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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', build_vignettes = TRUE)

When running under Windows, you will need to install the Rtools package to build the vignettes locally.

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Version

Install

install.packages('sads')

Monthly Downloads

1,333

Version

0.6.3

License

GPL-2

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/piLaboratory/sads

Maintainer

Paulo I Prado

Last Published

January 16th, 2024

Functions in sads (0.6.3)

Puyeo's Power-bend discrete distribution

Compound Poisson-gamma distribution

Poisson-lognormal distribution

Metacommunity zero-sum multinomial distribution

Pareto distribution

Zipf-Mandelbrodt distribution

Left-truncation of density, probability and quantile of distributions

Compound Poisson-Exponential distribution

Power discrete distribution

Neutral Biodiversity Theory distribution by Volkov et al.

Class "fitsadC" for maximum likelihood fitting of species abundance distributions from data in abundance classes

ML fitting of species abundance distributions to data pooled in abundance classes

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

Zipf distribution

ML fitting of species abundance distributions

ML fitting of species rank-abundance distributions

Moths caught with light traps at Rothamsted 1933-1936

likelregions-class

Class "likelregions" for likelihood profiles of maximum likelihood fits

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

Coverages of plants species in a plot in Southern Brazilian Grasslands

octavpred-methods

Predicted frequencies of species in octaves

Rank-abundance data frame

Predicted number of species by Fisher's Logseries

plotprofmle-methods

Log-likelihood profiles at original scale

Abundances of land snail species in Norway

Class "rad" for rank-abundance data

qqsad and qqrad methods

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

ppsad and pprad methods

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

Frequencies of species in octaves

Class "octav" for frequencies in abundance octaves

radpred-methods

Predicted ranked abundance of species

summary.sads-class

Summary for fitsad/fitrad calls

Updating of MLE fits by profiling

tools:::Rd_package_title("sads")

True likelihood for continuous variables

Sampling from a species abundance distribution

coefficients,fitsad-method

Standard stats methods

Abundances of breeding birds in Quacker Run Valley, NY

Continuous or discrete distributions

Geometric series distribution

MacArthur's Broken-stick distribution

Compute table of information criteria and auxiliary info

Fisher's Log-series distribution

coverpred-methods

~~ Methods for Function coverpred in Package sads ~~

Tree species abundance in Barro Colorado Island Plot

Biomass of marine animals in colonizing experiments in Baltic Sea

coverpred-class

Class "coverpred" for predicted values for abundance classes