This repository contains the necessary code and data to reproduce all results in the happi manuscript. preprint available here. The code and data contained in this repository can also be found at: 
The most recent happi R package is available: here. happi version 0.8.7 can be used to produce the manuscript results and a static version has been made available: 
Below you'll find a description of the R scripts and what analyses can be reproduced with each script.
Please refer to the comments within the R scripts for the associated data files needed to run or generate the figures/results.
| Script | Description | Data Files Needed |
|---|---|---|
TM7_data_cleaning.R |
Data cleaning script that uses Saccharibacteria data from public repositories and creates data file TM7_presence_absence.RDS |
TM7_data_cleaning_files/ |
compare-nonparametric-f-options.R |
Script for evaluating estimators for f | logit_DRR102664.RDS accuracy_f_nonparametric.RDS |
type1-error-parallel.R |
Type 1 error simulations in parallel | logit_DRR102664.RDS type1_results.RDS |
type2-error-parallel.R |
Type 2 error simulations in parallel | logit_DRR102664.RDS type2_results.RDS |
tm7-data-analysis.R |
Data analysis of Saccharibacteria MAGs and creation of Figure 1 | TM7_presence_absence.RDS tm7_hyp_results_summary.RDS |
happi-simulation-figures.R |
Creation of Figures 2 & 3 | logit_DRR102664.RDS type1_results.RDS type2_results.RDS |