Package: StratPal 0.1.1.9000
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_0.1.1.9000.tar.gz
StratPal_0.1.1.9000.zip(r-4.5)StratPal_0.1.1.9000.zip(r-4.4)StratPal_0.1.1.9000.zip(r-4.3)
StratPal_0.1.1.9000.tgz(r-4.4-any)StratPal_0.1.1.9000.tgz(r-4.3-any)
StratPal_0.1.1.9000.tar.gz(r-4.5-noble)StratPal_0.1.1.9000.tar.gz(r-4.4-noble)
StratPal_0.1.1.9000.tgz(r-4.4-emscripten)StratPal_0.1.1.9000.tgz(r-4.3-emscripten)
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
- scenarioA - Example data, scenario A from Hohmann et al.
palaeobiologypalaeontologypaleobiologypaleontologystratigraphic-paleobiologystratigraphy
Last updated 5 days agofrom:c6a44cc6ef. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Sep 13 2024 |
R-4.5-win | OK | Sep 13 2024 |
R-4.5-linux | OK | Sep 13 2024 |
R-4.4-win | OK | Sep 13 2024 |
R-4.4-mac | OK | Sep 13 2024 |
R-4.3-win | OK | Sep 13 2024 |
R-4.3-mac | OK | Sep 13 2024 |
Exports:apply_nicheapply_taphonomybounded_nicheornstein_uhlenbeckp3p3_var_raterandom_walkrej_sampsnd_nichestasisthin
Advanced Functionality and Writing Extensions
Rendered fromadvanced_functionality.Rmd
usingknitr::rmarkdown
on Sep 13 2024.Last update: 2024-08-26
Started: 2024-07-19
Intoduction to the StratPal package
Rendered fromStratPal.Rmd
usingknitr::rmarkdown
on Sep 13 2024.Last update: 2024-08-26
Started: 2024-07-15
Stratigraphic Paleobiology for Event Data
Rendered fromevent_data.Rmd
usingknitr::rmarkdown
on Sep 13 2024.Last update: 2024-08-26
Started: 2024-07-19
Stratigraphic Paleobiology for Phenotypic Evolution
Rendered fromphenotypic_evolution.Rmd
usingknitr::rmarkdown
on Sep 13 2024.Last update: 2024-08-26
Started: 2024-07-19
Readme and manuals
Help Manual
Help page | Topics |
---|---|
apply niche model to events | apply_niche |
model taphonomic effects | apply_taphonomy |
define niche from boundaries | bounded_niche |
simulate ornstein-uhlenbeck (OU) process | ornstein_uhlenbeck |
simulate Poisson point process | p3 |
simulate variable rate Poisson point process | p3_var_rate |
continuous time random walk | random_walk |
rejection sampling | rej_samp |
example data, scenario A from Hohmann et al. (2024) | scenarioA |
simple niche model | snd_niche |
simulate phenotypic stasis | stasis |
thin a series of events (e.g. fossil occurrences) | thin |