simMixedAssemblageSample {paleoAM}R Documentation

Simulate a Mixed Fossil Assemblage Composed of Communities at Different Gradient Values, and Sample the Lumped Assemblage

Description

This function simulate a mixed fossil assemblage by simulating a series of communities across a defined range of gradient values, lumps them into a single mixed assemblage, and then samples that assemblage as defined by the user.

Usage

simMixedAssemblageSample(
  kdeRescaled,
  probSpeciesOccur,
  gradientValues,
  specimensPerTimestep,
  nSpecimens
)

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.

nSpecimens

The number of specimens selected in each individual sample.

Details

This function is mainly written for simulating what artificial mixtures of assemblages at different gradient values would look like if sampled and assumed to be a single cohesive assemblage.

Value

A matrix containing the species abundances in the resulting mixed assemblage.


[Package paleoAM version 1.0.1 Index]