amertens/IMiC-intervention-effects-public

Analysis code for "Nutritional interventions' impacts on human milk: three trials in low-resource settings" (MISAME-III, Mumta-LW, ELICIT). TMLE effect estimation, pathway/enrichment analysis, and figure builds. No individual-level participant data. # IMiC — intervention effects on human milk composition Analysis code for: > Dailey-Chwalibóg, Mertens, et al. **"Nutritional interventions' impacts on human milk: > three trials in low-resource settings."** *Science* (submitted). The pipeline estimates the effects of three maternal-nutrition randomized trials — **MISAME-III** (Burkina Faso), **Mumta-LW** (Pakistan), and **ELICIT** (Tanzania) — on multi-omics human-milk outcomes: macronutrients, micronutrients, B-vitamins, HMOs, bioactive proteins, targeted and untargeted metabolomics, proteomics, and microbiome. A cross-compartment extension follows the same signals along maternal diet → maternal blood → milk → infant blood. --- ## 1. What is and is not in this repository This is a **code archive**, not a data archive. **Included** | | | |---|---| | `src/`, `functions/`, `figure-scripts/` | The complete analysis and figure-building code | | `metadata/` | Data dictionaries, milk/blood component groupings, WHO growth-velocity standards. No participant records. | | `data/msea/`, `data/untargeted_annotation/` | Aggregate enrichment (ORA/MSEA) exports and metabolite name maps | | `results/*_clean.RDS`, `*_clean.csv` | Per-outcome **effect estimates** (point estimate, CI, p, FDR) for the named-outcome analyses — one row per outcome × study × visit. No participant records. | | `results/metaboanalyst/`, `results/compartment_tracking/` | Pathway / ORA / mummichog / GO enrichment output — pathway- and compound-level, no participant records. | **Deliberately excluded** | | Why | |---|---| | `data/` participant files, `merged_analysis_datasets.RDS` | **Individual-level trial data.** Governed by the IMiC consortium and the three trials' data-access agreements — not publicly redistributable. | | Feature-level untargeted metabolomics and blood-compartment result files (~670 MB) | Size. These are aggregate (no participant rows) but too large for a code archive. Available on request. | | `figure-data/*.RDS` | Saved `ggplo …