Set Size Supplement

Estimating the Size of a Set Using Cascading Exclusion - Supplementary Materials

Author

Susan Holmes

Overview

This repository contains all supplementary materials, code, and analyses for the paper “Estimating the Size of a Set Using Cascading Exclusion.” by Sourav Chatterjee, Persi Diaconis and Susan Holmes, August 2025.

Data

silva_nr99_v138.2_toGenus_trainset.fa: Original SILVA database version
silva_aligned_bacteria_sequences.fasta: Aligned bacterial DNA sequences
silva_sequence_info.csv: Sequence metadata and taxonomic information

Reproducibility

Clone this repository and run render or build.

---
title: "Set Size Supplement"
subtitle: "Estimating the Size of a Set Using Cascading Exclusion - Supplementary Materials"
author: "Susan Holmes"
---

## Overview

This repository contains all supplementary materials, code, and analyses for the paper "Estimating the Size of a Set Using Cascading Exclusion." by
Sourav Chatterjee, Persi Diaconis and Susan Holmes, August 2025.

## Navigation

- **[Convex Hulls](analysis/01-convex-hulls.qmd)**: Geometric approaches to set size estimation
- **[Coincidence Detection](analysis/02-coincidence-detection.qmd)**: Distance-based methods and Anderson-Darling analysis
- **[Coincidence Detection on SILVA data](analysis/03-bacterialdata.qmd)**: Detection of coincident bacterial species from SILVA data example
- **[Prediction Sets](analysis/04-prediction-sets-regression.qmd)**: Regression-based estimation approaches


## Data

- `silva_nr99_v138.2_toGenus_trainset.fa`: Original SILVA database version
- `silva_aligned_bacteria_sequences.fasta`: Aligned bacterial DNA sequences
- `silva_sequence_info.csv`: Sequence metadata and taxonomic information

## Reproducibility

Clone this repository and run `render` or `build`.