Maximum Likelihood Models for Species Abundance Distributions

Maximum likelihood tools to fit and compare models of species abundance distributions and of species rank-abundance distributions.


Travis-CI Build Status AppVeyor Build Status CRAN Status

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.

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', build_vignettes = TRUE)

More info

News

0.4.2 (2018-06-16)

  • fixed bug that does not allow zero values in non-truncated poilog, geom, nbinom
  • fix: diagnostic octav plot Plot #1 returned by plot methods for fitsad and fitrad methods had a truncated bar for the first octave.
  • sads-package.Rd updated to be syncronized with package metadata
  • rsads now allows a numeric vector in argument 'sads', to define an arbitrary community to be sampled

0.4.1 (2017-10-17)

  • fixed fitpareto to have 2 degrees of freedom
  • added Svolkov function
  • removed deprecated "representation" from class definitions
  • removed some checks for bugs in previous bbmle versions

0.4.0 (2017-06-11)

  • added a "prop" argument for plotting relative rank abundances
  • changed many details in plotting functions related to above change
  • fixed registering external calls for R version 3.4
  • fixed qbs not accepting non-integer N
  • added continuous integration tests with TravisCI/AppVeyor
  • added clarifications for building vignettes on README
  • fixed a bug where plotprofmle would ignore input parameters
  • tweaked fitgeom optimization a bit

0.3.1 (2016-05-12)

  • Fixed a CRAN link on README

0.3.0 (2016-05-11)

  • new functions for density, distribution, quantile and random generators function for the Pueyo's powerbend distribution
  • several new functionalities for random sad generation (rsad)
  • now providing random generator functions for all distributions in the package (such as rls, rmzsm, rzipf, etc)
  • octav is now a S4 method, and octav plots have a new argument "mid=TRUE"
  • new function and class for likelregions; also changed the spline method for plotting in plotprofmle
  • better optimization and vectorization of several discrete quantile and distribution functions
  • fixed the support of Zipf, Zipf-Mandelbrot and geometric series to not include zero abundances or zero-th rank
  • added He & Tang's formula for initial parameter estimate of the geometric series
  • more robust checking for invalid data in the fitting functions
  • fixed bugs in octav, octavpred and dmzsm

0.2.4 (2015-11-02)

  • octavpred now accepts a 'preston' argument (as does 'octav')
  • fixes a bug in fitvolkov under Windows
  • added a friendlier error message when the octavs provided in octavpred do not cover the data
  • deprecated the slot "distr" on fitsad/fitrad objects. Now users should use the distr function (see ?distr)
  • fixed signature errors on several methods dealing with the trunc parameter
  • now providing the coefficients, fitted, fitted.values, residuals methods on fitsad/fitrad methods
  • providing a summary method for fitsad/fitrad classes that allows for fixed parameters (such as produced by fitls, fitvolkov, etc)

0.2.3 (2015-09-24)

  • fitgeom, fitpoilog and fitnbinom now can get argument trunc=NULL to avoid zero-truncation (the default)
  • fitgeom uses default optimization method from mle2 instead of Brent's method, to avoid some overflow errors for large datasets (e.g. moths)
  • dmzsm and dvolkov now returns zero for any abundance larger than the community size J. Accordingly, pzsm and pvolkov now return 1 for any q>J and lower.tail=TRUE and zero for lower.tail=FALSE.
  • fixes important bugs in AICc

0.2.2 (2015-07-12)

  • plotprofmle is now a S4 method with mle2 and profile.mle2 signatures
  • Fixed the way \dots are handled by some of the fitting functions
  • Better starting values for fitting Weibull distributions

0.2.1 (2015-06-14)

  • Fixed some errors in the documentation

0.2.0 (2015-06-01)

  • Reworked the Volkov distribution for performance.
  • Reworked density, quantile and distribution functions for more consistent behaviour, error handling and large performance gains.
  • Added some missing functions for mzsm, poig and poix families.
  • New function updatesad to update a fitsad with better fit from profile.
  • radpred now uses exact solutions for extreme data points.
  • Reimplemented the AIC and AICc functions for better integration with fitsad and fitrad classes.
  • Removed trueLL method to an experimental branch
  • Improved grammar and clearer text in some manual pages and vignette.
  • Improved starting values for several distributions.
  • Replaced table(cut(x)) for hist for improved performance.
  • octav and rad classes now have validation functions and are more consistent.
  • More informative calls in show and summary.
  • Reduced code redundancy and improved readability.
  • Changed some "Depends" and "Imports" to make the package more light-weight, but still reliable
  • Fixed the Broken-Stick family to behave like a Discrete distribution.
  • Small but importante fixes in octavpred.
  • Workarounds for bugs and issues of the bbmle package.

0.1.10 (2014-07-02)

  • Initial release on CRAN.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("sads")

0.4.2 by Paulo I. Prado, 10 months ago


http://piLaboratory.github.io/sads, https://github.com/piklprado/sads


Report a bug at https://github.com/piLaboratory/sads/issues


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


Authors: Paulo I. Prado , Murilo Dantas Miranda and Andre Chalom


Documentation:   PDF Manual  


GPL-2 license


Imports MASS, methods, graphics, grDevices, VGAM, poilog, GUILDS

Depends on stats, bbmle

Suggests vegan


Imported by mobsim.

Depended on by ebimetagenomics.


See at CRAN