Repositories list

• MindTheGap-ERC.github.io

  Public
  Project webpage

  CSS

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  Apache License 2.0

  •0•0•0•0•Updated Aug 18, 2025Aug 18, 2025

• vm_setup

  Public
  Shell

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  Apache License 2.0

  •0•0•0•0•Updated Aug 12, 2025Aug 12, 2025

• CarboKitten.jl

  Public
  Julia implementation of carbonate platform model

  Julia

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  GNU General Public License v3.0

  •0•5•33•2•Updated Aug 9, 2025Aug 9, 2025

• stratcols

  Public
  Stratigraphic columns in R

  geologystratigraphy

  R

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  Apache License 2.0

  •0•2•1•0•Updated Jul 31, 2025Jul 31, 2025

• revbayes

  Public
  Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

  C++

  •

  GNU General Public License v3.0

  •25•0•0•0•Updated Jul 29, 2025Jul 29, 2025

• age_depth_modeling_r

  Public
  Code and materials for the workshop "Age-depth modeling in R"

  HTML

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  Apache License 2.0

  •0•0•0•0•Updated Jun 25, 2025Jun 25, 2025

• CarboKitten_Denudation_paper

  Public
  Julia

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  Apache License 2.0

  •0•0•0•0•Updated Jun 10, 2025Jun 10, 2025

• PalAss_StratPal

  Public
  Stratigraphic paleobiology and phylogenetics - supplementary material for article in the PalAss newsletter

  R

  •

  Apache License 2.0

  •0•0•0•0•Updated May 22, 2025May 22, 2025

• nonparam_est_adm_supp

  Public
  Supplementary data and code for "Nonparametric estimation of age-depth models from sedimentological and stratigraphic data"

  R

  •

  Apache License 2.0

  •0•0•0•0•Updated May 22, 2025May 22, 2025

• admtools

  Public
  Estimate Age-Depth Models and Transform Data

  geochronologystratigraphyage-depth-model+ 1sedimentology

  R

  •

  GNU General Public License v3.0

  •0•4•5•0•Updated May 21, 2025May 21, 2025

• StratPal

  Public
  R package for Stratigraphic Paleobiology

  paleobiologypalaeobiologystratigraphy+ 3paleontologypalaeontologystratigraphic-paleobiology

  R

  •

  Apache License 2.0

  •0•1•0•0•Updated May 21, 2025May 21, 2025

• stratorder

  Public
  Quantify stratigraphic order

  geologystratigraphy

  R

  •

  Apache License 2.0

  •0•0•1•0•Updated May 15, 2025May 15, 2025

• StratPal_ms_supp

  Public
  Supplementary code for the manuscript "StratPal: An R package for creating stratigraphic paleobiology modeling pipelines"

  R

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  Apache License 2.0

  •0•1•0•0•Updated May 15, 2025May 15, 2025

• ShellbedCondensator

  Public
  Shiny app visualizing the effects of sedimentary condensation

  geologypaleobiologypalaeobiology+ 6paleontologytaphonomysedimentologypalaeontologyrshiny

  R

  •

  Apache License 2.0

  •0•0•1•0•Updated Mar 3, 2025Mar 3, 2025

• DarwinCAT

  Public
  Shiny app visualizing the effects of carbonate stratigraphy on trait evolution

  rshinygeology+ 9palaeobiologystratigraphypaleontologyevolutionary-biologysedimentologytrait-evolutionpalaeontology+ 2

  R

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  Apache License 2.0

  •1•2•0•0•Updated Mar 3, 2025Mar 3, 2025

• reactive-transport-model-for-limestone-marl-sequences

  Public
  Integrating diagenetic equations using Python, inspired by LMA-Matlab, which was created by Niklas Hohmann

  calcitecarbonatesediment+ 10permeabilitygeochemistryoscillationssedimentologyreactive-transportporositydiagenesis+ 3

  Python

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  Apache License 2.0

  •1•2•0•0•Updated Nov 26, 2024Nov 26, 2024

• StratPal_data_prep

  Public
  Data preparation for StratPal workshop and package

  MATLAB

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  Apache License 2.0

  •1•0•0•0•Updated Nov 11, 2024Nov 11, 2024

• CarboKittenData

  Public
  Auxiliary data files for use with CarboKitten

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

• StratPal_paleoverse_materials

  Public
  Materials and examples for the Paleoverse lecture "Building modeling pipelines for stratigraphic paleobiology in R" (Oct 31st 2024)

  R

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  Apache License 2.0

  •0•1•0•0•Updated Oct 31, 2024Oct 31, 2024

• StratPal_workshop_materials

  Public
  Workshop materials for modeling pipelines in stratigraphic paleobiology using the StratPal package

  HTML

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  Apache License 2.0

  •0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

• phylo_stratpal

  Public
  Rudimentary shiny app transforming phylogenetic trees using age-depth models

  R

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  Apache License 2.0

  •1•0•0•0•Updated Oct 28, 2024Oct 28, 2024

• .github

  Public
  MindTheGap: Quantifying the completeness of the stratigraphic record and its role in reconstructing the tempo and mode of evolution

  0•0•0•0•Updated Aug 24, 2024Aug 24, 2024

• PartiMoDe

  Public
  Modeling Particle Movement and Destruction in the sediment surface mixed layer.

  mixingsedimentology

  MATLAB

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  Apache License 2.0

  •0•0•0•0•Updated Aug 4, 2024Aug 4, 2024

• Cross-comparison

  Public
  Comparing the outputs of implementations of the diagenetic model by Ivan L'Heureux (2018)

  Python

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  Apache License 2.0

  •0•1•0•0•Updated Jul 25, 2024Jul 25, 2024

• LMA-Matlab

  Public
  Matlab implementation of the model by L'Heureux (2018) generating self-organized Limestone-Marl Alternations

  MATLAB

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  Apache License 2.0

  •0•1•0•0•Updated Jul 24, 2024Jul 24, 2024

• rhythmite

  Public
  FDM-based code which solves the 5 coupled nonlinear diagenetic PDEs of L'Heureux (2018) https://doi.org/10.1155/2018/4968315

  Python

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  GNU General Public License v3.0

  •1•0•0•0•Updated Jul 12, 2024Jul 12, 2024

• R.Pijnenburg_BSc

  Public
  BSc thesis of Robin Pijnenburg

  PLSQL

  •0•0•3•0•Updated Jul 5, 2024Jul 5, 2024

• CarboCAT_utils

  Public
  Extracting data from CarboCAT model outputs

  MATLAB

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  Apache License 2.0

  •0•0•0•0•Updated Jul 1, 2024Jul 1, 2024

• anchoring-late-devonian-mass-extinction

  Public
  Code and data for

  R

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  Apache License 2.0

  •0•1•0•0•Updated Jun 24, 2024Jun 24, 2024

• CarbonateStratPalEvo

  Public
  Code for "Identification of the Mode of Evolution in Incomplete Carbonate Successions"

  biologyevolutionbiological-simulations+ 7geoscienceearth-sciencegeosciencesstratigraphyaicsedimentologyfossils

  R

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  Apache License 2.0

  •0•0•0•0•Updated May 30, 2024May 30, 2024