Welcome to stdvoidsim

Population genetic simulations for the Cthulhu Mythos.

stdvoidsim is a library of demographic and genome models for Lovecraftian entities and eldritch horrors. Simulate Deep Ones, Shoggoths, Mi-Go, and dozens more with made-up but population-genetically plausible parameters — powered by msprime and SLiM and built on the stdpopsim framework.

That is not dead which can eternal lie, And with strange aeons even death may die. — H.P. Lovecraft, The Nameless City

First steps

• Install: Installation — get stdvoidsim on your machine.

• Explore: Catalog — 40 species and demographic models.

• Run: Tutorial — examples and workflows.

Quick run

Install and simulate 10 Deep One samples over 100 kb:

$ pip install stdvoidsim
$ stdvoidsim DagHyd -d InnsmouthDecline_1M27 -o deep_ones.trees -L 100000 DeepOnes:10

Then open deep_ones.trees in tskit or continue with the tutorial.

Catalog at a glance

The full catalog lists every species and demographic model. By category:

• Outer Gods & Great Old Ones - Azathoth primordia, Cthulhu greatoldone, Chaugnarus faugnis, Dagonus maximus, Hastur carcosensis, Nyarlathotep azathothspawn, Shubniggurath fertilitas, Tsathoggua somnolentis, Yogsothoth dimensionalis

• Servitor Races & Engineered Species - Byakhee voidwing, Obscurus silvanus, Igneus vampirus, Informis generatus, Venator obscurus, Shoggoth nigrumplasma, Starspawn cthulhidae

• Ancient Civilizations - Elderium antarcticae, Polypus volantis, Migo fungoides, Serpentis valusiensis, Yithianus temporalis

• Amphibious & Aquatic - Chromatis extraspatiala, Dagonus hydridae

• Subterranean Horrors - Dholos subterraneus, Ghastus cavernicola, Ghoulish necrophagus, Gugus underworldis, Degeneratus subterraneus

• Dreamlands Creatures - Felis ultharensis, Araneus lengensis, Lunaris bestialis, Nightgauntus mantaformis, Shantakus dreamlandis, Zoogus sylvaticus

• Interdimensional & Temporal - Dimensius shambleris, Houndus tindalosi

• Arctic & Desert - Gnophkehus arcticus, Arenicola abyssalis

• Human-Adjacent Horrors - Rattus magicus, Tsathoggua choriensis

• Generic models - Generic demographic models (any species)

Contents:

• Introduction
  • First steps
  • Citations
  • Licence and usage
• Installation
  • Requirements
  • Conda
  • Pip
  • Running the CLI
• Catalog
  • Outer Gods & Great Old Ones
  • Servitor Races & Engineered Species
  • Ancient Civilizations
  • Amphibious & Aquatic
  • Subterranean Horrors
  • Dreamlands Creatures
  • Interdimensional & Temporal
  • Arctic & Desert
  • Human-Adjacent Horrors
  • Generic models
• Tutorials
  • Running stdvoidsim with the command-line interface (CLI)
  • Running stdvoidsim with the Python interface (API)
  • Example analyses with stdvoidsim
• Command-line options
  • Positional Arguments
  • Named Arguments
  • msprime specific parameters
  • SLiM specific parameters
  • Sub-commands
• API
  • Quick reference
  • Species definitions
  • Demographic Models
  • Gene conversion and bacterial recombination
  • Selection and DFEs
  • Selection and sweeps
  • Generic models
  • Simulation Engines
• Development
  • Installation
  • GitHub workflow
  • Adding a new species
  • Adding a new demographic model
  • Adding a recombination/genetic map or annotation
  • Lifting over a recombination/genetic map
  • Adding a DFE model
  • Coding standards
  • Naming conventions
  • Unit tests
  • Code Coverage
  • Documentation
  • Making a new release
• Changelogs
  • Upcoming
  • [0.3.0] - 2025-03-18
  • [0.2.1a] - 2024-07-06
  • [0.2.0] - 2022-11-01
  • [0.1.2] - 2020-05-29
  • [0.1.1] - 2020-01-02
  • [0.1.0] - 2019-12-18

Indices and tables

• Index

• Module Index

• Search Page