Package: StratPal 0.3.0
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:
StratPal_0.3.0.tar.gz
StratPal_0.3.0.tar.gz(r-4.5-noble)StratPal_0.3.0.tar.gz(r-4.4-noble)
StratPal_0.3.0.tgz(r-4.4-emscripten)StratPal_0.3.0.tgz(r-4.3-emscripten)
StratPal.pdf |StratPal.html✨
StratPal/json (API)
NEWS
| # Install 'StratPal' in R: |
| install.packages('StratPal', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mindthegap-erc/stratpal/issues
- scenarioA - Example data, scenario A from Hohmann et al.
Last updated 4 days agofrom:760a97b73b. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 22 2024 |
| R-4.5-linux | OK | Nov 22 2024 |
Exports:apply_nicheapply_taphonomybounded_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 Nov 22 2024.Last update: 2024-10-05
Started: 2024-08-24
Documentation of defined S3 classes
Rendered fromStratPal_docs.Rmdusingknitr::rmarkdownon Nov 22 2024.Last update: 2024-10-05
Started: 2024-10-05
Introduction to the StratPal package
Rendered fromStratPal.Rmdusingknitr::rmarkdownon Nov 22 2024.Last update: 2024-10-05
Started: 2024-08-24
Stratigraphic Paleobiology for Event Data
Rendered fromevent_data.Rmdusingknitr::rmarkdownon Nov 22 2024.Last update: 2024-11-21
Started: 2024-08-24
Stratigraphic Paleobiology for Phenotypic Evolution
Rendered fromphenotypic_evolution.Rmdusingknitr::rmarkdownon Nov 22 2024.Last update: 2024-10-05
Started: 2024-08-24
Usage with the paleoTS package
Rendered frompaleoTS_functionality.Rmdusingknitr::rmarkdownon Nov 22 2024.Last update: 2024-11-21
Started: 2024-10-05
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| apply niche model | apply_niche |
| model taphonomic effects | apply_taphonomy |
| define niche from boundaries | bounded_niche |
| simulate ornstein-uhlenbeck (OU) process | ornstein_uhlenbeck |
| simulate ornstein-uhlenbeck (OU) process (specimen level) | ornstein_uhlenbeck_sl |
| simulate Poisson point process | p3 |
| simulate variable rate Poisson point process | p3_var_rate |
| plot pre-paleoTS objects | plot.pre_paleoTS |
| probabilistic removal of elements | prob_remove |
| simulate (un)biased random walk | random_walk |
| simulate (un)biased random walk (specimen level) | random_walk_sl |
| reduce pre-paleoTS format to paleoTS | reduce_to_paleoTS |
| random numbers from rejection sampling | rej_samp |
| example data, scenario A from Hohmann et al. (2024) | scenarioA |
| simple niche model | snd_niche |
| simulate phenotypic stasis | stasis |
| simulate phenotypic stasis (specimen level) | stasis_sl |
| simulate strict phenotypic stasis (specimen level) | strict_stasis_sl |
| thin a series of events (e.g. fossil occurrences) | thin |
