Package: StratPal 0.7.1

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, phylogenetic trees), 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, biostratigraphy 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_0.7.1.tar.gz
StratPal_0.7.1.zip(r-4.7)StratPal_0.7.1.zip(r-4.6)StratPal_0.7.1.zip(r-4.5)
StratPal_0.7.1.tgz(r-4.6-any)StratPal_0.7.1.tgz(r-4.5-any)
StratPal_0.7.1.tar.gz(r-4.7-any)StratPal_0.7.1.tar.gz(r-4.6-any)
StratPal_0.7.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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/docs site:https://mindthegap-erc.github.io

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

On CRAN:

Conda:

palaeobiologypalaeontologypaleobiologypaleontologystratigraphic-paleobiologystratigraphy

6.05 score 2 stars 35 scripts 150 downloads 29 exports 12 dependencies

Last updated from:f18bef06db. Checks:8 OK, 1 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK127
source / vignettesOK181
linux-release-x86_64OK136
macos-release-arm64ERROR88
macos-oldrel-arm64OK85
windows-develOK83
windows-releaseOK77
windows-oldrelOK68
wasm-releaseOK103

Exports:all_preservedapply_nicheapply_taphonomyas_char_matbounded_nichediscrete_gradientdiscrete_nichegradient_from_datais_char_matlast_occornstein_uhlenbeckornstein_uhlenbeck_slp3p3_var_rateperfect_preservationprob_removerandom_walkrandom_walk_slrange_offsetreduce_to_paleoTSrej_sampsnd_nichestasisstasis_slstrat_filterstrict_stasis_slthintrivial_gradienttrivial_niche

Dependencies:admtoolsapecodetoolsdigestdoParallelforeachiteratorslatticemnormtnlmepaleoTSRcpp

Advanced Functionality and Writing Extensions

Rendered fromadvanced_functionality.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2025-12-04
Started: 2024-07-19

Documentation of defined S3 classes

Rendered fromStratPal_docs.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2025-12-04
Started: 2024-10-03

Example Stratigraphic Architecture

Rendered fromstratigraphic_architecture.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2025-12-04
Started: 2025-12-04

Integration with the FossilSim and paleotree packages

Rendered fromFossilSim_integration.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2025-08-27
Started: 2025-03-20

Introduction to the StratPal package

Rendered fromStratPal.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2025-12-04
Started: 2024-07-15

Stratigraphic Paleobiology for Event Data

Rendered fromevent_data.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2025-12-04
Started: 2024-07-19

Stratigraphic Paleobiology for Phenotypic Evolution

Rendered fromphenotypic_evolution.Rmdusingknitr::rmarkdownon May 28 2026.

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

Usage with the paleoTS and evoTS package

Rendered frompaleoTS_functionality.Rmdusingknitr::rmarkdownon May 28 2026.

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