sivirep: A package for strengthening epidemiological surveillance and report generation—Use case in Colombia
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
Bibliographic record
Abstract
This paper presents sivirep , an open-source R package created to streamline epidemiological surveillance and reporting in public health. sivirep is part of the Epiverse TRACE-LAC initiative, which aims to strengthen the infrastructure and epidemic response to infectious diseases in Latin America and the Caribbean. This package automates the downloading, preprocessing, and preparation of data from Colombia’s epidemiological surveillance and reporting system, “SIVIGILA”. sivirep also provides a customizable R Markdown template for subsequent analysis and automatic generation of epidemiological reports. sivirep was developed in Spanish to improve the engagement of local users, but can be used worldwide, keeping both potential global uses aligned with local needs. This tool also can facilitate teaching and learning on SIVIGILA data source for students and researchers from various fields.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.001 | 0.006 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 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 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| 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 it