Package: sads 0.6.5

Paulo I. Prado

sads: 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.

Authors:Paulo I. Prado [aut, cre], Murilo Dantas Miranda [aut], Andre Chalom [aut]

sads_0.6.5.tar.gz
sads_0.6.5.zip(r-4.7)sads_0.6.5.zip(r-4.6)sads_0.6.5.zip(r-4.5)
sads_0.6.5.tgz(r-4.6-x86_64)sads_0.6.5.tgz(r-4.6-arm64)sads_0.6.5.tgz(r-4.5-x86_64)sads_0.6.5.tgz(r-4.5-arm64)
sads_0.6.5.tar.gz(r-4.7-arm64)sads_0.6.5.tar.gz(r-4.7-x86_64)sads_0.6.5.tar.gz(r-4.6-arm64)sads_0.6.5.tar.gz(r-4.6-x86_64)
sads_0.6.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
sads/json (API)

# Install 'sads' in R:

install.packages('sads', repos = c('https://pilaboratory.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pilaboratory/sads/issues

Datasets:

ARN82.eB.apr77 - Biomass of marine animals in colonizing experiments in Baltic Sea
bci - Tree species abundance in Barro Colorado Island Plot
birds - Abundances of breeding birds in Quacker Run Valley, NY
grasslands - Coverages of plants species in a plot in Southern Brazilian Grasslands
moths - Moths caught with light traps at Rothamsted 1933-1936
okland - Abundances of land snail species in Norway

On CRAN:

9.74 score 24 stars 11 packages 199 scripts 1.3k downloads 9 mentions 116 exports 14 dependencies

Last updated from:462e9d4e2f. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	172
linux-devel-x86_64	OK	150
source / vignettes	OK	203
linux-release-arm64	OK	144
linux-release-x86_64	OK	154
macos-release-arm64	OK	219
macos-release-x86_64	OK	306
macos-oldrel-arm64	OK	170
macos-oldrel-x86_64	OK	314
windows-devel	OK	111
windows-release	OK	118
windows-oldrel	OK	139
wasm-release	OK	107

Exports:AIC AICc coefficients coverpred dbs dgs distr dls dmand dmzsm dpareto dpoig dpoilog dpoix dpowbend dpower drbs dtrunc dvolkov dzipf fitbs fitexp fitexpC fitgamma fitgammaC fitgeom fitgs fitlnorm fitlnormC fitls fitmand fitmzsm fitnbinom fitpareto fitparetoC fitpoilog fitpowbend fitpower fitrad fitrbs fitsad fitsadC fitted fitted.values fitvolkov fitweibull fitweibullC fitzipf likelregions lines nobs octav octavpred pbs pgs plot plotprofmle pls pmand pmzsm points ppareto ppoig ppoilog ppoix ppowbend ppower pprad ppsad prbs pred.logser ptrunc pvolkov pzipf qbs qgs qls qmand qmzsm qpareto qpoig qpoilog qpoix qpowbend qpower qqrad qqsad qrbs qtrunc qvolkov qzipf rad radpred rbs residuals rgs rls rmand rmzsm rpareto rpoig rpoilog rpoix rpowbend rpower rrbs rsad rtrunc rvolkov rzipf show summary Svolkov trueLL updaterad updatesad

Dependencies:bbmle bdsmatrix GUILDS lattice MASS Matrix mvtnorm nloptr numDeriv poilog poweRlaw pracma Rcpp VGAM

