getSpeciesSpecificRescaledKDE {paleoAM}R Documentation

This is a function for Fitting a KDE to a specific species in Community Ecology Data

Description

This function fits a KDE to the abundance data of a particular species from community data given some ecological gradient variable.

Usage

getSpeciesSpecificRescaledKDE(
  gradientOrigDCA,
  origAbundData,
  abundanceFloorRatio = 0.5,
  nBreaksGradientHist = 20,
  modeledSiteAbundance = 10000
)

Arguments

gradientOrigDCA

The environmental gradient along which abundance varies, which you are fitting a KDE to.

origAbundData

The abundance data of the data you wish to model the abundance of.

abundanceFloorRatio

The minimum value for the abundance in a given interval along the gradient – a probably arbitration value that is set to 0.5 by default.

nBreaksGradientHist

The default is 20. Twenty what they asked? Twenty something.

modeledSiteAbundance

The number of abundances the relative abundances will by multiplied by to formulate the KDE. The default is 10000.

Details

In many ways, this is an attempt to measure empirical representations of the abundance response curves relative to environmental gradients, as portrayed in figure within Patzkowsky & Holland (2012).

The ecological gradient variable is often an environmental gradient, such as depth, oxygenation, altitude, precipitation, but this is not necessarily so.

Value

A list containing the KDEs describing change in abundance for each species across the specified gradient.

References

Patzkowsky, M.E. and Holland, S.M., 2012. Stratigraphic Paleobiology: Understanding the Distribution of Fossil Taxa in Time and Space. University of Chicago Press. 259 pages.

See Also

getProbOccViaPresAbs, plotGradientKDE

Examples


# load data
data(gulfOfAlaska)

alaskaKDEs <- getSpeciesSpecificRescaledKDE(
    gradientOrigDCA = DCA1_GOA, 
    origAbundData = abundData_GOA, 
    abundanceFloorRatio = 0.5, 
    nBreaksGradientHist = 20, 
    modeledSiteAbundance = 10000
    )
    
plotGradientKDE(
    speciesKDEs = alaskaKDEs,
    fullGradientRange = c(min(DCA1_GOA), max(DCA1_GOA))
    )


[Package paleoAM version 1.0.1 Index]