A century of weekly notifiable disease incidence data by province in Canada
Bibliographic record
Abstract
Canadian notifiable disease surveillance programmes have recorded communicable disease incidence data, dating back to the late 19th century. A Public Health Agency of Canada web-portal provides summaries of these data from 1924-2023, but lacks details on how incidence varies seasonally and geographically among provinces. The sub-annual (weekly, monthly, quarterly) and sub-national (provincial, territorial) data required to study such patterns appear in government documents, but are available only in typewritten or handwritten hard copies. We digitized and collated these sources to make sub-annual and sub-national Canadian disease incidence data conveniently available for researchers. We manually transcribed hard copies into digital spreadsheets resembling the originals, enabling accurate transcription through easier cross-checking. We supplemented these historical data sources with more recent digital spreadsheets obtained directly from two provincial agencies. We standardized and combined these spreadsheets into consistent, machine-readable CSV files containing 1,631,380 incidence values from 1903-2021. Because multiple publications and agencies reproduced case counts from the same surveillance system, and many publications reported the same cases at multiple levels of aggregation, many cases were counted more than once among these 1,631,380 incidence values. We reconciled overlapping counts to produce a dataset containing 934,010 unique incidence values at sub-national and sub-annual scales (829,689 weekly; 567 2-weekly; 82,267 monthly; 20,967 quarterly; 520 3-quarterly) covering 139 diseases stratified by province or territory. We illustrate the value of these sub-annual and sub-national data using two examples: synchronized annual cycles of poliomyelitis across provinces and spatially heterogeneous resurgence of whooping cough in the 1990s. Canada's infectious disease surveillance has produced a detailed record of sub-annual and sub-national disease incidence data that remains largely unexplored. This record is now available as the Canadian Notifiable Disease Incidence Dataset (CANDID), hosted on a publicly accessible website along with code to reproduce it, and scans of the original sources.
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How this classification was reachedexpand
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 | 0.003 | 0.018 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.012 | 0.041 |
| Science and technology studies | 0.003 | 0.001 |
| Scholarly communication | 0.003 | 0.001 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.005 | 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, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), 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".