Package: paleoAM 1.0.1

paleoAM: Simulating Assemblage Models of Abundance for the Fossil Record

Provides functions for fitting abundance distributions over environmental gradients to the species in ecological communities, and tools for simulating the fossil assemblages from those abundance models for such communities, as well as simulating assemblages across various patterns of sedimentary history and sampling. These tools are for particular use with fossil records with detailed age models and abundance distributions used for calculating environmental gradients from ordinations or other indices based on fossil assemblages.

Authors:David W Bapst [aut, cre], Christina L Belanger [aut]

paleoAM_1.0.1.tar.gz
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paleoAM_1.0.1.tgz(r-4.4-any)paleoAM_1.0.1.tgz(r-4.3-any)
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paleoAM.pdf |paleoAM.html✨
paleoAM/json (API)

# Install 'paleoAM' in R:
install.packages('paleoAM', repos = c('https://dwbapst.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/dwbapst/paleoam/issues

Datasets:
  • DCA1_GOA - Benthic Foram Abundances from the Gulf of Alaska Reported by Sharon et al 2021
  • abundData_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
  • graptCommData - Katian-Hirnantian Graptolite Assemblages Reported by Sheets et al.
  • graptSampleInfo - Katian-Hirnantian Graptolite Assemblages Reported by Sheets et al.

On CRAN:

4.38 score 4 stars 1 scripts 402 downloads 14 exports 8 dependencies

Last updated 1 months agofrom:c65529ee5d. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 09 2024
R-4.5-winOKNov 09 2024
R-4.5-linuxOKNov 09 2024
R-4.4-winOKNov 09 2024
R-4.4-macOKNov 09 2024
R-4.3-winOKNov 09 2024
R-4.3-macOKNov 09 2024

Exports:calculateImplicitParametersgetProbOccViaPresAbsgetRecoveredTransitionDurationgetSampleDCAgetSpeciesSpecificRescaledKDEgetTimestepAbundancesplotFossilAssemblageSeriesDCAplotGradientKDEplotHeatmapComparisonsampleFossilSeriessetupSimulatedGradientChangesimMixedAssemblageSamplesimulateFossilAssemblageSeriessimulateGradientQuantile

Dependencies:clusterlatticeMASSMatrixmgcvnlmepermutevegan

Readme and manuals

Help Manual

Help pageTopics
Calculate Implicit Parameters for Modeling Time-Series of Fossil AssemblagescalculateImplicitParameters
Estimate the Per-Species Probability of Occurrence as a Function of an Environmental Gradient from Presence-Absence DatagetProbOccViaPresAbs
Measure the Duration of a Transition Period from Recovered Sequence of Fossil Assemblages with DCA-1 ScoresgetRecoveredTransitionDuration
Get the Detrended correspondence Analysis (DCA) Score Value for A Single SamplegetSampleDCA
This is a function for Fitting a KDE to a specific species in Community Ecology DatagetSpeciesSpecificRescaledKDE
Simulate Fossil Assemblages with Abundances at each Time-StepgetTimestepAbundances
Benthic Foram Abundances from the Gulf of Alaska Reported by Sharon et al 2021abundData_GOA DCA1_GOA fullDataTable_GOA gulfOfAlaska
Katian-Hirnantian Graptolite Assemblages Reported by Sheets et al. (2016)graptCommData graptSampleInfo hirnantian
Plot the Recovered DCA Values of a Fossil Assemblage SeriesplotFossilAssemblageSeriesDCA
Plot Kernel Density Estimates of Species Abundance Across a Focal GradientplotGradientKDE
Plots a Heatmap ComparisonplotHeatmapComparison
Sample Fossil Assemblage SeriessampleFossilSeries
Create a Stochastic Time-Series of Gradient Change For Use in Simulating Assemblage ChangesetupSimulatedGradientChange
Simulate a Mixed Fossil Assemblage Composed of Communities at Different Gradient Values, and Sample the Lumped AssemblagesimMixedAssemblageSample
Simulate Time-Series of Successive Fossil AssemblagessimulateFossilAssemblageSeries
Repeatedly Simulate Sampled Assemblages at some Gradient Value, and Return a Quantile Based on Recovered Gradient ValuessimulateGradientQuantile