Package: sads 0.6.3

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, Murilo Dantas Miranda and Andre Chalom

sads_0.6.3.tar.gz
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sads.pdf |sads.html✨
sads/json (API)
NEWS

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

Peer review:

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:

8.36 score 23 stars 2 packages 186 scripts 432 downloads 9 mentions 116 exports 14 dependencies

Last updated 10 months agofrom:df7ec19747. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-win-x86_64NOTENov 12 2024
R-4.5-linux-x86_64NOTENov 12 2024
R-4.4-win-x86_64OKNov 12 2024
R-4.4-mac-x86_64OKNov 12 2024
R-4.4-mac-aarch64OKNov 12 2024
R-4.3-win-x86_64OKNov 12 2024
R-4.3-mac-x86_64OKNov 12 2024
R-4.3-mac-aarch64OKNov 12 2024

Exports:AICAICccoefficientscoverpreddbsdgsdistrdlsdmanddmzsmdparetodpoigdpoilogdpoixdpowbenddpowerdrbsdtruncdvolkovdzipffitbsfitexpfitexpCfitgammafitgammaCfitgeomfitgsfitlnormfitlnormCfitlsfitmandfitmzsmfitnbinomfitparetofitparetoCfitpoilogfitpowbendfitpowerfitradfitrbsfitsadfitsadCfittedfitted.valuesfitvolkovfitweibullfitweibullCfitzipflikelregionslinesnobsoctavoctavpredpbspgsplotplotprofmleplspmandpmzsmpointspparetoppoigppoilogppoixppowbendppowerppradppsadprbspred.logserptruncpvolkovpzipfqbsqgsqlsqmandqmzsmqparetoqpoigqpoilogqpoixqpowbendqpowerqqradqqsadqrbsqtruncqvolkovqzipfradradpredrbsresidualsrgsrlsrmandrmzsmrparetorpoigrpoilogrpoixrpowbendrpowerrrbsrsadrtruncrvolkovrzipfshowsummarySvolkovtrueLLupdateradupdatesad

Dependencies:bbmlebdsmatrixGUILDSlatticeMASSMatrixmvtnormnloptrnumDerivpoilogpoweRlawpracmaRcppVGAM

Introduction to sads

Rendered fromsads_intro.Rnwusingutils::Sweaveon Nov 12 2024.

Last update: 2024-01-16
Started: 2014-07-02

Readme and manuals

Help Manual

Help pageTopics
Maximum Likelihood Models for Species Abundance Distributionssads-package sads
Biomass of marine animals in colonizing experiments in Baltic SeaARN82.eB.apr77
Tree species abundance in Barro Colorado Island Plotbci
Abundances of breeding birds in Quacker Run Valley, NYbirds
Standard stats methodscoefficients,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 classescoverpred-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 distributiondbs drbs pbs prbs qbs qrbs rbs rrbs
Geometric series distributiondgs pgs qgs rgs
Continuous or discrete distributionsdistr
Fisher's Log-series distributiondls pls qls rls
Zipf-Mandelbrodt distributiondmand pmand qmand rmand
Metacommunity zero-sum multinomial distributiondmzsm pmzsm qmzsm rmzsm
Pareto distributiondpareto ppareto qpareto rpareto
Compound Poisson-gamma distributiondpoig ppoig qpoig rpoig
Poisson-lognormal distributiondpoilog ppoilog qpoilog rpoilog
Compound Poisson-Exponential distributiondpoix ppoix qpoix rpoix
Puyeo's Power-bend discrete distributiondpowbend ppowbend qpowbend rpowbend
Power discrete distributiondpower ppower qpower rpower
Left-truncation of density, probability and quantile of distributionsdtrunc ptrunc qtrunc rtrunc
Neutral Biodiversity Theory distribution by Volkov _et al._dvolkov pvolkov qvolkov rvolkov Svolkov
Zipf distributiondzipf pzipf qzipf rzipf
ML fitting of species rank-abundance distributionsfitgs fitmand fitrad fitrbs fitzipf
Class '"fitrad"' for maximum likelihood fitting of species rank-abundance distributionsfitrad-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 distributionsfitbs fitexp fitgamma fitgeom fitlnorm fitls fitmzsm fitnbinom fitpareto fitpoilog fitpowbend fitpower fitsad fitvolkov fitweibull
Class '"fitsad"' for maximum likelihood fitting of species abundance distributionsfitsad-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 classesfitexpC fitgammaC fitlnormC fitparetoC fitsadC fitweibullC
Class '"fitsadC"' for maximum likelihood fitting of species abundance distributions from data in abundance classesfitsadC-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 Grasslandsgrasslands
Compute table of information criteria and auxiliary infoAIC 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 fitslikelregions-class show,likelregions-method
Moths caught with light traps at Rothamsted 1933-1936moths
Class '"octav"' for frequencies in abundance octaveslines,octav-method octav-class plot,octav,ANY-method plot,octav-method points,octav-method
Frequencies of species in octavesoctav octav,fitrad-method octav,fitsad-method octav,numeric-method
Predicted frequencies of species in octavesoctavpred 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 Norwayokland
Log-likelihood profiles at original scalelikelregions likelregions,mle2-method likelregions,profile.mle2-method plotprofmle plotprofmle,mle2-method plotprofmle,profile.mle2-method
Percentile-percentile plots for species-abundance and rank-abundance modelspprad 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 Logseriespred.logser
Quantile-quantile plots for species-abundance and rank-abundance modelsqqrad 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 framerad
Class '"rad"' for rank-abundance datalines,rad-method plot,rad,ANY-method plot,rad-method points,rad-method rad-class
Predicted ranked abundance of speciesradpred 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 distributionrsad
Summary for fitsad/fitrad callsshow,summary.sads-method summary,fitrad-method summary,fitsad-method summary.sads-class
True likelihood for continuous variablestrueLL 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 profilingupdaterad updatesad