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:
sads_0.6.3.tar.gz
sads_0.6.3.zip(r-4.5)sads_0.6.3.zip(r-4.4)sads_0.6.3.zip(r-4.3)
sads_0.6.3.tgz(r-4.4-x86_64)sads_0.6.3.tgz(r-4.4-arm64)sads_0.6.3.tgz(r-4.3-x86_64)sads_0.6.3.tgz(r-4.3-arm64)
sads_0.6.3.tar.gz(r-4.5-noble)sads_0.6.3.tar.gz(r-4.4-noble)
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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')) |
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
Last updated 8 months agofrom:df7ec19747. Checks:OK: 7 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 13 2024 |
| R-4.5-win-x86_64 | NOTE | Sep 13 2024 |
| R-4.5-linux-x86_64 | NOTE | Sep 13 2024 |
| R-4.4-win-x86_64 | OK | Sep 13 2024 |
| R-4.4-mac-x86_64 | OK | Sep 13 2024 |
| R-4.4-mac-aarch64 | OK | Sep 13 2024 |
| R-4.3-win-x86_64 | OK | Sep 13 2024 |
| R-4.3-mac-x86_64 | OK | Sep 13 2024 |
| R-4.3-mac-aarch64 | OK | Sep 13 2024 |
Exports:AICAICccoefficientscoverpreddbsdgsdistrdlsdmanddmzsmdparetodpoigdpoilogdpoixdpowbenddpowerdrbsdtruncdvolkovdzipffitbsfitexpfitexpCfitgammafitgammaCfitgeomfitgsfitlnormfitlnormCfitlsfitmandfitmzsmfitnbinomfitparetofitparetoCfitpoilogfitpowbendfitpowerfitradfitrbsfitsadfitsadCfittedfitted.valuesfitvolkovfitweibullfitweibullCfitzipflikelregionslinesnobsoctavoctavpredpbspgsplotplotprofmleplspmandpmzsmpointspparetoppoigppoilogppoixppowbendppowerppradppsadprbspred.logserptruncpvolkovpzipfqbsqgsqlsqmandqmzsmqparetoqpoigqpoilogqpoixqpowbendqpowerqqradqqsadqrbsqtruncqvolkovqzipfradradpredrbsresidualsrgsrlsrmandrmzsmrparetorpoigrpoilogrpoixrpowbendrpowerrrbsrsadrtruncrvolkovrzipfshowsummarySvolkovtrueLLupdateradupdatesad
Dependencies:bbmlebdsmatrixGUILDSlatticeMASSMatrixmvtnormnloptrnumDerivpoilogpoweRlawpracmaRcppVGAM
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 |
