simulateGradientQuantile {paleoAM}R Documentation

Repeatedly Simulate Sampled Assemblages at some Gradient Value, and Return a Quantile Based on Recovered Gradient Values

Description

This function simulates assemblages at a single given gradient value, and returns a specified quantile on the recovered gradient values for the sake of defining an envelope around on recovered gradient values.

Usage

simulateGradientQuantile(
  quantileProbs = c(0.95),
  nSamplesSim,
  gradientValue,
  origAbundData,
  kdeRescaled,
  probSpeciesOccur,
  powerRootTransform = 1,
  specimensPerTimestep = 10000,
  nSpecimens
)

Arguments

quantileProbs

The quantile for which to return on the recovered gradient values from the simulated assemblages. (Technically multiple quantiles can be given, for which a value will be returned for each.

nSamplesSim

The number of samples to simulate.

gradientValue

The gradient value to simulate assemblages at.

origAbundData

The original matrix of abundance data, to be used to project the simulated data into the same detrended correspondence analysis (DCA) space.

kdeRescaled

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

probSpeciesOccur

The output from getProbOccViaPresAbs

powerRootTransform

The power-root transform to be used on the abundance data before applying the DCA. By default this is 1, which means the data is not transformed at all. Note that the power-root transform is only performed if useTransformedRelAbundance = TRUE.

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 most useful with applications like getRecoveredTransitionDuration which use envelope values to define features of a recovered sequence of gradient values for comparing simulated and empirical data.

Value

A value for each quantile specified in quantileProbs. May be multiple values if quantileProbs is a vector with more than one value.


[Package paleoAM version 1.0.1 Index]