Our team is developing multiple open-source software packages. These are all freely available from here or other sources (e.g. CRAN) and constantly being updated.
BAT – Biodiversity Assessment Tools
An R package that includes algorithms to assess alpha and beta diversity in all their dimensions (taxon, phylogenetic and functional diversity), whether communities are completely sampled or not. It allows performing a number of analyses based on either species identities or phylogenetic/functional trees or hypervolumes depicting species relationships.
Cardoso, P., Rigal, F. & Carvalho, J.C. (2015) BAT – Biodiversity Assessment Tools, an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity. Methods in Ecology and Evolution, 6: 232-236. https://doi.org/10.1111/2041-210X.12310
Cardoso, P., Guillerme, T., Mammola, S., Matthews, T.J., Rigal, F., Graco-Roza, C., Stahls, G. & Carvalho, J.C. (subm.) Calculating functional diversity metrics using neighbor-joining trees. bioRxiv. https://doi.org/10.1101/2022.11.27.518065
Mammola, S. & Cardoso, P. (2020) Functional diversity metrics using kernel density n-dimensional hypervolumes. Methods in Ecology and Evolution, 11: 986-995. https://doi.org/10.1111/2041-210X.13424
Download: https://cran.r-project.org/package=BAT
Manual: https://cran.r-project.org/web/packages/BAT/BAT.pdf
RED – IUCN Redlisting Tools
An R package that includes algorithms to facilitate the assessment of extinction risk of species according to the IUCN (International Union for Conservation of Nature, see http://www.iucn.org for more information) red list criteria.
Cardoso, P. (2017) Red – an R package to facilitate species red list assessments according to the IUCN criteria. Biodiversity Data Journal, 5: e20530. https://doi.org/10.3897/BDJ.5.e20530
Download: https://CRAN.R-project.org/package=red
Manual: https://cran.r-project.org/web/packages/red/red.pdf
ARAKNO – Arachnid Knowledge Online
An R package that allows the user to connect with the World Spider Catalogue (WSC; <https://wsc.nmbe.ch/>) and the World Spider Trait (WST; <https://spidertraits.sci.muni.cz/>) databases. Also performs several basic functions such as checking names validity, retrieving coordinate data from the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/>), and mapping.
Cardoso, P. & Pekar, S. (2022) arakno – An R package for effective spider nomenclature, distribution, and trait data retrieval from online resources. Journal of Arachnology, 50: 30-32. https://doi.org/10.1636/JoA-S-21-024
Download: https://CRAN.R-project.org/package=arakno
Manual: https://cran.r-project.org/web/packages/arakno/arakno.pdf
RAT – Research Assessment Tools
An R package that includes algorithms to assess research productivity and patterns, such as the h-index and i-index.
Cardoso, P., Fukushima, C.S. & Mammola, S. (2022) Quantifying the internationalization and representativeness in research. Trends in Ecology and Evolution., 37: 725-728. https://doi.org/10.1016/j.tree.2022.06.011
Download: https://CRAN.R-project.org/package=RAT
Manual: https://cran.r-project.org/web/packages/arakno/RAT.pdf
GECKO – Geographical Ecology and Conservation Knowledge Online
An R package aimed primarily at ecology and conservation science studies, allowing processing of both point and raster data. Now integrates SPECTRE, the high resolution species threat dataset.
Download: https://cran.r-project.org/web/packages/gecko/index.html
Manual: https://cran.r-project.org/web/packages/gecko/gecko.pdf
PRION – PRIority Optimization aNalysis
A standalone Java software and graphical user interface to calculate and map multiple algorithms for prioritization of areas for conservation. The main analysis uses spatially-explicit genetic algorithms to optimize spatial distribution of protected areas.
No manual is available as the development has been halted.