beta_plot: Plot the beta profile for each community.

In BioFTF: Biodiversity Assessment Using Functional Tools

Description

This function provides a plot of the diversity profiles of the considered communities. The domain "beta" represents the sensibility to changes in the presence of rare species. It is a decreasing and concave upward curve showing different values of biodiversity for each value of beta. The most frequently used indices of biodiversity are special cases of this function. The diversity profile displays a complete picture of biodiversity. Its plot allows the analyst to rank different communities when the curves do not intersect. Indeed, the higher curve highlights biological populations with higher diversity and vice versa. The function tends towards a straight line, decreasing for beta values in the range -1 to 1. The profile tends to be more curved if there is a prevalence of few species over the others.

Usage

beta_plot(x,n)

Arguments

x

A data matrix with the abundance of the species (the rows are the communities and the columns indicate the species living in a community). The user can freely choose to use the absolute or relative frequencies.

n

The number of points of the domain [-1,1] that the user wants to consider in computing the functional tools. It is suggested to choose a number in the interval [3,10000] because a value of less than 3 has little sense; indeed, the major indices of biodiversity are the richness index, the index of Shannon and the index of Simpson (that we get for beta equal to -1, 0, +1, respectively). On the other hand, a value greater than 10000 is not very interesting because with a value of approximately 100 we already have a good approximation. The examples provided in this package always divide the domain into 20 intervals. The default value is n=20.

Author(s)

Fabrizio Maturo, Francesca Fortuna, Tonio Di Battista

Source

ENVIRONMENTAL MONITORING THROUGH FUNCTIONAL BIODIVERSITY TOOLS - T. Di Battista, F. Fortuna, F. Maturo - Ecological Indicators (2016) 60, 237-247 - online (2015). DOI: 10.1016/j.ecolind.2015.05.056.

PARAMETRIC FUNCTIONAL ANALYSIS OF VARIANCE FOR FISH BIODIVERSITY ASSESSMENT - T. Di Battista, F. Fortuna, F. Maturo - Journal of Environmental Informatics. Special issue of Marine and Freshwater Environmental Engineering and Management, Journal of Environmental Informatics. In press.

Examples

a=c(0.35,0.35,0.27,0.01,0.02)
b=c(0.54,0.20,0.17,0.06,0.03)
c=c(0.35,0.35,0.30,0,0)
d=c(0.51,0.31,0.07,0.10,0.01)
e=c(0.40,0.20,0.10,0.30,0)
x=matrix(rbind(a,b,c,d,e),5,5)
x
beta_plot(x,20)

Example output

Attaching package: ‘BioFTF’

The following object is masked from ‘package:base’:

    beta

     [,1] [,2] [,3] [,4] [,5]
[1,] 0.35 0.35 0.27 0.01 0.02
[2,] 0.54 0.20 0.17 0.06 0.03
[3,] 0.35 0.35 0.30 0.00 0.00
[4,] 0.51 0.31 0.07 0.10 0.01
[5,] 0.40 0.20 0.10 0.30 0.00

BioFTF documentation built on May 1, 2019, 10:26 p.m.