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StratPal

INFRA · APIS
Velocity0.0

Stratigraphic Paleobiology Modeling Pipelines

github.com/mindthegap-erc/stratpal ↗

Building the pipeline that carries simulated evolution into stratigraphic position

paleobiologystratigraphysimulationfossilsiminteroperability
◆Current state
StratPal provides pipelines for stratigraphic paleobiology: simulate trait evolution or event data at specimen level, apply niche and taphonomic effects, then push the result through an age-depth model into stratigraphic position. The pre_paleoTS S3 class introduced in 0.2.0 is the interchange format the design rests on, with reduce_to_paleoTS() connecting it to the paleoTS package for downstream fitting. The two most recent releases extend the pipeline outward: FossilSim integration in 0.4.0, and in 0.6.0 the last_occ and range_offset wrappers that express biostratigraphic precision as a function of taphonomy, ecology, abundance and stratigraphy.
◆Where it's heading
This package develops in lockstep with admtools, its sibling from the same group — admtools 0.4.0 added pre_paleoTS transformations fifty-seven minutes before StratPal 0.2.0 shipped the class itself, and both picked up FossilSim integration in spring 2025. The direction is consistently outward: rather than adding simulation models, StratPal adds adapters so its output can feed established paleontology packages and be fed by them. Releases are small and frequent, and each names a specific connection or wrapper.
◆Prediction
Expect the next release to add another adapter or convenience wrapper rather than a new simulation model, following the paleoTS and FossilSim pattern, with the matching change in admtools landing within weeks either side.

◆Recent moves

  1. 11mo ago

    Wrappers for last occurrences and biostratigraphic precision

    Adds last_occ and range_offset to determine the position and timing of last occurrences and to express biostratigraphic precision in terms of taphonomy, ecology, abundance and stratigraphy. It turns what the pipeline could already compute into two direct answers to questions paleontologists actually ask.

    View source ↗
  2. 1y ago

    FossilSim integration and discrete-category niche utilities

    Connects the pipeline to FossilSim and adds utilities for niches defined by discrete categories rather than continuous gradients. The FossilSim link arrived here a month before the matching transformation support in sibling package admtools.

    View source ↗
  3. 1y ago

    Citation and vignette update after manuscript publication

    Updates citation information and vignettes now that the accompanying manuscript is published. No code change, but it marks the point where the package became citable in its own right.

    View source ↗
  4. 1y ago

    Fixes for apply_niche, apply_taphonomy and pre_paleoTS plotting

    Bug fixes in the two effect functions for the pre_paleoTS format, plus repaired plotting for that class. Consolidation of the class introduced two releases earlier.

    View source ↗
  5. 1y ago

    pre_paleoTS class links specimen-level simulation to paleoTS

    Introduces the pre_paleoTS S3 class with specimen-level trait evolution simulation, and reduce_to_paleoTS() to hand results to the paleoTS package. This is the structural decision the rest of the package and its sibling admtools have been built around.

    View source ↗
  6. 2y ago

    First release: phenotypic evolution, niche models and taphonomy

    The initial release, carrying models of phenotypic evolution and event-type data, simple niche and taphonomy models, example data from the group's own 2024 paper, and workflow vignettes. The pipeline framing was present from the start.

    View source ↗