getProbOccViaPresAbs {paleoAM}R Documentation

Estimate the Per-Species Probability of Occurrence as a Function of an Environmental Gradient from Presence-Absence Data

Description

This function calculates how species presence (not abundance) varies as a function of an underlying environmental gradient, using only the pattern of presence-absence observed in a given data set (usually data on species abundance).

Usage

getProbOccViaPresAbs(
  origAbundData,
  gradientOrigDCA,
  occurrenceFloor = 0,
  nBreaksGradientHist = 20
)

Arguments

origAbundData

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

gradientOrigDCA

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

occurrenceFloor

The minimum occurrence for every species, in every bin. The default is zero – increasing this value means every species has a non-zero chance of occurring in every bin, which tends to result in wildly more diverse assemblages than what is observed in the fossil record, so use with caution.

nBreaksGradientHist

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

Details

The rationale for this function was that simulating assemblages using the KDEs of species abundance alone (calculated with getSpeciesSpecificRescaledKDE tended to create very diversity-high assemblages that did not reflect reality. Accounting for species presence at all using separate models brings simulated assemblages much closer to real assemblages.

Value

An approximate function, created with approx that describes the relationship between gradient and probability of occurrence for all species.

See Also

getSpeciesSpecificRescaledKDE

Examples


# load data
data(gulfOfAlaska)

alaskaProbOccur <- getProbOccViaPresAbs(
   gradientOrigDCA = DCA1_GOA, 
   origAbundData = abundData_GOA
   )


[Package paleoAM version 1.0.1 Index]