Package: StratPal 0.8.0

Emilia Jarochowska

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], Emilia Jarochowska [cre]

StratPal_0.8.0.tar.gz
StratPal_0.8.0.zip(r-4.7-any)StratPal_0.8.0.zip(r-4.6-any)StratPal_0.8.0.zip(r-4.5-any)
StratPal_0.8.0.tgz(r-4.6-any)StratPal_0.8.0.tgz(r-4.5-any)
StratPal_0.8.0.tar.gz(r-4.7-any)StratPal_0.8.0.tar.gz(r-4.6-any)
StratPal_0.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
StratPal/json (API)

# 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

6.17 score 2 stars 46 scripts 298 downloads 30 exports 12 dependencies

Last updated from:1394466470. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develNOTE135
source / vignettesOK194
linux-releaseNOTE119
macos-releaseNOTE114
macos-oldrelNOTE95
windows-develNOTE84
windows-releaseNOTE87
windows-oldrelNOTE92
wasm-releaseOK99

Exports:all_preservedapply_nicheapply_taphonomyas_char_matbounded_nichediscrete_gradientdiscrete_nichegap_filtergradient_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
Different forward models | Empirical age-depth models | Other ecological gradients and niche definitions | Different models of phenotypic evolution | Different models of event type data | Transforming data from the stratigraphic domain to the time domain | Taphonomy | Transform different types of data | References
Rendered fromadvanced_functionality.Rmdusingknitr::rmarkdown

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

Documentation of defined S3 classes
S3 class pre_paleoTS | Structure | Construction | Modification | Transformation into other S3 classes | Plotting | S3 class char_mat
Rendered fromStratPal_docs.Rmdusingknitr::rmarkdown

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

Example Stratigraphic Architecture
Introduction | Stratigraphic Context | Dataset structure | Simulation settings | Platform visualization | References
Rendered fromstratigraphic_architecture.Rmdusingknitr::rmarkdown

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

Introduction to the StratPal package
Overview | Installation | CRAN | GitHub | Dependencies | Example data | Piping | Motivation and usage | Advanced usage | Age-depth models | Defining age-depth models | Plotting | Extracting information | Transforming data | Getting started | References
Rendered fromStratPal.Rmdusingknitr::rmarkdown

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

Stratigraphic Paleobiology for Event Data
Introduction | Modeling fossil occurrences and first/last fossil occurrences | Age-depth models | Stratigraphic distortions of "event" type data | Fossil specimens | First/Last occurrences of common taxa | Range offset | Niche modeling | Taphonomic effects | Further reading | References
Rendered fromevent_data.Rmdusingknitr::rmarkdown

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

Integration with the FossilSim and paleotree packages
Integration with the FossilSim package | Stratigraphic basis | Trees with fossils | Ecological effects | Stratigraphic effects | Combined stratigraphic and ecological effects | Technical notes | Integration with paleotree | References
Rendered fromFossilSim_integration.Rmdusingknitr::rmarkdown

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

Stratigraphic Paleobiology for Phenotypic Evolution
Introduction | Modes of evolution in the time domain | Implemented modes of evolution | Visualization | Stratigraphic domain | Age-depth models | Stratigraphic expression of phenotypic evolution | Prescribing a sampling strategy | Further reading | References
Rendered fromphenotypic_evolution.Rmdusingknitr::rmarkdown

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

Usage with the paleoTS and evoTS package
Quick summary | Motivation | Modeling trait evolution on specimen level, complexity reduction, and plotting | Modeling of ecological, taphonomic, and stratigraphic effects | References
Rendered frompaleoTS_functionality.Rmdusingknitr::rmarkdown

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

Readme and manuals

Help Manual

Help pageTopics
Indestructible fossilsall_preserved
apply niche modelapply_niche
model taphonomic effectsapply_taphonomy
construct character matrixas_char_mat
define niche from boundariesbounded_niche
construct discretized gradientdiscrete_gradient
niche from discrete datadiscrete_niche
remove data associated with gapsgap_filter
gradient or taphonomic conditions from datagradient_from_data
validity of character matricesis_char_mat
last occurrence of taxonlast_occ
simulate ornstein-uhlenbeck (OU) processornstein_uhlenbeck
simulate ornstein-uhlenbeck (OU) process (specimen level)ornstein_uhlenbeck_sl
simulate Poisson point processp3
simulate variable rate Poisson point processp3_var_rate
perfect taphonomic conditionsperfect_preservation
plot pre-paleoTS objectsplot.pre_paleoTS
probabilistic removal of elementsprob_remove
simulate (un)biased random walkrandom_walk
simulate (un)biased random walk (specimen level)random_walk_sl
range offset of taxonrange_offset
reduce pre-paleoTS format to paleoTSreduce_to_paleoTS
random numbers from rejection samplingrej_samp
example data, emulates scenario A from Hohmann et al. (2024)scenarioA
simple niche modelsnd_niche
simulate phenotypic stasisstasis
simulate phenotypic stasis (specimen level)stasis_sl
generate basic stratigraphic filterstrat_filter
simulate strict phenotypic stasis (specimen level)strict_stasis_sl
thin a series of events (e.g. fossil occurrences)thin
model absence of environmental gradientstrivial_gradient
trivial niche modeltrivial_niche