Package: StratPal 0.4.0.9000

Niklas Hohmann

StratPal: Stratigraphic Paleobiology Modeling Pipelines

The fossil record is a joint expression of ecological, taphonomic, evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012, ISBN:978-0226649382). This package allowing to simulate biological processes in the time domain (e.g., trait evolution, fossil abundance), and examine how their expression in the rock record (stratigraphic domain) is influenced based on age-depth models, ecological niche models, and taphonomic effects. Functions simulating common processes used in modeling trait evolution or event type data such as first/last occurrences are provided and can be used standalone or as part of a pipeline. The package comes with example data sets and tutorials in several vignettes, which can be used as a template to set up one's own simulation.

Authors:Niklas Hohmann [aut, cre]

StratPal_0.4.0.9000.tar.gz
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StratPal.pdf |StratPal.html✨
StratPal/json (API)
NEWS

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

Bug tracker:https://github.com/mindthegap-erc/stratpal/issues

Pkgdown site:https://mindthegap-erc.github.io

Datasets:
  • scenarioA - Example data, scenario A from Hohmann et al.

On CRAN:

Conda:

palaeobiologypalaeontologypaleobiologypaleontologystratigraphic-paleobiologystratigraphy

6.00 score 1 stars 18 scripts 222 downloads 19 exports 12 dependencies

Last updated 4 days agofrom:394160056a. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 28 2025
R-4.5-winOKMar 28 2025
R-4.5-macOKMar 28 2025
R-4.5-linuxOKMar 28 2025
R-4.4-winOKMar 28 2025
R-4.4-macOKMar 28 2025
R-4.4-linuxOKMar 28 2025
R-4.3-winOKMar 28 2025
R-4.3-macOKMar 28 2025

Exports:apply_nicheapply_taphonomybounded_nichediscrete_gradientdiscrete_nicheornstein_uhlenbeckornstein_uhlenbeck_slp3p3_var_rateprob_removerandom_walkrandom_walk_slreduce_to_paleoTSrej_sampsnd_nichestasisstasis_slstrict_stasis_slthin

Dependencies:admtoolsapecodetoolsdigestdoParallelforeachiteratorslatticemnormtnlmepaleoTSRcpp

Advanced Functionality and Writing Extensions

Rendered fromadvanced_functionality.Rmdusingknitr::rmarkdownon Mar 28 2025.

Last update: 2025-03-27
Started: 2024-07-19

Documentation of defined S3 classes

Rendered fromStratPal_docs.Rmdusingknitr::rmarkdownon Mar 28 2025.

Last update: 2024-10-04
Started: 2024-10-03

Integration with the FossilSim and paleotree packages

Rendered fromFossilSim_integration.Rmdusingknitr::rmarkdownon Mar 28 2025.

Last update: 2025-03-20
Started: 2025-03-20

Introduction to the StratPal package

Rendered fromStratPal.Rmdusingknitr::rmarkdownon Mar 28 2025.

Last update: 2025-03-20
Started: 2024-07-15

Stratigraphic Paleobiology for Event Data

Rendered fromevent_data.Rmdusingknitr::rmarkdownon Mar 28 2025.

Last update: 2025-03-27
Started: 2024-07-19

Stratigraphic Paleobiology for Phenotypic Evolution

Rendered fromphenotypic_evolution.Rmdusingknitr::rmarkdownon Mar 28 2025.

Last update: 2025-01-14
Started: 2024-07-19

Usage with the paleoTS and evoTS package

Rendered frompaleoTS_functionality.Rmdusingknitr::rmarkdownon Mar 28 2025.

Last update: 2025-01-14
Started: 2024-10-03