R: Simulating Assemblage Models of Abundance for the Fossil Record

# Simulating Assemblage Models of Abundance for the Fossil Record

## Documentation for package ‘paleoAM’ version 1.0.1

- DESCRIPTION file
- Package README

## Help Pages

abundData_GOA | Benthic Foram Abundances from the Gulf of Alaska Reported by Sharon et al 2021
calculateImplicitParameters | Calculate Implicit Parameters for Modeling Time-Series of Fossil Assemblages
DCA1_GOA | Benthic Foram Abundances from the Gulf of Alaska Reported by Sharon et al 2021
fullDataTable_GOA | Benthic Foram Abundances from the Gulf of Alaska Reported by Sharon et al 2021
getProbOccViaPresAbs | Estimate the Per-Species Probability of Occurrence as a Function of an Environmental Gradient from Presence-Absence Data
getRecoveredTransitionDuration | Measure the Duration of a Transition Period from Recovered Sequence of Fossil Assemblages with DCA-1 Scores
getSampleDCA | Get the Detrended correspondence Analysis (DCA) Score Value for A Single Sample
getSpeciesSpecificRescaledKDE | This is a function for Fitting a KDE to a specific species in Community Ecology Data
getTimestepAbundances | Simulate Fossil Assemblages with Abundances at each Time-Step
graptCommData | Katian-Hirnantian Graptolite Assemblages Reported by Sheets et al. (2016)
graptSampleInfo | Katian-Hirnantian Graptolite Assemblages Reported by Sheets et al. (2016)
gulfOfAlaska | Benthic Foram Abundances from the Gulf of Alaska Reported by Sharon et al 2021
hirnantian | Katian-Hirnantian Graptolite Assemblages Reported by Sheets et al. (2016)
plotFossilAssemblageSeriesDCA | Plot the Recovered DCA Values of a Fossil Assemblage Series
plotGradientKDE | Plot Kernel Density Estimates of Species Abundance Across a Focal Gradient
plotHeatmapComparison | Plots a Heatmap Comparison
sampleFossilSeries | Sample Fossil Assemblage Series
setupSimulatedGradientChange | Create a Stochastic Time-Series of Gradient Change For Use in Simulating Assemblage Change
simMixedAssemblageSample | Simulate a Mixed Fossil Assemblage Composed of Communities at Different Gradient Values, and Sample the Lumped Assemblage
simulateFossilAssemblageSeries | Simulate Time-Series of Successive Fossil Assemblages
simulateGradientQuantile | Repeatedly Simulate Sampled Assemblages at some Gradient Value, and Return a Quantile Based on Recovered Gradient Values