Simulating Assemblage Models of Abundance for the Fossil Record

[Up] [Top]

Documentation for package ‘paleoAM’ version 1.0.1

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