Appendix A. Method Summary – Basically the “methods” section as we had it in the Nature version, a bit updated.
- These sections are as before, with minor updates from the reviewers, etc. They’re also probably the most important part:
- Appendix B. The data sets
- Appendix C. Model Derivations
- Appendix D. Likelihood calculations
Appendix E. The likelihood statistic
Appendix F. The distributions for the ROC curves – these are the former figure 1b/c distributions used to make the ROC curve.
Appendix G. On a hypothesis-testing framework – A new section. Really let me know if this part is okay, I try to address some issues more directly then we had space for in the main text.
Appendix H. Model choice and model adequacy – I don’t currently include examples of this. I could add them, I think they are interesting, but a bit tangential to the topic. I want to acknowledge that the models we use are general but not completely general, and that this is a sensible way of checking when they are reasonable. I think it’s important to point out how one could check for model adequacy, but let me know what you think. I could remove the whole section too. Referenced in second-to-last paragraph though. Attempting runs on cluster, unlikely to finish though.
Appendix I. R package tutorial – this is super minimal at the moment. I may try and flush it out more.
Appendix J. Examples – I add the analysis for two more data sets, exactly as in the paper. I put almost all the text in the captions, let me know if it needs more background on the data, etc in the body of this section.