F-Diversity

f-Diversity is a software that implements a user-friendly interface to open source routines for the estimation and analysis of functional diversity indices. The authors: Di Rienzo, J.A., Casanoves F., and Pla L., are bio-statisticians form Argentina, Costa Rica and Venezuela, working within the . Development of f-Diversity was partially supported by the Interamerican Institute for Global Change Research, IAI (CRN-II 2015), which is supported by US National Science Foundation (Grant GEO-0452325). The open source platform is R with an interface written in Delphi® using DCOM-R (a way to run R in the background, due to Thomas Baier and Erich Neuwirth). DCOM-R is accessed via Delphi routines written by Dieter Menne.
Next the contents of the menu tool bar is described:
Implemented functional diversity indices
Unidimensional-single traits indices
All these indices use the relative abundance of each species. The Community Weighted Mean is a metric to represent the expected functional value of a random community sample trait by trait (Garnier et al. 2004, Díaz et al. 2007, Lavorell et al. 2008), the index FDvar is essentially the variance in the attribute values of the species present at a site (Mason et al. 2003). The Functional Regularity index measures how much a community of S species differs from maximum functional regularity (Mouillot et al. 2005).
Unidimensional-multiple traits indices
Some of these indices take into account species abundance others are based only on trait values. Among them FAD1 (Functional Attribute Diversity) is the number of different attribute combinations that occur in the community (Walker et al. 1999). FAD2 (Walker et al. 1999) and FD are based on a distance or dissimilarity matrix among pairs of species with one value by trait (Petchey and Gaston 2002, 2006) or several values by trait (Cianciaruso et al. 2009). The convex hull hyper-volume (Cornwell et al. 2006) is a crude multivariate representation of the range in a community. Other authors use the species abundance distribution to weight the traits: Q and Qrel (Rao 1982). All these indices allow the use of several traits in a multiple trait domain.
Multidimensional-multiple traits indices
Functional diversity summarized by a single number may not include components of richness, evenness and divergence at the same time. Under this framework functional diversity comprises three components: functional richness, functional evenness, and functional divergence (Villéger et al. 2008). The three components provide more detail in examining the mechanisms linking biodiversity to ecosystem functioning. Functional dispersion (FDis) is an another component of the multidimensional approach to functional diversity recently proposed by Laliberté and Legendre (2009).
It also includes tools to compare the estimated index among a set of conditions using a built-in linear model facility base on lm library of R.
Data handling facilities
As usual, the file menu contains the list of actions for handling data sets, like creating a new table or opening an existing one, saving, saving as, closing a table, and quitting the application. The default file format that f-Diversity uses to save tables is a proprietary file format with an .FDDB extension. However, f-Diversity can read Excel files (*.xls), text files (*.txt, *.dat), dbase files (*.dbf), InfoStat files (*.idb, *.idb2) and R scripts (*.r). It also has the ability to export data tables to all previously mentioned data formats. the Data menu contains a list of links to procedures that apply to the current active table. These procedures are intended to manage usual actions on a data sheets, such as: inserting, adding and deleting rows and columns, arranging rows according to different sorting criteria, activating and deactivating cases to allow or disallow participation in calculations, changing columns names, modify the number of decimal numbers displayed and the alignment and width of columns. It also contains links to more specialized procedures that allow categorizing numerical variables, editing the names of categories of categorical variables, writing formulas and searching for cases according to logical rules. Moreover, there are links to procedures on how to merge tables side by side according to matching criteria (Merge horizontally) and on how to merge tables appending one to the other (Merge vertically). Several transformation are implemented to make trait scales comparable.
How to get f-Diversity
The software is free and can be downloaded at: .

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