Maximum Likelihood Models for Species Abundance Distributions

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Documentation for package ‘sads’ version 0.6.3

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A B C D F G L M N O P Q R S T U

sads-package Maximum Likelihood Models for Species Abundance Distributions

-- A --

AIC Compute table of information criteria and auxiliary info
AIC-method Compute table of information criteria and auxiliary info
AIC-methods Compute table of information criteria and auxiliary info
AICc Compute table of information criteria and auxiliary info
AICc-method Compute table of information criteria and auxiliary info
AICc-methods Compute table of information criteria and auxiliary info
ARN82.eB.apr77 Biomass of marine animals in colonizing experiments in Baltic Sea

-- B --

bci Tree species abundance in Barro Colorado Island Plot
birds Abundances of breeding birds in Quacker Run Valley, NY

-- C --

coefficients-method Standard stats methods
coverpred ~~ Methods for Function 'coverpred' in Package 'sads' ~~
coverpred-class Class '"coverpred"' for predicted values for abundance classes
coverpred-method ~~ Methods for Function 'coverpred' in Package 'sads' ~~
coverpred-methods ~~ Methods for Function 'coverpred' in Package 'sads' ~~

-- D --

dbs MacArthur's Broken-stick distribution
dgs Geometric series distribution
distr Continuous or discrete distributions
dls Fisher's Log-series distribution
dmand 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
drbs MacArthur's Broken-stick distribution
dtrunc Left-truncation of density, probability and quantile of distributions
dvolkov Neutral Biodiversity Theory distribution by Volkov _et al._
dzipf Zipf distribution

-- F --

fitbs ML fitting of species abundance distributions
fitexp ML fitting of species abundance distributions
fitexpC ML fitting of species abundance distributions to data pooled in abundance classes
fitgamma ML fitting of species abundance distributions
fitgammaC ML fitting of species abundance distributions to data pooled in abundance classes
fitgeom ML fitting of species abundance distributions
fitgs ML fitting of species rank-abundance distributions
fitlnorm ML fitting of species abundance distributions
fitlnormC ML fitting of species abundance distributions to data pooled in abundance classes
fitls ML fitting of species abundance distributions
fitmand ML fitting of species rank-abundance distributions
fitmzsm ML fitting of species abundance distributions
fitnbinom ML fitting of species abundance distributions
fitpareto ML fitting of species abundance distributions
fitparetoC ML fitting of species abundance distributions to data pooled in abundance classes
fitpoilog ML fitting of species abundance distributions
fitpowbend ML fitting of species abundance distributions
fitpower ML fitting of species abundance distributions
fitrad ML fitting of species rank-abundance distributions
fitrad-class Class '"fitrad"' for maximum likelihood fitting of species rank-abundance distributions
fitrbs ML fitting of species rank-abundance distributions
fitsad ML fitting of species abundance distributions
fitsad-class Class '"fitsad"' for maximum likelihood fitting of species abundance distributions
fitsadC ML fitting of species abundance distributions to data pooled in abundance classes
fitsadC-class Class '"fitsadC"' for maximum likelihood fitting of species abundance distributions from data in abundance classes
fitted-method Standard stats methods
fitted.values-method Standard stats methods
fitvolkov ML fitting of species abundance distributions
fitweibull ML fitting of species abundance distributions
fitweibullC ML fitting of species abundance distributions to data pooled in abundance classes
fitzipf ML fitting of species rank-abundance distributions

-- G --

grasslands Coverages of plants species in a plot in Southern Brazilian Grasslands

-- L --

likelregions Log-likelihood profiles at original scale
likelregions-class Class '"likelregions"' for likelihood profiles of maximum likelihood fits
likelregions-method Log-likelihood profiles at original scale
lines-method Class '"octav"' for frequencies in abundance octaves
lines-method Class '"rad"' for rank-abundance data

-- M --

moths Moths caught with light traps at Rothamsted 1933-1936

-- N --

nobs Compute table of information criteria and auxiliary info
nobs-method Compute table of information criteria and auxiliary info
nobs-method Class '"fitsadC"' for maximum likelihood fitting of species abundance distributions from data in abundance classes
nobs-methods Compute table of information criteria and auxiliary info

-- O --

octav Frequencies of species in octaves
octav-class Class '"octav"' for frequencies in abundance octaves
octav-method Frequencies of species in octaves
octavpred Predicted frequencies of species in octaves
octavpred-method Predicted frequencies of species in octaves
okland Abundances of land snail species in Norway

