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.

AuthorPaulo I. Prado, Murilo Dantas Miranda and Andre Chalom
Date of publication2016-05-13 00:47:12
MaintainerPaulo I. Prado <prado@ib.usp.br>
LicenseGPL-2
Version0.3.1
http://piLaboratory.github.io/sads, https://github.com/piklprado/sads

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

Functions

AIC Man page
AICc Man page
AICc-methods Man page
AICc,mle2-method Man page
AIC-methods Man page
AIC,mle2-method Man page
ARN82.eB.apr77 Man page
bci Man page
birds Man page
coefficients,fitrad-method Man page
coefficients,fitsad-method Man page
dbs Man page
dgs Man page
distr Man page
dls Man page
dmand Man page
dmzsm Man page
dpareto Man page
dpoig Man page
dpoilog Man page
dpoix Man page
dpowbend Man page
dpower Man page
drbs Man page
dtrunc Man page
dvolkov Man page
dzipf Man page
fitbs Man page
fitgamma Man page
fitgeom Man page
fitgs Man page
fitlnorm Man page
fitls Man page
fitmand Man page
fitmzsm Man page
fitnbinom Man page
fitpareto Man page
fitpoilog Man page
fitpowbend Man page
fitpower Man page
fitrad Man page
fitrad-class Man page
fitrbs Man page
fitsad Man page
fitsad-class Man page
fitted,fitrad-method Man page
fitted,fitsad-method Man page
fitted.values,fitrad-method Man page
fitted.values,fitsad-method Man page
fitvolkov Man page
fitweibull Man page
fitzipf Man page
likelregions Man page
likelregions-class Man page
likelregions,mle2-method Man page
likelregions,profile.mle2-method Man page
lines,octav-method Man page
lines,rad-method Man page
moths Man page
nobs Man page
nobs,fitrad-method Man page
nobs,fitsad-method Man page
nobs-methods Man page
octav Man page
octav-class Man page
octav,fitrad-method Man page
octav,fitsad-method Man page
octav,numeric-method Man page
octavpred Man page
octavpred,fitrad,missing,missing,missing,missing,ANY,missing,mis Man page
octavpred,fitrad,missing,missing,missing,missing,ANY,missing,mis Man page
octavpred,fitrad,missing,missing,missing,missing,ANY,missing,mis Man page
octavpred,fitsad,missing,missing,missing,missing,ANY,missing,mis Man page
octavpred,fitsad,missing,missing,missing,missing,ANY,missing,mis Man page
octavpred-methods Man page
octavpred,missing,character,missing,list,ANY,ANY,numeric,numeric Man page
octavpred,missing,missing,character,list,ANY,ANY,numeric,numeric Man page
octavpred,numeric,character,missing,list,ANY,ANY,missing,missing Man page
octavpred,numeric,missing,character,list,ANY,ANY,missing,missing Man page
okland Man page
pbs Man page
pgs Man page
plot,fitrad,ANY-method Man page
plot,fitsad,ANY-method Man page
plot,octav,ANY-method Man page
plot,octav-method Man page
plotprofmle Man page
plotprofmle,mle2-method Man page
plotprofmle,profile.mle2-method Man page
plot,rad,ANY-method Man page
pls Man page
pmand Man page
pmzsm Man page
points,octav-method Man page
points,rad-method Man page
ppareto Man page
ppoig Man page
ppoilog Man page
ppoix Man page
ppowbend Man page
ppower Man page
pprad Man page
pprad,fitrad-method Man page
pprad,fitrad-method Man page
pprad,fitrad,missing,missing-method Man page
pprad,fitrad,missing,missing-method Man page
pprad,fitrad,missing,missing,missing,missing-method Man page
pprad,fitrad,missing,missing,missing,missing-method Man page
pprad-methods Man page
pprad,numeric,character,list,ANY,character-method Man page
pprad,numeric,character,list-method Man page
pprad,numeric-method Man page
pprad,rad,character,list,ANY,character-method Man page
pprad,rad,character,list-method Man page
pprad,rad,character,list-method Man page
pprad,rad-method Man page
ppsad Man page
ppsad,fitsad-method Man page
ppsad,fitsad-method Man page
ppsad,fitsad,missing,missing-method Man page
ppsad,fitsad,missing,missing-method Man page
ppsad,fitsad,missing,missing,missing-method Man page
ppsad,fitsad,missing,missing,missing-method Man page
ppsad-methods Man page
ppsad,numeric,character,list,ANY-method Man page
ppsad,numeric,character,list-method Man page
ppsad,numeric-method Man page
prbs Man page
pred.logser Man page
ptrunc Man page
pvolkov Man page
pzipf Man page
qbs Man page
qgs Man page
qls Man page
qmand Man page
qmzsm Man page
qpareto Man page
qpoig Man page
qpoilog Man page
qpoix Man page
qpowbend Man page
qpower Man page
qqrad Man page
qqrad,fitrad-method Man page
qqrad,fitrad-method Man page
qqrad,fitrad,missing,missing,missing-method Man page
qqrad,fitrad,missing,missing,missing,missing-method Man page
qqrad,fitrad,missing,missing,missing,missing-method Man page
qqrad,integer-method Man page
qqrad-methods Man page
qqrad,numeric,character,list,ANY,character-method Man page
qqrad,numeric,character,list,ANY-method Man page
qqrad,numeric-method Man page
qqrad,rad,character,list,ANY,character-method Man page
qqrad,rad,character,list,ANY,character-method Man page
qqrad,rad,character,list,ANY-method Man page
qqrad,rad,character,list,ANY-method Man page
qqrad,rad,character,list,ANY-method Man page
qqrad,rad-method Man page
qqrad,rad-method Man page
qqsad Man page
qqsad,fitsad-method Man page
qqsad,fitsad-method Man page
qqsad,fitsad,missing,missing,missing,missing-method Man page
qqsad,fitsad,missing,missing,missing,missing-method Man page
qqsad,integer-method Man page
qqsad-methods Man page
qqsad,numeric,character,list,ANY,ANY-method Man page
qqsad,numeric-method Man page
qrbs Man page
qtrunc Man page
qvolkov Man page
qzipf Man page
rad Man page
rad-class Man page
radpred Man page
radpred,fitrad,missing,missing,missing,missing,missing,missing,m Man page
radpred,fitrad,missing,missing,missing,missing,missing,missing,m Man page
radpred,fitsad,missing,missing,missing,missing,missing,missing,m Man page
radpred,fitsad,missing,missing,missing,missing,missing,missing,m Man page
radpred-methods Man page
radpred,missing,character,missing,list,ANY,ANY,numeric,numeric-m Man page
radpred,missing,missing,character,list,ANY,missing,numeric,numer Man page
radpred,numeric,character,missing,list,ANY,ANY,missing,missing-m Man page
radpred,numeric,missing,character,list,ANY,missing,missing,missi Man page
rbs Man page
residuals,fitrad-method Man page
residuals,fitsad-method Man page
rgs Man page
rls Man page
rmand Man page
rmzsm Man page
rpareto Man page
rpoig Man page
rpoilog Man page
rpoix Man page
rpowbend Man page
rpower Man page
rrbs Man page
rsad Man page
rtrunc Man page
rvolkov Man page
rzipf Man page
sads Man page
sads-package Man page
show,fitrad-method Man page
show,fitsad-method Man page
show,likelregions-method Man page
show,summary.sads-method Man page
summary,fitrad-method Man page
summary,fitsad-method Man page
summary.sads-class Man page
updaterad Man page
updatesad Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.