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) . '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.


The gambin R package

Build Status Downloads CRAN codecov.io

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")

News

Version 2.4.0

  • Bug fix: confidence intervals for alpha
  • New tests included
  • Adding a new 'deconstruct_modes' function to enable more in depth analysis of a multimodal gambin model fit
  • Confidence intervals for multi-component gambin model parameters

Version 2.3.0

  • Adding a new 'mult_abundances' function to fit gambin to muliple sites and calculate standardised alpha

Version 2.2.0

  • Adding a new dataset (Brazilian flies)

Version 2.1.0

  • Adding support for mixture models

Version 2.0.0

  • Code refactored
  • Create r/q/p/d gambin functions
  • Number of considered free parameters increased from 1 to 2
  • Created an initial vignette.
  • Created an initial test suite
  • Hooked up to travis and codecov
  • Created d/r/p/q functions
  • Minor optimisation on fitGam
  • Move plot to barplot, lines, points. You can now pass standard plotting arguments and everything will work as expected.
  • Created README.Rmd to generate README.md
  • Created NEWS.md
  • Updated DESCRIPTION with URL

Version 1.4.0

  • Initial version

Reference manual

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install.packages("gambin")

2.4.0 by Thomas Matthews, 4 months ago


https://github.com/txm676/gambin/


Report a bug at https://github.com/txm676/gambin/issues


Browse source code at https://github.com/cran/gambin


Authors: Thomas Matthews [aut, cre] , Michael Krabbe Borregaard [aut] , Karl Ugland [aut] , Colin Gillespie [aut]


Documentation:   PDF Manual  


Task views: Probability Distributions


GPL-3 license


Imports stats, graphics, doParallel, gtools, foreach, parallel

Suggests testthat, knitr


Suggested by fitteR.


See at CRAN