sads-package: tools:::Rd_package_title("sads")

Description

tools:::Rd_package_description("sads")

Arguments

Author

tools:::Rd_package_author("sads")

Maintainer: tools:::Rd_package_maintainer("sads")

Details

The distribution of abundances of species is one of the basic patterns of ecological communities. The empirical distributions of abundances (SADs) or their ranks (RADs) are traditionally modelled through probability distributions. Hence, the maximum likelihood method can be used to fit and compare competing models for SADs and RADs. The sads package provides functions, classes and methods to:

Fit classic SAD models: log-series, lognormal, broken-stick, ... ;
Fit classic rank-abundance (RADs) models: geometric, broken-stick, Zipf, Zipf-Mandelbrodt, ... ;
Tools for quick diagnostic and comparison of models;
Tools to simulate Poisson and Negative Binomial samples from abundances in communities.

References

Magurran, A.E. 2004. Measuring Biological Diversity. Blackwell.

Magurran, A.E. and McGill, B.J. 2011. Biological Diversity -- Frontiers in measurement and assessment. Oxford University Press.

May, R.M. 1975. Patterns of Species Abundance and Diversity. In M. L. Cody and J. M. Diamond (Eds.), (pp. 81--120). Harvard University Press.

Green,J. and Plotkin, J.B. 2007 A statistical theory for sampling species abundances. Ecology Letters 10:1037--1045.

Saether, B.E., Engen, S. and Grotan, V. 2013. Species diversity and community similarity in fluctuating environments: parametric approaches using species abundance distributions. Journal of Animal Ecology, 82(4): 721--738.

Examples

Run this code

## Rank-abundance plot
plot( rad(moths) )
## Preston's plots
plot (octav(moths) )
## Fit logseries model
moths.ls <-  fitsad(moths, sad = 'ls')
## Diagnostic plots
par(mfrow=c(2,2))
plot(moths.ls)
par(mfrow = c(1,1))
## Model summary
summary(moths.ls)
## Confidence interval
confint(moths.ls)