Reproducibility of Research During COVID‐19: Examining the Case of Population Density and the Basic Reproductive Rate from the Perspective of Spatial Analysis
Bibliographic record
Abstract
The emergence of the novel SARS-CoV-2 coronavirus and the global COVID-19 pandemic in 2019 led to explosive growth in scientific research. Alas, much of the research in the literature lacks conditions to be reproducible, and recent publications on the association between population density and the basic reproductive number of SARS-CoV-2 are no exception. Relatively few papers share code and data sufficiently, which hinders not only verification but additional experimentation. In this article, an example of reproducible research shows the potential of spatial analysis for epidemiology research during COVID-19. Transparency and openness means that independent researchers can, with only modest efforts, verify findings and use different approaches as appropriate. Given the high stakes of the situation, it is essential that scientific findings, on which good policy depends, are as robust as possible; as the empirical example shows, reproducibility is one of the keys to ensure this.
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How this classification was reachedexpand
Direct model labels (unvalidated)
Per-model category and study-design labels from the labeling rounds. They are machine output, unvalidated, and the disagreement between models ships as data. No study design here is MEDLINE-validated yet.
| Model arm | Categories | Study design | Confidence |
|---|---|---|---|
| gemma | Metaresearch Domain: Reproducibility · Genre: Empirical About the Canadian research system: no · About a Canadian topic: no | Observational | low |
| gpt | Metaresearch Domain: Reproducibility · Genre: Empirical About the Canadian research system: no · About a Canadian topic: yes | Observational | high |
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.324 | 0.727 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.005 |
| Bibliometrics | 0.005 | 0.009 |
| Science and technology studies | 0.004 | 0.027 |
| Scholarly communication | 0.010 | 0.013 |
| Open science | 0.004 | 0.010 |
| Research integrity | 0.004 | 0.006 |
| Insufficient payload (model declined to judge) | 0.004 | 0.001 |
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, unvalidatedLabeled directly by 2 models reading the full record.
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".