Introduction to sads

Rendered fromsads_intro.Rnwusingutils::Sweave

Last update: 2025-08-18
Started: 2014-07-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Maximum Likelihood Models for Species Abundance Distributions	sads-package sads
Biomass of marine animals in colonizing experiments in Baltic Sea	ARN82.eB.apr77
Tree species abundance in Barro Colorado Island Plot	bci
Abundances of breeding birds in Quacker Run Valley, NY	birds
Standard stats methods	coefficients,fitrad-method coefficients,fitsad-method coefficients,fitsadC-method fitted,fitrad-method fitted,fitsad-method fitted,fitsadC-method fitted.values,fitrad-method fitted.values,fitsad-method fitted.values,fitsadC-method residuals,fitrad-method residuals,fitsad-method residuals,fitsadC-method
Class '"coverpred"' for predicted values for abundance classes	coverpred-class points,coverpred-method
~~ Methods for Function 'coverpred' in Package 'sads' ~~	coverpred coverpred,fitsadC,missing,missing,missing,missing,missing,missing-method coverpred,histogram,character,list,ANY,missing,missing,missing-method coverpred,missing,character,list,ANY,numeric,ANY,numeric-method coverpred-methods
MacArthur's Broken-stick distribution	dbs drbs pbs prbs qbs qrbs rbs rrbs
Geometric series distribution	dgs pgs qgs rgs
Continuous or discrete distributions	distr
Fisher's Log-series distribution	dls pls qls rls
Zipf-Mandelbrodt distribution	dmand pmand qmand rmand
Metacommunity zero-sum multinomial distribution	dmzsm pmzsm qmzsm rmzsm
Pareto distribution	dpareto ppareto qpareto rpareto
Compound Poisson-gamma distribution	dpoig ppoig qpoig rpoig
Poisson-lognormal distribution	dpoilog ppoilog qpoilog rpoilog
Compound Poisson-Exponential distribution	dpoix ppoix qpoix rpoix
Puyeo's Power-bend discrete distribution	dpowbend ppowbend qpowbend rpowbend
Power discrete distribution	dpower ppower qpower rpower
Left-truncation of density, probability and quantile of distributions	dtrunc ptrunc qtrunc rtrunc
Neutral Biodiversity Theory distribution by Volkov _et al._	dvolkov pvolkov qvolkov rvolkov Svolkov
Zipf distribution	dzipf pzipf qzipf rzipf
ML fitting of species rank-abundance distributions	fitgs fitmand fitrad fitrbs fitzipf
Class '"fitrad"' for maximum likelihood fitting of species rank-abundance distributions	fitrad-class plot,fitrad,ANY-method pprad,fitrad,missing,missing,missing,missing-method pprad,fitrad,missing,missing-method qqrad,fitrad,missing,missing,missing,missing-method show,fitrad-method
ML fitting of species abundance distributions	fitbs fitexp fitgamma fitgeom fitlnorm fitls fitmzsm fitnbinom fitpareto fitpoilog fitpowbend fitpower fitsad fitvolkov fitweibull
Class '"fitsad"' for maximum likelihood fitting of species abundance distributions	fitsad-class plot,fitsad,ANY-method ppsad,fitsad,missing,missing,missing-method ppsad,fitsad,missing,missing-method qqsad,fitsad,missing,missing,missing,missing-method show,fitsad-method
ML fitting of species abundance distributions to data pooled in abundance classes	fitexpC fitgammaC fitlnormC fitparetoC fitsadC fitweibullC
Class '"fitsadC"' for maximum likelihood fitting of species abundance distributions from data in abundance classes	fitsadC-class nobs,fitsadC-method plot,fitsadC,ANY-method ppsad,fitsadC,missing,missing,missing-method qqsad,fitsadC,missing,missing,missing,missing-method show,fitsadC-method
Coverages of plants species in a plot in Southern Brazilian Grasslands	grasslands
Compute table of information criteria and auxiliary info	AIC AIC,mle2-method AIC-methods AICc AICc,mle2-method AICc-methods nobs nobs,fitrad-method nobs,fitsad-method nobs-methods
Class '"likelregions"' for likelihood profiles of maximum likelihood fits	likelregions-class show,likelregions-method
Moths caught with light traps at Rothamsted 1933-1936	moths
Class '"octav"' for frequencies in abundance octaves	lines,octav-method octav-class plot,octav,ANY-method plot,octav-method points,octav-method
Frequencies of species in octaves	octav octav,fitrad-method octav,fitsad-method octav,numeric-method
Predicted frequencies of species in octaves	octavpred octavpred,fitrad,missing,missing,missing,missing,ANY,missing,missing-method octavpred,fitsad,missing,missing,missing,missing,ANY,missing,missing-method octavpred,missing,character,missing,list,ANY,ANY,numeric,numeric-method octavpred,missing,missing,character,list,ANY,ANY,numeric,numeric-method octavpred,numeric,character,missing,list,ANY,ANY,missing,missing-method octavpred,numeric,missing,character,list,ANY,ANY,missing,missing-method
Abundances of land snail species in Norway	okland
Log-likelihood profiles at original scale	likelregions likelregions,mle2-method likelregions,profile.mle2-method plotprofmle plotprofmle,mle2-method plotprofmle,profile.mle2-method
Percentile-percentile plots for species-abundance and rank-abundance models	pprad pprad,fitrad-method pprad,numeric,character,list,ANY,character-method pprad,numeric,character,list-method pprad,numeric-method pprad,rad,character,list,ANY,character-method pprad,rad,character,list-method pprad,rad-method ppsad ppsad,fitsad-method ppsad,numeric,character,list,ANY-method ppsad,numeric,character,list-method ppsad,numeric-method
Predicted number of species by Fisher's Logseries	pred.logser
Quantile-quantile plots for species-abundance and rank-abundance models	qqrad qqrad,fitrad,missing,missing,missing-method qqrad,fitrad-method qqrad,integer-method qqrad,numeric,character,list,ANY,character-method qqrad,numeric,character,list,ANY-method qqrad,numeric-method qqrad,rad,character,list,ANY,character-method qqrad,rad,character,list,ANY-method qqrad,rad-method qqsad qqsad,fitsad-method qqsad,integer-method qqsad,numeric,character,list,ANY,ANY-method qqsad,numeric-method
Rank-abundance data frame	rad
Class '"rad"' for rank-abundance data	lines,rad-method plot,rad,ANY-method plot,rad-method points,rad-method rad-class
Predicted ranked abundance of species	radpred radpred,fitrad,missing,missing,missing,missing,missing,missing,missing-method radpred,fitsad,missing,missing,missing,missing,missing,missing,missing-method radpred,fitsadC,missing,missing,missing,missing,missing,missing,missing-method radpred,missing,character,missing,list,ANY,ANY,numeric,numeric-method radpred,missing,missing,character,list,ANY,missing,numeric,numeric-method radpred,numeric,character,missing,list,ANY,ANY,missing,missing-method radpred,numeric,missing,character,list,ANY,missing,missing,missing-method
Sampling from a species abundance distribution	rsad
Summary for fitsad/fitrad calls	show,summary.sads-method summary,fitrad-method summary,fitsad-method summary.sads-class
True likelihood for continuous variables	trueLL trueLL,fitrad,missing,missing,missing,ANY,ANY-method trueLL,fitsad,missing,missing,missing,ANY,ANY-method trueLL,histogram,character,list,ANY,missing,missing-method trueLL,numeric,character,list,ANY,ANY,ANY-method trueLL-methods
Updating of MLE fits by profiling	updaterad updatesad