semialg-hypothesis-test-with-incomplete-u-stats
https://github.com/marinagarrote/semialg-hypothesis-test-with-incomplete-u-stats
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Repository
Basic Info
- Host: GitHub
- Owner: marinagarrote
- License: mit
- Language: C++
- Default Branch: main
- Size: 16.9 MB
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Metadata Files
README.md
Methodological considerations for semialgebraic hypothesis testing with incomplete U-statistics
V.1.0 Update: July/2025
This repository contains code implementing methods described in the paper:
[1] Methodological considerations for semialgebraic hypothesis testing with incomplete U-statistics,
D. Barnhill, M. Garrote-López, E. Gross, M. Hill, B. Kagy, J. A. Rhodes, and J. Z. Zhang.
Available at arxiv.org/abs/2507.13531.
A portion of the R and C++ code in this repository is adapted from the
implementation in the TestGGM R package, which is available at
github.com/NilsSturma/TestGGM. We
gratefully acknowledge the authors of TestGGM for their work and allowing us
to use their code.
This repository includes code implemented in R, C++ and Macaulay2.
Code for hypothesis testing with incomplete U-statistics:
The code is based on the following files, all of which contain additional detailed documentation:
src/SDL-test.R
Contains the main high-level functiontest_U_stat, which runs the SDL test.
└src/SDL-test_functions.cpp: Additional C++ functions for implementing the SDL test.src/trinomial-models_main_SDL-test.R
Code for running experiments for the trinomial models (see Section 3 in [1]).
└src/trinomial-models_utils.RAdditional functions for generating data and plotting trinomial models.src/CFN-model_main_SDL-test.R
This file contains code for how to use the SDL test with the CFN 4-leaf tree model (see Section 4 in [1]).
└src/CFN-model_utils.R: Additional functions for working with the CFN model.src/plot-CFN-results.R
This file contains code with examples illustrating how to generate the p-value histograms and treespace plots in Section 4 of [1].
└ The dataset used for this is Collection 1, seethe data readme.
Additional Macaulay2 code:
docs/singular_locus_CFN.m2
This file can be used to compute the singular locus of the CFN model on a 4-leaf binary tree.docs/generating_sets_CFN.m2
This file contains the code presented in Appendix C.1, used to compute the 5 different constrain sets (CDD, CDM, PDM, CDR and PDR) used thoughout the paper. It also contains the list of invariants for the CFN model for the 3 tree topologies of 4-leaf binary trees.
To discuss: Add docs/TestModels.pdf? or similar R code?
Owner
- Name: Marina Garrote-López
- Login: marinagarrote
- Kind: user
- Website: https://sites.google.com/view/marinagarrotelopez/
- Repositories: 1
- Profile: https://github.com/marinagarrote
PhD Researcher at UPC
Citation (CITATION.cff)
cff-version: 1.0.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Barnhill
given-names: David
- family-names: Garrote-López
given-names: Marina
- family-names: Gross
given-names: Elizabeth
- family-names: Hill
given-names: Max
- family-names: Kagy
given-names: Bryson
- family-names: Rhodes
given-names: John A.
- family-names: Zhang
given-names: Joy Z.
title: "Code repository for the paper: Methodological considerations for semialgebraic hypothesis testing with incomplete U-statistics"
version: 1.0.0
date-released: 2025-07-08
url: "https://github.com/marinagarrote/Semialg-Hypothesis-Test-with-Incomplete-U-Stats"
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