BioFresh project

Member of the

Freshwater Information Platform

A selection of useful tools in freshwater biodiversity research

The aim of this page is to bundle the tools used and developed in the framework of the BioFresh-project.


  • EFI+ (Improvement and Spatial extension of the European Fish Index)
    • The EFI+-tool (Improvement and Spatial extension of the European Fish Index) allows assessing the ecological status of rivers in accordance with the EU Water Framework Directive. The tool is based on the European Fish Index (EFI) developed within the FAME and EFI+ project as a standardized fish-based assessment method applicable across a wide range of European rivers. The EFI employs a number of environmental descriptors (see documentation on the data input matrix) to predict biological reference conditions and quantifies the deviation from reference conditions on a statistical basis.
    • More info: documentation page, pdf manual
    • On-line tool: at BOKU
  • Freshwater Key Biodiversity Areas search

Freshwater AquaMaps

  • AquaMaps for Europe
    • Freshwater AquaMaps is an approach to generating model-based, large-scale predictions of freshwater species and is based on a methodology, which was originally developed for marine mammals. Models for the freshwater AquaMaps are constructed from estimates of the environmental tolerance of a given species with respect to elevation, temperature, soil pH, soil moisture, soil carbon, precipitation and the Compound Topographic Index (a wetness index) and occurrence data available through FishBase and GBIF. Maps show the colour-coded relative likelihood of a species to occur in a global grid of half-degree latitude/longitude cell dimensions, which corresponds to about 50 km near the equator.
    • Predictions are generated by matching habitat usage of species, termed environmental envelopes, against local environmental conditions to determine the relative suitability of specific geographic areas for a given species. Knowledge of species' distributions within FishBase, FAO areas or bounding boxes is also used to exclude potentially suitable habitats in which the species is not known to occur.
    • Environmental parameter layers and drainage basins based on the Pfaffstetter system have been established for European freshwater fishes, amphibians, and mammals. Parameters were tested by calculating their relative contribution to the predicted distribution patterns for different organisms. Predicted ranges have been tested against IUCN shapefile boundaries based on known distributions. AquaMaps is relatively insensitive to gaps in occurrence data and uses presence only for calculation of ranges.
    • The European AquaMaps are currently available for a dozen of freshwater species and will be produced for a wider range of species in the near future. These maps can be consulted at:
    • European AquaMaps at
    • Within the Freshwater Biodiversity Data Portal you can either use the dedicated AquaMaps viewer or visualise the AquaMaps during occurrence searches (if available).
    • More background information on AquaMaps in general is available at

European Alien Species Information Network (EASIN) tool

  • The European Alien Species Information Network (EASIN) is an initiative of the Joint Research Centre of the European Commission, and aims to enable easy access to data and information on Alien Species (AS) in Europe from existing on-line databases to assist policy makers and scientists in their efforts to tackle AS invasions.
  • EASIN facilitates the exploration of existing alien species information from a variety of distributed information sources by developing and making freely available tools and interoperable web services compliant with internationally recognized standards. The EASIN web tools and services can be utilized freely and independently by any website, while ownership of the data remains with its source, which is properly cited and linked.
  • More info at
  • On-line tool:
  • More to come...
    The information available through EASIN will be integrated on the species pages in the Freshwater Biodiversity Data Portal.

Ecological assessment tools

  • Assessing the ecological quality of rivers - ASTERICS
  • Taxa Entry Tool
    • Tool to produce a standardized taxalist for Macrophytes, Fish, Phytoplankton or Diatoms.
    • On-line tool: at
  • WISER methods database
    • The WISER methods database details national assessment methods used to classify the ecological status of rivers, lakes, coastal and transitional waters from different EU member states.
    • Access database: at
  • STREAMES-EDSS: STream REAch Management: an Expert System:
    • STREAMES-EDSS 1.0 is an Environmental Decision Support System, a computer application that supports the decision-making processes in stream reach management by encompassing heuristic (expert) and empirical information.
    • More info at:
  • FORECASTER: Facilitating the application of Output from REsearch and CAse STudies on Ecological Responses to hydro-morphological degradation and rehabilitation

Literature analysis tools

  • Eco-Evidence
    • Eco Evidence is a unique tool for performing systematic literature review. It allows users to document and extract causes and effects and their response direction in a standardized manner. As such, the tool helps users to perform a systematic review of the scientific literature focussing on a specific cause-and-effect hypothesis. Eco Evidence consist of an online database and a desktop application for data analysis.
    • On-line database tool: at eWater Toolkit (access is registration based)
    • More info: on the desktop analyser software (Windows) at eWater Toolkit