-- P --

pbs MacArthur's Broken-stick distribution
pgs Geometric series distribution
plot-method Class '"fitrad"' for maximum likelihood fitting of species rank-abundance distributions
plot-method Class '"fitsad"' for maximum likelihood fitting of species abundance distributions
plot-method Class '"fitsadC"' for maximum likelihood fitting of species abundance distributions from data in abundance classes
plot-method Class '"octav"' for frequencies in abundance octaves
plot-method Class '"rad"' for rank-abundance data
plotprofmle Log-likelihood profiles at original scale
plotprofmle-method Log-likelihood profiles at original scale
pls Fisher's Log-series distribution
pmand Zipf-Mandelbrodt distribution
pmzsm Metacommunity zero-sum multinomial distribution
points-method Class '"coverpred"' for predicted values for abundance classes
points-method Class '"octav"' for frequencies in abundance octaves
points-method Class '"rad"' for rank-abundance data
ppareto Pareto distribution
ppoig Compound Poisson-gamma distribution
ppoilog Poisson-lognormal distribution
ppoix Compound Poisson-Exponential distribution
ppowbend Puyeo's Power-bend discrete distribution
ppower Power discrete distribution
pprad Percentile-percentile plots for species-abundance and rank-abundance models
pprad-method Class '"fitrad"' for maximum likelihood fitting of species rank-abundance distributions
pprad-method Percentile-percentile plots for species-abundance and rank-abundance models
ppsad Percentile-percentile plots for species-abundance and rank-abundance models
ppsad-method Class '"fitsad"' for maximum likelihood fitting of species abundance distributions
ppsad-method Class '"fitsadC"' for maximum likelihood fitting of species abundance distributions from data in abundance classes
ppsad-method Percentile-percentile plots for species-abundance and rank-abundance models
prbs MacArthur's Broken-stick distribution
pred.logser Predicted number of species by Fisher's Logseries
ptrunc Left-truncation of density, probability and quantile of distributions
pvolkov Neutral Biodiversity Theory distribution by Volkov _et al._
pzipf Zipf distribution

-- Q --

qbs MacArthur's Broken-stick distribution
qgs Geometric series distribution
qls Fisher's Log-series distribution
qmand Zipf-Mandelbrodt distribution
qmzsm Metacommunity zero-sum multinomial distribution
qpareto Pareto distribution
qpoig Compound Poisson-gamma distribution
qpoilog Poisson-lognormal distribution
qpoix Compound Poisson-Exponential distribution
qpowbend Puyeo's Power-bend discrete distribution
qpower Power discrete distribution
qqrad Quantile-quantile plots for species-abundance and rank-abundance models
qqrad-method Class '"fitrad"' for maximum likelihood fitting of species rank-abundance distributions
qqrad-method Quantile-quantile plots for species-abundance and rank-abundance models
qqsad Quantile-quantile plots for species-abundance and rank-abundance models
qqsad-method Class '"fitsad"' for maximum likelihood fitting of species abundance distributions
qqsad-method Class '"fitsadC"' for maximum likelihood fitting of species abundance distributions from data in abundance classes
qqsad-method Quantile-quantile plots for species-abundance and rank-abundance models
qrbs MacArthur's Broken-stick distribution
qtrunc Left-truncation of density, probability and quantile of distributions
qvolkov Neutral Biodiversity Theory distribution by Volkov _et al._
qzipf Zipf distribution

-- R --

rad Rank-abundance data frame
rad-class Class '"rad"' for rank-abundance data
radpred Predicted ranked abundance of species
radpred-method Predicted ranked abundance of species
rbs MacArthur's Broken-stick distribution
residuals-method Standard stats methods
rgs Geometric series distribution
rls Fisher's Log-series distribution
rmand Zipf-Mandelbrodt distribution
rmzsm Metacommunity zero-sum multinomial distribution
rpareto Pareto distribution
rpoig Compound Poisson-gamma distribution
rpoilog Poisson-lognormal distribution
rpoix Compound Poisson-Exponential distribution
rpowbend Puyeo's Power-bend discrete distribution
rpower Power discrete distribution
rrbs MacArthur's Broken-stick distribution
rsad Sampling from a species abundance distribution
rtrunc Left-truncation of density, probability and quantile of distributions
rvolkov Neutral Biodiversity Theory distribution by Volkov _et al._
rzipf Zipf distribution

-- S --

sads Maximum Likelihood Models for Species Abundance Distributions
show-method Class '"fitrad"' for maximum likelihood fitting of species rank-abundance distributions
show-method Class '"fitsad"' for maximum likelihood fitting of species abundance distributions
show-method Class '"fitsadC"' for maximum likelihood fitting of species abundance distributions from data in abundance classes
show-method Class '"likelregions"' for likelihood profiles of maximum likelihood fits
show-method Summary for fitsad/fitrad calls
summary-method Summary for fitsad/fitrad calls
summary.sads-class Summary for fitsad/fitrad calls
Svolkov Neutral Biodiversity Theory distribution by Volkov _et al._

-- T --

trueLL True likelihood for continuous variables
trueLL-method True likelihood for continuous variables
trueLL-methods True likelihood for continuous variables

-- U --

updaterad Updating of MLE fits by profiling
updatesad Updating of MLE fits by profiling