markov-null-design

Generate Markov null models with explicit order for trajectory TDA permutation tests.

1|Updated Dec 13, 2025
One-click install
npx skills add https://github.com/stephendor/TDL --skill markov-null-design
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: markov-null-design
Source: https://github.com/stephendor/TDL/tree/main/.agents/skills/markov-null-design
Command: npx skills add https://github.com/stephendor/TDL --skill markov-null-design

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) components.

What problem does it solve?

This Skill helps in designing and scaffolding Markov null models for the trajectory TDA permutation pipeline, ensuring explicit Markov order and automating the permutation test call and result logging.

Core Features & Use Cases

  • Markov Null Model Design: Generates Markov null models with explicit Markov order.
  • Permutation Test Automation: Automates the permutation_test_trajectories call.
  • Result Logging: Provides a stub for logging results and a reminder to log seeds.
  • Use Case: For a researcher looking to create a Markov null model with order 2 for a trajectory TDA permutation test, this Skill can be used to generate the necessary model and automation calls.

Quick Start

Run /markov-null-design markov 2 to scaffold a Markov-2 null model.

Frequently Asked Questions about markov-null-design

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I design a Markov null model for trajectory topology permutation tests?

You can design a Markov null model for trajectory topology permutation tests by generating a model with an explicit Markov order, which scaffolds the necessary structure for your TDA analysis pipeline.

How do I automate permutation test calls for trajectory TDA analysis?

You can automate permutation test calls for trajectory TDA analysis by using a skill that wraps the permutation_test_trajectories function, automatically invoking it and logging the results along with the random seeds.

What is a Markov null model used for in TDA permutation pipelines?

A Markov null model in TDA permutation pipelines is used to generate randomized trajectory data preserving Markov properties, serving as a statistical baseline to test whether observed trajectory topology is statistically significant.

Can I specify the Markov order when generating a null model for trajectory analysis?

Yes, you can specify the Markov order when generating a null model for trajectory analysis by providing the desired order value as a command argument, such as setting it to 2 for a Markov-2 model.

Do I need to manually log random seeds when running trajectory TDA permutation tests?

No, manual seed logging is not required because the permutation test automation includes a stub for logging results and provides a reminder to log seeds, ensuring reproducibility of your trajectory TDA analysis.

What are the limitations of using Markov null models for trajectory topology analysis?

Markov null models for trajectory topology analysis enforce an explicit Markov order, meaning they assume trajectory dependencies only exist up to that specified order and may not capture complex long-range dependencies present in your data.