Best practices for estimating and reporting epidemiological delay distributions of infectious diseases using public health surveillance and healthcare data
Bibliographic record
Abstract
Epidemiological delays, such as incubation periods, serial intervals, and hospital lengths of stay, are among key quantities in infectious disease epidemiology that inform public health policy and clinical practice. This information is used to inform mathematical and statistical models, which in turn can inform control strategies. There are three main challenges that make delay distributions difficult to estimate. First, the data are commonly censored (e.g., symptom onset may only be reported by date instead of the exact time of day). Second, delays are often right truncated when being estimated in real time (not all events that have occurred have been observed yet). Third, during a rapidly growing or declining outbreak, overrepresentation or underrepresentation, respectively, of recently infected cases in the data can lead to bias in estimates. Studies that estimate delays rarely address all these factors and sometimes report several estimates using different combinations of adjustments, which can lead to conflicting answers and confusion about which estimates are most accurate. In this work, we formulate a checklist of best practices for estimating and reporting epidemiological delays with a focus on the incubation period and serial interval. We also propose strategies for handling common biases and identify areas where more work is needed. Our recommendations can help improve the robustness and utility of reported estimates and provide guidance for the evaluation of estimates for downstream use in transmission models or other analyses.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.018 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.002 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".