Statistical Inference
This folder contains two analyses:
- Figures3_4.ipynb: processes and analyses the estimated latent positions for the mice, studying the effects of genotypes, sex, age, and immunity (HN and non-HN). This produces figures 3 and 4 in the manuscript, and the associated pvalue table analysis-hn.csv.
- Figures5_6.ipynb](./Figures5_6.ipynb): processes and analyses the estimated latent positions for mice, exploring the effects of genotypes, sex, age, and diet (control and HFD). This produces figures 5 and 6 in the manuscript, and the associated pvalue table analysis-diet.csv.
These analyses were conducted separately for immunity and diet due to the fact that mice with certain combinations of risk factors (e.g., high-fat diet + non-HN immunity) were not collected.