R-packages and modeling tools used within the project

  • R software
    • R is a powerful, free cross-platform environment for statistical computing and graphics. This software is required to use the packages mentioned below.
    • More info: at r-project
    • Download software: at one of the cran-mirrors
  • Bioclim - Bioclimatic Variables
    • bioclim recreates the standard 19 bioclimatic variables (BIOCLIM) created using ANUCLIM or used by Worldclim.
    • More info: at R-forge
    • Download variables: at R-forge or install using the command install.packages("bioclim",repos="")
  • Biomod
    • BIOMOD is R-package for ensemble forecasting of species distributions, enabling the treatment of a range of methodological uncertainties in models and the examination of species-environment relationships.
    • More info: at R-forge
    • Download package: install using the command install.packages("BIOMOD",repos="")
  • dismo: Species distribution modeling
    • Functions for species distribution modelling, predicting entire geographic distributions from occurrences at a number of sites.
    • More info: pdf manual at CRAN
    • Download package: at cran or install using the command install.packages("spatstat",repos="")
  • gam: Generalized Additive Models
    • Functions for fitting and working with generalized additive models, as described in chapter 7 of "Statistical Models in S" (Chambers and Hastie (eds), 1991), and "Generalized Additive Models" (Hastie and Tibshirani, 1990).
    • More info: pdf manual at cran
    • Download package: at cranor install using the command install.packages("gam",repos="")
  • gbm
    • Generalized Boosted Regression Models. gbm package, found in Elith, J, J. R. Leathwick and T. Hastie. 2008. A working guide to boosted regression trees. Journal of Animal Ecology. 77: 802-813.
    • More info: pdf manual at cran
    • Download package: at cran or install using the command install.packages("gbm",repos="")
  • MASS: Support Functions and Datasets for Venables and Ripley's MASS
    • Functions and datasets to support Venables and Ripley, 'Modern Applied Statistics with S' (4th edition, 2002).
    • More info: pdf manual at cran
    • Download package: at cran or install using the command install.packages("MASS",repos="")
  • randomForest: Breiman and Cutler's random forests for classification and regression
    • Classification and regression based on a forest of trees using random inputs.
    • More info: pdf manual at cran
    • Download package: at cran or install using the command install.packages("randomForest",repos="")
  • rpart: Recursive Partitioning and Regression Trees
    • Recursive partitioning for classification, regression and survival trees. An implementation of most of the functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.
    • More info: pdf manual at cran
    • Download package: at cran or install using the command install.packages("rpart",repos="")
  • spdep
    • Spatial dependence: weighting schemes, statistics and models
    • More info: at cran
    • Download package: install using the command install.packages("spdep",repos="")
  • spatstat
    • An R library for spatial statistics
    • More info: at spatstat
    • Download package: at cran or install using the command install.packages("spatstat",repos="")
  • raster: Geographic data analysis and modeling
    • Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
    • More info: pdf manual at cran
    • Download package: at cran or install using the command install.packages("raster",repos="")
  • vegan
    • Vegan: R functions for vegetation ecologists. Useful tool for vegetation/community analysis. Contains the major ordination methods, dissimilarity indices and tools for biodiversity, species richness and abundance analysis.
    • More info: at OULU, pdf tutorial at OULU, pdf reference manual at cran
    • Download package: at cran or install using the command install.packages("vegan")
    • ... or get the development version: at R-forge or install using the command install.packages("vegan",repos="")
  • Reol: R interface to the Encyclopedia of Life
    • An R interface to the Encyclopedia of Life API. Includes functions for downloading and extracting information off the EOL pages.
    • More info: Barbara L. Banbury & Brian C. O’Meara (2014) Reol: R interface to the Encyclopedia of Life. Ecology and Evolution 4(12):2577–2583. doi:10.1002/ece3.1109
    • Download package: at cran or install using the command install.packages("reol",repos="")
  • Packages used for statistical testing of model parameters
    • These packages where for instance used in the parameter selection for AquaMaps
    • HH: Statistical Analysis and Data Display: Heiberger and Holland - see details: at cran
    • ROCR: prediction - performance - plot - see details: at mpi

Other (spatial) modeling tools

  • Maxent
    • Maxent software for species habitat modeling. Software based on the maximum-entropy approach for species habitat modeling.
    • More info and download form: at princeton
  • Spatial Analysis in Macroecology (SAM)
    • SAM (Spatial Analysis in Macroecology) is a Windows program designed as a package of tools for spatial statistical analysis, mainly for applications in Surface Pattern Spatial Analysis.
    • More info: at ufg, pdf article
    • Download form: at ufg
  • Geospatial Modelling Environment
    • GME is an analysis and modeling environment for geospatial analysis that is designed to facilitate rigorous analysis of geospatial data. Windows program requiring the statistical software R and ESRI ArcGIS to drive geospatial analyses.
    • More info: at
    • Download page: at
  • ModestR
    • ModestR: a software tool for managing and analyzing species distribution map databases
    • More info, download and installation instructions for Windows: at IPez
    • Associated EnvNicheR R package: at IPez
  • Distance sampling
    • The Distance project provides software for the design and analysis of distance sampling surveys of wildlife populations. This software takes two forms: a Windows-based program and a suite of packages for the statistical programming language R.
    • More info:
    • Distance R packages

On-line GIS tools

  • Earthpoint Excel to KML
    • Simple on-line tool to convert coordinates in Excel to a KML-file which can be viewed in Google Earth
    • More info and on-line tool: at
  • The World Coordinate Converter
    • A tool to convert geodetic coordinates in a wide range of reference systems
    • More info and on-line tool: at

Open source GIS tools

  • Quantum GIS
    • User friendly Open Source Geographic Information System (GIS)
    • More info: at qgis
    • Geographic Resources Analysis Support System. Commonly referred to as GRASS, this is free Geographic Information System (GIS) software used for geospatial data management and analysis, image processing, graphics/maps production, spatial modeling, and visualization.
    • More info: at fbk
  • PostGIS