationale, and alternatives at each pipeline step | reproducible-ecology-pipeline |
+| **parameter manifest** | manifesto de parâmetros | manifiesto de parámetros | Complete record of all settings used to produce a given model or output file | reproducible-ecology-pipeline |
+| **provenance** | procedência | procedencia | Traceable history of how a dataset or output was produced, from raw data to final result | reproducible-ecology-pipeline |
+| **ODMAP** | ODMAP | ODMAP | Overview, Data, Model, Assessment, Prediction — standard SDM reporting protocol (Zurell et al. 2020) | reproducible-ecology-pipeline |
+| **DOI** | DOI | DOI | Digital Object Identifier; persistent link to a citable dataset or publication | ecological-data-foundation |
+| **renv** | renv | renv | R package for project-level dependency management and reproducible environments | reproducible-ecology-pipeline |
+| **SPDX** | SPDX | SPDX | Software Package Data Exchange standard for expressing license information in source files | reproducible-ecology-pipeline |