gambin v2.4.0

Monthly downloads

by Thomas Matthews View Source

Fit the Gambin Model to Species Abundance Distributions

Fits unimodal and multimodal gambin distributions to species-abundance distributions from ecological data, as in in Matthews et al. (2014) <DOI:10.1111/ecog.00861>. 'gambin' is short for 'gamma-binomial'. The main function is fit_abundances(), which estimates the 'alpha' parameter(s) of the gambin distribution using maximum likelihood. Functions are also provided to generate the gambin distribution and for calculating likelihood statistics.

Readme

The gambin R package

This package fits the gambin distribution to species-abundance distributions from ecological data. 'gambin' is short for 'gamma-binomial'. The main functions are fit_abundances, which estimates the alpha parameter of the gambin distribution using maximum likelihood, and mult_abundances which estimates alpha for multiple sites / samples after standardising for the number of individuals. Recent functions are also provided to generate the gambin distribution and for calculating likelihood statistics. The package now provides functionality to fit multimodal gambin distributions.

The package is currently on CRAN and can be installed via

install.packages("gambin")

Alternatively, you can install the developmental version via

devtools::install_github("txm676/gambin")

Functions in gambin

Name	Description
moths	Williams' Rothamsted moth data
deconstruct_modes	Deconstruct a multimodal gambin model fit
summary.gambin	Summarising the results of a gambin model fit
gambin-package	Fit the gambin model to species abundance distributions
create_octaves	Reclassify a vector of species' abundances into abundance octaves
fit_abundances	Fit a unimodal or multimodal gambin model to a species abundance distribution
dgambin	The mixture gambin distribution
AIC.gambin	Likelihood statistics for the GamBin model
categ	Simulated bird SAD dataset with species classification data
mult_abundances	Fit a unimodal gambin model to multiple species abundance distributions
fly	Brazilian Horse Fly Data
No Results!

Vignettes of gambin

Name
overview.Rmd
refs.bib
No Results!

Last month downloads

Details

Type	Package
URL	https://github.com/txm676/gambin/
BugReports	https://github.com/txm676/gambin/issues
License	GPL-3
RoxygenNote	6.0.1
VignetteBuilder	knitr
NeedsCompilation	no
Packaged	2018-07-12 15:19:46 UTC; Tom
Repository	CRAN
Date/Publication	2018-07-12 15:30:03 UTC

imports	doParallel , foreach , graphics , gtools , parallel , stats
suggests	knitr , testthat
depends	R (>= 3.0.0)
Contributors	Michael Krabbe Borregaard, Colin Gillespie, Karl Ugland