Date
30 Nov 2018
The software is of increasing importance in measuring biodiversity globally
The BiodiversityR package was created by Roeland Kindt, a senior ecologist at the World Agroforestry Centre, to accompany the Tree Diversity Analysis manual for common statistical methods for ecological and biodiversity studies.
Based on daily package downloads made available for the RStudio mirror server since 1 October 2012, BiodiversityR has been installed more than 100,000 times to the end of October 2018.
It is not known what the actual total number of installations has been because the R base software and its contributing packages can be downloaded from a large number of mirror sites and also because the first version of BiodiversityR was released over ten years ago, in July 2007. The vegan package, for which BiodiversityR is a companion, has been installed more than 1,200,000 times, according to the same download statistics from the RStudio server.
The Tree Diversity Analysis manual focuses on the analysis of species’ survey data, providing a comprehensive review of methods, such as species’ accumulation curves, accumulated Rényi diversity profiles, constrained ordination techniques or generalized additive models.
Despite the manual’s title, the statistical methods described within can be used for a wider range of organisms, for different hierarchical levels of biodiversity and for a variety of environments. Both manual and software can be accessed openly and without charge.
One of the features of BiodiversityR is a graphical user interface developed specifically for training students and researchers who are not familiar with the command-style programming of R. Since its release in 2007, the graphical user interface has been developed in parallel with the vegan community ecology package, a package that contains recommended statistical tools for the analysis of dissimilarities and diversity, which has been widely cited (> 16,000 times according to recent Google Scholar statistics). Roeland Kindt is also a co-author.
Since 2012 and version 2.0, BiodiversityR has been expanded with new functions for ensemble suitability modelling. These new species’ distribution modelling functions were typically applied in studies of the potential effects of climate change on tree distributions, including a recently published climate change atlas for 54 tree species that are widely used in Central America for shade in coffee or cocoa agroforestry systems.
Improving the relevance of the package is a continuous process. Users can look forward to updates as they are released.
If you would like to discuss any aspect of BiodiversityR, please contact Roeland Kindt: r.kindt@cgiar.org.
The World Agroforestry Centre (ICRAF) is a centre of scientific excellence that harnesses the benefits of trees for people and the environment. Knowledge produced by ICRAF enables governments, development agencies and farmers to utilize the power of trees to make farming and livelihoods more environmentally, socially and economically sustainable at multiple scales. ICRAF is one of the 15 members of the CGIAR, a global research partnership for a food-secure future. We thank all donors who support research in development through their contributions to the CGIAR Fund.