Upload Data Files
Upload your CSV data files following the MARBEFES guidance format.
Data Validation
Run Functional Diversity Analysis
Calculate functional diversity indices (Rao's Q, FDis, FRic, FEve, FDiv) and Community Weighted Means (CWM) using the FD package.
Functional Diversity Indices
Community Weighted Means (CWM)
Rao's Q by EUNIS Habitat
FDis by EUNIS Habitat
Summary Statistics per EUNIS Habitat
Spatial Map: Rao's Q
Spatial Map: FDis
Trait Biogeography Settings
Visualize the spatial distribution of individual traits in the BBT. CWM trait categories are combined into a single value per trait using the standardized formula from the guidance.
Combined Trait Formula
(CWM.cat1 * 1 + CWM.cat2 * 2 + ... + CWM.catn * n) / n
Where n = total number of categories for that trait (including absent categories).
Download Combined Traits CSV
Trait Biogeography Map
CWM Trait Categories per Sample
Combined Trait Values per Sample
Trait Distribution by EUNIS Habitat
Environmental Raster Layers
Upload environmental raster layers (.tif) for spatial modelling. These are used by Random Forest and GAM models to predict trait distributions across the BBT area.
Based on: RF vs GAM new.R (Puntila-Dodd, Jan 2026)
Model Performance Comparison
RF Variable Importance
GAM Smooth Terms
Spatial Prediction: Random Forest
Spatial Prediction: GAM
RF - GAM Difference Map
Cross-Validation Diagnostics
About This Application
MARBEFES WP3 - Broadscale Biological Trait Methods
This Shiny application implements the guidance from the MARBEFES project (EU Horizon Europe, Grant Agreement no 101060937) for broadscale biological trait methods analysis.
Task Leaders: Marie Nordström & Anna Törnroos, Åbo Akademi University
Activity 1: Functional Diversity Assessment
- Calculates functional diversity indices: Rao's Q, FDis, FRic, FEve, FDiv
- Computes Community Weighted Means (CWM) for all trait categories
- Compares functional diversity across EUNIS Level 3 habitats
- Generates spatial maps of diversity indices
Activity 2: Trait Biogeographies
- Visualizes spatial distribution of individual traits
- Combines trait categories into single values using the standardized formula
- Generates trait biogeography maps across the BBT
Advanced: RF/GAM Spatial Modelling (sections 3.2.6-3.2.7)
- Upload environmental raster layers (depth, slope, salinity, temperature, chla, sediment)
- Fit Random Forest and GAM models to predict trait distributions from environmental variables
- Spatial cross-validation using blockCV
- Variable importance and model diagnostics
- Spatial prediction maps with downloadable rasters
- Based on: RF vs GAM new.R (Puntila-Dodd, Jan 2026)
Data Format Requirements
Abundance Data (CSV)
Rows = samples, Columns = taxa. First column must be the sample identifier.
SampleID, Macoma_balthica, Mytilus_trossulus, ...
S001, 3, 5, ...
S002, 2, 3, ...
S003, 1, 4, ...
Trait Data (CSV)
Rows = taxa (matching abundance columns), Columns = trait categories. First column = taxon name. Values should be 0 (not expressed) or fuzzy-coded (0-1) with each trait group summing to 1 per taxon.
Taxon, size_s, size_sm, size_m, size_ml, size_l, ...
Macoma_balthica, 0, 0, 1, 0, 0, ...
Mytilus_trossulus, 0, 0, 0, 1, 0, ...
Metadata (CSV, optional)
Must contain SampleID matching the abundance file.
SampleID, Longitude, Latitude, EUNIS_habitat, Year
S001, 21.5, 60.2, MC63_infralittoral_mud, 2020
S002, 21.8, 60.1, MC53_infralittoral_sand, 2019
Trait Categories (Table 1)
Invertebrate Traits
| Trait | Categories | Labels | Relevance |
|---|---|---|---|
| Body size | small (1-5mm), small-medium (5mm-1cm), medium (1-3cm), medium-large (3-5cm), large (>5cm) | s, sm, m, ml, l | Productivity, feeding, respiration |
| Longevity | very short (<1yr), short (1-2yr), long (2-5yr), very long (5-10yr) | vsho, sho, lon, vlon | Production, elemental cycling |
| Reproductive freq. | annual episodic, annual protracted, semelparous | anep, anpr, sem | Production |
| Living habit | attached, burrow dweller, free, tube dweller | att, budw, free, tub | Elemental cycling, dispersal |
| Movement type | no movement, swimmer, rafter-drafter, crawler, byssus threads, tube dweller, burrower | nom, swim, raft, crawl, byss, tube, burr | Mobility, dispersal |
| Feeding position | suspension, surface, sub-surface, selection, miner, parasite | sus, sur, sub, sel, min, par | Production, elemental cycling |
| Feeding habit | detrivore, omnivore, herbivore, carnivore, scavenger, parasite | detr, omni, herb, car, sca, para | Production, trophic |
Key References
- Frelat et al. (2022) Tutorial for analysing trait-environment relationships
- de Juan et al. (2022) Biological traits approaches in benthic marine ecology
- Laliberte et al. (2022) FD: Measuring functional diversity from multiple traits
- Törnroos & Bonsdorff (2012) Developing the multitrait concept for functional diversity