Learn R Programming

⚠️There's a newer version (0.6.3) of this package.Take me there.

sads

R package for fitting species abundance distributions

Paulo I. Prado, Murilo Miranda and Andre Chalom

Installation

install.packages('sads')
library(sads)

Or download binaries from CRAN.

Developer version

Master branch on GitHub has the release version, as available on CRAN.

If you want to install the developer version:

library(devtools)
install_github(repo = 'piLaboratory/sads', ref= 'dev')

An experimental branch implementing Lindsey's (1999) correction for the log-likelihood of continuous density distributions when used for discrete data can be installed by:

library(devtools)
install_github(repo = 'piLaboratory/sads', ref= 'trueLL')

More info

Project page on GitHub
Research project at our Lab wiki

Copy Link

Version

Install

install.packages('sads')

Monthly Downloads

919

Version

0.3.2

License

GPL-2

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/piklprado/sads

Homepage

http://piLaboratory.github.io/sads

Maintainer

Paulo I Prado

Last Published

June 12th, 2017

Functions in sads (0.3.2)

Continuous or discrete distributions

Fisher's Log-series distribution

MacArthur's Broken-stick distribution

Geometric series distribution

Zipf-Mandelbrodt distribution

Metacommunity zero-sum multinomial distribution

Tree species abundance in Barro Colorado Island Plot

Abundances of breeding birds in Quacker Run Valley, NY

Biomass of marine animals in colonizing experiments in Baltic Sea

Compute table of information criteria and auxiliary info

Puyeo's Power-bend discrete distribution

Power discrete distribution

Pareto distribution

Left-truncation of density, probability and quantile of distributions

Neutral Biodiversity Theory distribution by Volkov et al.

Abundances of land snail species in Norway

Zipf distribution

Class "fitrad" for maximum likelihood fitting of species rank-abundance distributions

Rank-abundance data frame

radpred-methods

Predicted ranked abundance of species

Moths caught with light traps at Rothamsted 1933-1936

Class "octav" for frequencies in abundance octaves

qqsad and qqrad methods

Quantile-quantile plots for species-abundance and rank-abundance models

Compound Poisson-gamma distribution

Frequencies of species in octaves

octavpred-methods

Predicted frequencies of species in octaves

Sampling from a species abundance distribution

Modeling Species Abundance Distributions

Class "rad" for rank-abundance data

plotprofmle-methods

Log-likelihood profiles at original scale

coefficients,fitsad-method

Standard stats methods

summary.sads-class

Summary for fitsad/fitrad calls

Poisson-lognormal distribution

Compound Poisson-Exponential distribution

Class "fitsad" for maximum likelihood fitting of species abundance distributions

ML fitting of species abundance distributions

likelregions-class

Class "likelregions" for likelihood profiles of maximum likelihood fits

ppsad and pprad methods

Percentile-percentile plots for species-abundance and rank-abundance models

Predicted number of species by Fisher's Logseries

ML fitting of species rank-abundance distributions

Updating of MLE fits by profiling