getTimestepAbundances {paleoAM} | R Documentation |
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.
getTimestepAbundances(
kdeRescaled,
probSpeciesOccur,
gradientValues,
specimensPerTimestep
)
kdeRescaled |
The list of modeled KDEs for species abundance, output from |
probSpeciesOccur |
The output from |
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
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
.
A matrix containing abundances for species as a series of simulated assemblages.
This function is generally run before running sampleFossilSeries
.
Most users will likely never run either function, instead running simulateFossilAssemblageSeries
.