phylostrat

Effects of stratigraphy of phylogenetic inference

Authors

Niklas Hohmann
Utrecht University
email: n.h.hohmann [at] uu.nl
Web page: uu.nl/staff/NHohmann
Orcid: 0000-0003-1559-1838

Emilia Jarochowska
Utrecht University
email: e.b.jarochowska [at] uu.nl
Web page: www.uu.nl/staff/EBJarochowska
ORCID: 0000-0001-8937-9405

Raoul Schram
Utrecht University

Requirements and reproduction

Requires Julia, revBayes as rb, bash, snakemake, and R. Details for full instructions are given in the REPRODUCEME.md.

Repository structure

• code/
  • bugreports/: bugreports issued for revBayes
  • strat_architectures/: Julia & R code to generate strat architectures, plot them, and do postprocessing
  • bash, revBayes, and R code for phylogenetic simulation and inference, including postprocessing and plotting
• dag/: folder for model dags (content not tracked)
• data/
  • strat/: data from stratigraphic forward models
  • further folders generated by the phylogenetic simulation pipelines, specifically fbd_base/, fbd_strat/, fbd_gap_est, and fbd_gap_prior. Contain both simulation data, trace files from inference, and MAP trees
  • convergence_assessment.RData: mcmc convergence statistics
  • post_values.RData: posterior & MAP statistics from traces
• figs/
  • ms/: figures in the main manuscript. Initially empty
  • sm/: figures for supplementary materials. Initially empty
• logs/: folder for log files of mcmc runs (content not tracked)
• .gitignore: untracked files
• LICENSE: Apache 2.0 license text
• README: you are here
• REPRODUCEME.md: Instructions for reproduction of study
• phylostrat.RProj: R project file for RStudio
• Manifest.toml: Julia deps
• Project.toml: Julia project info
• snakefile_[suffix]: various snakemake workflows, specifically
  • fbd_base: cFBD + CFS simulation and inference
  • fbd_strat: cFBD + MSG and cFBD + FLG simulation and inference
  • fbd_gap_est: sFBDw + FLG simulation and inference
  • fbd_gap_est: sFBDs + FLG simulation and inference
  • tree_summary: generage MAP trees

License

Apache 2.0, see LICENSE file for license text.

Citation

To cite this repository, please use

• Hohmann, N., & Jarochowska, E. (2026). Supplementary code for "Phylogenetic inference from an incomplete fossil record". Zenodo. https://doi.org/10.5281/zenodo.20393226

To cite the associated data, please use

• Hohmann, N. (2026). Simulation and inference data for "Phylogenetic inference from an incomplete fossil record". YoDa. https://doi.org/10.24416/UU01-6ON0QY

Funding information

Funded by the European Union (ERC, MindTheGap, StG project no 101041077). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them.