sads: Maximum Likelihood Models for Species Abundance Distributions

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

Author
Paulo I. Prado, Murilo Dantas Miranda and Andre Chalom
Date of publication
2016-05-13 00:47:12
Maintainer
Paulo I. Prado <prado@ib.usp.br>
License
GPL-2
Version
0.3.1
URLs

View on CRAN

Man pages

ARN82
Biomass of marine animals in colonizing experiments in Baltic...
bci
Tree species abundance in Barro Colorado Island Plot
birds
Abundances of breeding birds in Quacker Run Valley, NY
dbs
MacArthur's Broken-stick distribution
dgs
Geometric series distribution
distr
Continuous or discrete distributions
dls
Fisher's Log-series distribution
dman
Zipf-Mandelbrodt distribution
dmzsm
Metacommunity zero-sum multinomial distribution
dpareto
Pareto distribution
dpoig
Compound Poisson-gamma distribution
dpoilog
Poisson-lognormal distribution
dpoix
Compound Poisson-Exponential distribution
dpowbend
Puyeo's Power-bend discrete distribution
dpower
Power discrete distribution
dtrunc
Left-truncation of density, probability and quantile of...
dvolkov
Neutral Biodiversity Theory distribution by Volkov _et al._
dzipf
Zipf distribution
fitrad
ML fitting of species rank-abundance distributions
fitrad-class
Class '"fitrad"' for maximum likelihood fitting of species...
fitsad
ML fitting of species abundance distributions
fitsad-class
Class '"fitsad"' for maximum likelihood fitting of species...
ICtab
Compute table of information criteria and auxiliary info
likelregions-class
Class '"likelregions"' for likelihood profiles of maximum...
moths
Moths caught with light traps at Rothamsted 1933-1936
octav
Frequencies of species in octaves
octav-class
Class '"octav"' for frequencies in abundance octaves
octavpred
Predicted frequencies of species in octaves
okland
Abundances of land snail species in Norway
plotprofmle
Log-likelihood profiles at original scale
ppsad
Percentile-percentile plots for species-abundance and...
pred.logser
Predicted number of species by Fisher's Logseries
qqsad
Quantile-quantile plots for species-abundance and...
rad
Rank-abundance data frame
rad-class
Class '"rad"' for rank-abundance data
radpred
Predicted ranked abundance of species
rsad
Sampling from a species abundance distribution
sads-package
Modeling Species Abundance Distributions
stats
Standard stats methods
summary.sads-class
Summary for fitsad/fitrad calls
updatesad
Updating of MLE fits by profiling

Files in this package

sads
sads/inst
sads/inst/doc
sads/inst/doc/sads_intro.Rnw
sads/inst/doc/sads_intro.pdf
sads/inst/doc/sads_intro.R
sads/src
sads/src/gauss_legendre.h
sads/src/volkov.c
sads/src/gauss_legendre.c
sads/NAMESPACE
sads/NEWS
sads/data
sads/data/birds.rda
sads/data/okland.rda
sads/data/ARN82.eB.apr77.rda
sads/data/bci.rda
sads/data/moths.rda
sads/R
sads/R/dpoig.R
sads/R/dpoix.R
sads/R/qmzsm.R
sads/R/qrbs.R
sads/R/fitpareto.R
sads/R/fitzipf.R
sads/R/utils.R
sads/R/fitbs.R
sads/R/fitpoilog.R
sads/R/pred.logser.R
sads/R/dls.R
sads/R/prbs.R
sads/R/updatesad.R
sads/R/pls.R
sads/R/qmand.R
sads/R/rad.R
sads/R/dpower.R
sads/R/dvolkov.R
sads/R/qpoig.R
sads/R/plotprofmle.R
sads/R/ppower.R
sads/R/dzipf.R
sads/R/fitrad.R
sads/R/fitvolkov.R
sads/R/pmand.R
sads/R/qpowbend.R
sads/R/ppoilog.R
sads/R/qpoix.R
sads/R/dpowbend.R
sads/R/rsad.R
sads/R/qgs.R
sads/R/qtrunc.R
sads/R/fitmzsm.R
sads/R/dpareto.R
sads/R/sads-methods.R
sads/R/dmzsm.R
sads/R/fitgeom.R
sads/R/pbs.R
sads/R/qpower.R
sads/R/dpoilog.R
sads/R/pvolkov.R
sads/R/ppareto.R
sads/R/pzipf.R
sads/R/pmzsm.R
sads/R/sads-classes.R
sads/R/fitpowbend.R
sads/R/fitlnorm.R
sads/R/fitmand.R
sads/R/fitls.R
sads/R/ppoix.R
sads/R/fitpower.R
sads/R/ppowbend.R
sads/R/pgs.R
sads/R/fitrbs.R
sads/R/dgs.R
sads/R/qvolkov.R
sads/R/qpoilog.R
sads/R/fitnbinom.R
sads/R/ppoig.R
sads/R/fitsad.R
sads/R/distr.R
sads/R/dtrunc.R
sads/R/fitweibull.R
sads/R/qbs.R
sads/R/drbs.R
sads/R/qls.R
sads/R/ptrunc.R
sads/R/fitgs.R
sads/R/qpareto.R
sads/R/dmand.R
sads/R/qzipf.R
sads/R/fitgamma.R
sads/R/dbs.R
sads/vignettes
sads/vignettes/sads_intro.Rnw
sads/vignettes/ecology.bst
sads/vignettes/sads_intro.bib
sads/README.md
sads/MD5
sads/build
sads/build/vignette.rds
sads/DESCRIPTION
sads/man
sads/man/dvolkov.Rd
sads/man/summary.sads-class.Rd
sads/man/ppsad.Rd
sads/man/octavpred.Rd
sads/man/dpareto.Rd
sads/man/dgs.Rd
sads/man/plotprofmle.Rd
sads/man/octav.Rd
sads/man/dpoix.Rd
sads/man/updatesad.Rd
sads/man/dmzsm.Rd
sads/man/dman.Rd
sads/man/moths.Rd
sads/man/distr.Rd
sads/man/dtrunc.Rd
sads/man/ICtab.Rd
sads/man/dbs.Rd
sads/man/dpower.Rd
sads/man/ARN82.Rd
sads/man/bci.Rd
sads/man/fitrad.Rd
sads/man/pred.logser.Rd
sads/man/fitsad.Rd
sads/man/dzipf.Rd
sads/man/rad-class.Rd
sads/man/fitrad-class.Rd
sads/man/stats.Rd
sads/man/birds.Rd
sads/man/octav-class.Rd
sads/man/okland.Rd
sads/man/dpoig.Rd
sads/man/sads-package.Rd
sads/man/qqsad.Rd
sads/man/rsad.Rd
sads/man/radpred.Rd
sads/man/dpowbend.Rd
sads/man/dls.Rd
sads/man/dpoilog.Rd
sads/man/fitsad-class.Rd
sads/man/likelregions-class.Rd
sads/man/rad.Rd