getTimestepAbundances {paleoAM}R Documentation

Simulate Fossil Assemblages with Abundances at each Time-Step

Description

Given a set of KDEs fit to species abundance and models of species occurrence relative to an environmental gradient, and given a sequence of gradient values, and a number of specimens to sample at each time-step, obtains a matrix containing abundances for species as a series of simulated assemblages.

Usage

getTimestepAbundances(
  kdeRescaled,
  probSpeciesOccur,
  gradientValues,
  specimensPerTimestep
)

Arguments

kdeRescaled

The list of modeled KDEs for species abundance, output from getSpeciesSpecificRescaledKDE.

probSpeciesOccur

The output from getProbOccViaPresAbs

gradientValues

A vector of gradient values to simulate over. A separate 'true' assemblage / community will be simulated for each value in the respective vector.

specimensPerTimestep

The number of specimens returned in a given time-step by getTimestepAbundances, usually set to an unrealistically high number to represent the true 'unsampled' fossil assemblage.

Details

getTimestepAbundances represents simulating the original biotic community that was present at some given point in time, which is not the same thing as a fossil assemblage that might be collected from sediments today as finite samples. That is covered by feeding the output from this function to sampleFossilSeries.

Thus, this function is generally run before running sampleFossilSeries, however most users will likely never run either function, instead running simulateFossilAssemblageSeries.

Value

A matrix containing abundances for species as a series of simulated assemblages.

See Also

This function is generally run before running sampleFossilSeries. Most users will likely never run either function, instead running simulateFossilAssemblageSeries.


[Package paleoAM version 1.0.1 Index]