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fossilsim

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Velocity0.0

Simulation and Plots for Fossil and Taxonomy Data

github.com/fossilsim/fossilsim ↗

A fossil-record simulator that quietly grew a trait-evolution engine.

phylogeneticssimulationtrait-evolutionbirth-death-modelsr-package
◆Current state
FossilSim is a mature R package for simulating fossil records on phylogenetic trees, and its release cadence reflects that: long gaps punctuated by a single capability addition. The last four releases span three years, with the most recent being a compatibility sync to its companion Shiny front-end rather than new functionality. The core simulation surface has been stable since 2022.
◆Where it's heading
The arc runs from sampling mechanics toward simulating what the organisms actually were. Version 2.2.0 taught the package to handle occurrence data for occurrence birth-death models; 2.3.0 then added trait simulation under Mk, BM and OU, which is a different kind of output than fossil ages. Since then the work has been maintenance and keeping the FossilSimShiny GUI in step, suggesting the authors consider the current model set feature-complete.
◆Prediction
The pairing of the 2.3.3 release with a FossilSimShiny version bump points to the GUI, not the library, as where the next visible work lands. The entries do not show enough activity to predict a specific new model family.

◆Recent moves

  1. 2y ago

    Compatibility bump for FossilSimShiny 1.1.2

    A compatibility release that aligns the package with FossilSimShiny v1.1.2. Nothing changes for users calling the library directly; this exists so the GUI companion keeps working.

    View source ↗
  2. 4y ago

    Bug fixes and documentation cleanup

    Bug fixes and documentation improvements with no named user-facing change. Consolidation work in the gap between the trait-simulation release and the Shiny sync.

    View source ↗
  3. 4y ago

    Trait simulation arrives: Mk, BM and OU models

    ⚡ SPARK

    Trait simulation under Mk, BM and OU models lands, extending the package past fossil ages and sampling into simulating character evolution along the tree. This is the release that widened what FossilSim outputs rather than refining how it samples.

    View source ↗
  4. 5y ago

    Occurrence handling for the occurrence birth-death model

    Occurrence handling arrives so the package can feed the occurrence birth-death model, broadening the sampling schemes it supports. A real capability addition, but within the birth-death family the package was already built around.

    View source ↗