Share tools and databases

BETSI

Biological and ecological functional traits of soil invertebrates to link species assemblages to environmental factors

• Database on the biological and ecological traits for soil invertebrates: https://portail.betsi.cnrs.fr/node/2

• T-SITA – Thesaurus for Soil Invertebrate Trait-based Approaches (a controlled vocabulary of soil invertebrate trait names): https://t-sita.betsi.cnrs.fr/BETSI_vizIndex.jsp

FUNCTIONALWEBS
The functional diversity of food webs: linking ecology, physiology and biogeography

• Database on 12 functional traits of 852 aquatic invertebrate taxa collected in tank bromeliads from Mexico to Argentina: https://doi.org/10.5063/F1VD6WMF

• R code to analyze FunctionalWebs database: https://doi.org/10.5281/zenodo.1200194

GASPAR

A general approach to Species-Abundance relationships in a context of global change, reef fish species as a model

• Database of presence/absence of more than 6,300 coral reef species in more than 100 worldwide locations. Available on request (contact : Valeriano Parravicini).

IRBAS
Analysis and synthesis of intermittent river biodiversity

• Online database to collate, analyze, and synthesize data on the biodiversity and ecology of intermittent rivers worldwide: http://irbas.inrae.fr/contribute-n-and-access-data/how-explore-irbas-database

RAATD
Retrospective analysis of vertebrates’ tracking data in Antarctica to identify ecologically significant areas

• The RAATD project consolidated tracking data for multiple species of Antarctic meso- and top-predators to identify Areas of Ecological Significance. These datasets constitute the compiled tracking data from a large number of research groups that have worked in the Antarctic since the 1990s. https://doi.org/10.4225/15/5afcb927e8162

• R code to analyze RAATD database: https://github.com/SCAR/RAATD

RAINBIO
African biodiversity dynamics: interactions between ecological processes and conservation actions

• The RAINBIO mega database contains high quality georeferenced occurrences of vascular plants from sub-Saharan tropical Africa and is the compilation of thirteen public and non-public databases. The database was filtered, quality-checked and verified by the CESAB RAINBIO Consortium. The database holds 610 117 georeferenced occurrences for 25,356 species of vascular plants and 29,659 taxa (including subspecies and varieties), 3,158 genera and 273 families. http://rainbio.cesab.org/index.html#dataset

WOODIV

Origin and congruence of taxonomic, phylogenetic, functional and paleo-ecological diversity patterns: tree biodiversity in the European Mediterranean 

• Database of occurrences, functional traits, and phylogenetic data for all Euro-Mediterranean trees: https://figshare.com/articles/dataset/WOODIV_a_database_of_occurrences_functional_traits_and_phylogenetic_data_for_all_Euro-Mediterranean_trees/13952897/2

AFROBIODIVERS

African biodiversity dynamics: interactions between ecological processes and conservation actions

• popbayes : package to infer populations trends over time from series of counts under a Bayesian framework https://cran.r-project.org/package=popbayes

CESAB
R packages developed by the CESAB team

• rcompendium: R package to make easier the creation of R package or research compendium https://cran.r-project.org/web/packages/rcompendium/

• worldpa: R interface to the World Database on Protected Areas (WDPA) https://github.com/FRBCesab/worldpa

DIVERS

From reproductive strategies to species diversity: how evolution of breeding systems and associated traits shapes plant species diversity?

• papierRmache : package to help extracting information from scientific papers https://github.com/ajhelmstetter/papieRmache

FREE
Causes and consequences of functional rarity from local to global scales

• funrar: R package to characterize functional rarity https://cran.r-project.org/web/packages/funrar/index.html

• mFD : package to compute functional spaces and functional indices https://cran.r-project.org/package=mFD

GEISHA
Global Evaluation of the Impacts of Storms on freshwater Habitat and structure of phytoplankton Assemblages

• algaeClassify: R package to determine phytoplankton functional groups based on functional traits https://cran.r-project.org/web/packages/algaeClassify/index.html

RAINBIO
African biodiversity dynamics: interactions between ecological processes and conservation actions

• ConR:R package to assist large-scale multi-species preliminary conservation assessments using distribution data https://cran.r-project.org/web/packages/ConR/index.html