R: Maximum Likelihood Models for Species Abundance Distributions

# Maximum Likelihood Models for Species Abundance Distributions

## Documentation for package ‘sads’ version 0.6.5

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

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