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.
Note that this listing of spatial data links is no longer actively maintained here. This list has now been integrated in the Freshwater Information Platform pages.
BioFresh-tools
- 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
aquamaps.org
- 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
aquamaps.org
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
http://easin.jrc.ec.europa.eu/
- 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
- ASTERICS (version 3.1.1) calculates the ecological status of rivers
based on benthic invertebrate taxa lists. The assessment fulfills the
demands of the WFD. The German Assessment System PERLODES is part of
the software.
- More info:
at fliessgewaesserbewertung.de
- On-line tool:
at fliessgewaesserbewertung.de
- Taxa Entry Tool
- Tool to produce a standardized taxalist for Macrophytes, Fish,
Phytoplankton or Diatoms.
- On-line tool:
at freshwaterecology.info
- 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 wiser.eu
- 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:
streames.net
- 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="http://r-forge.r-project.org")
- 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="http://r-forge.r-project.org")
- 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="http://cran.r-project.org")
- 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="http://cran.r-project.org")
- 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="http://cran.r-project.org")
- 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="http://cran.r-project.org")
- 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="http://cran.r-project.org")
- 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="http://cran.r-project.org")
- spdep
- Spatial dependence: weighting schemes, statistics and models
- More info: at cran
- Download package: install using the command
install.packages("spdep",repos="http://cran.r-project.org")
- spatstat
- An R library for spatial statistics
- More info: at spatstat
- Download package: at cran or install using the
command
install.packages("spatstat",repos="http://cran.r-project.org")
- 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="http://cran.r-project.org")
- 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="http://r-forge.r-project.org")
- 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="http://cran.r-project.org")
- 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 spatialecology.com
- Download page: at spatialecology.com
- 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:
distancesampling.org
- Distance R packages
distancesampling.org
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 earthpoint.us
- The World Coordinate Converter
- A tool to convert geodetic coordinates in a wide range of
reference systems
- More info and on-line tool:
at twcc.free.fr
Open source GIS tools
- Quantum GIS
- User friendly Open Source Geographic Information System (GIS)
- More info: at qgis
- GRASS GIS
- 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