SpeciesDistributions: Species Distribution

In EricMarcon/SpatDiv: Spatially Explicit Measures of Diversity

Species Distribution

Description

A Species Distribution is a (preferably named) vector containing species abundances or probabilities. SpeciesDistribution objects include AbdVector and ProbaVector objects.

Usage

## S3 method for class 'wmppp'
as.SpeciesDistribution(x, ...)

## S3 method for class 'factor'
as.SpeciesDistribution(x, ...)

## S3 method for class 'character'
as.SpeciesDistribution(x, ...)

## S3 method for class 'wmppp'
as.ProbaVector(x, ...)

## S3 method for class 'factor'
as.ProbaVector(x, ...)

## S3 method for class 'character'
as.ProbaVector(x, ...)

## S3 method for class 'wmppp'
as.AbdVector(x, ...)

## S3 method for class 'factor'
as.AbdVector(x, ...)

## S3 method for class 'character'
as.AbdVector(x, ...)

Arguments

x	A wmppp.object with PointType values as species names, or a vector of factors or characters containing species names of each individual.
...	Further arguments. Unsused.

Details

as.AbdVector counts the number of individuals (points) per species (in marks$PointType).

as.ProbaVector normalizes the vector so that it sums to 1. If Correction is not "None", the observed abundance distribution is used to estimate the actual species distribution. The list of species will be changed: zero-abundance species will be cleared, and some unobserved species will be added. First, observed species probabilities are estimated folllowing \insertCiteChao2003;textualSpatDiv, i.e. input probabilities are multiplied by the sample coverage, or according to more sophisticated models: \insertCiteChao2013;textualSpatDiv, single-parameter model or \insertCiteChao2015;textualSpatDiv, two-parameter model. The total probability of observed species equals the sample coverage. Then, the distribution of unobserved species can be unveiled: their number is estimated according to RCorrection (if the Jackknife estimator is chosen, the JackOver argument allows using the order immediately over the optimal one). The coverage deficit (1 minus the sample coverage) is shared by the unobserved species equally: Unveiling = "unif", \insertCiteChao2013;textualSpatDiv or according to a geometric distribution: Unveiling = "geom", \insertCiteChao2015;textualSpatDiv.

SpeciesDistribution objects can be plotted. The plot method returns the estimated parameters of the fitted distribution. The broken stick has no parameter, so the maximum abundance is returned.

Value

A vector of species abundances (AbdVector) or probabilities (ProbaVector).

References

\insertAllCited

EricMarcon/SpatDiv documentation built on May 25, 2023, 12:54 p.m.