By name: sitrep-report description: "Render and deploy the MVE SitRep Quarto HTML report. Use when: rebuilding the report after new extraction data; Quarto render fails; R package missing or broken; publishing updated report to GitHub Pages via git push; the live report at bquilty25.github.io is out of date; diagnosing R or Quarto errors."
SitRep Report
Renders the Quarto HTML situation report from the master CSVs and deploys it to GitHub Pages.
When to Use
- After extraction has added new rows to
data/processed/master_combined_counts.csv - Diagnosing Quarto or R errors
- Publishing the updated report (always confirm with user before
git push)
Render Command
Run from the project root (not from inside scripts/):
cd /Users/billyquilty/Documents/Work/bvd_sitrep_extractor
quarto render sitrep_report.qmd
Output: outputs/sitrep_report.html
Config: _quarto.yml at project root sets output-dir: outputs
Expected terminal output ends with:
Output created: outputs/sitrep_report.html
R Dependency Check
If render fails with there is no package called 'X' or Error in library(X):
Rscript -e "if (!requireNamespace('pacman', quietly=TRUE)) install.packages('pacman'); pacman::p_load(tidyverse, lubridate, here, scales, ggrepel, flextable, ggh4x)"
Required packages: tidyverse, lubridate, here, scales, ggrepel, flextable, ggh4x
Deploy Workflow
Always confirm with the user before running git push.
# 1. Review what changed
git status
git diff --stat HEAD outputs/sitrep_report.html data/processed/master_combined_counts.csv
# 2. Commit
git add -A
git commit -m "Add SitRep NNN (YYYY-MM-DD), update report"
# 3. Push — triggers GitHub Actions deploy (CONFIRM WITH USER FIRST)
git push
After push, the GitHub Actions workflow (.github/workflows/deploy-report-pages.yml) fires automatically when outputs/sitrep_report.html has changed. Live URL: https://bquilty25.github.io/bvd_sitrep_extractor/sitrep_report.html
Error Table
| Error | Cause | Fix |
|---|---|---|
there is no package called 'X' |
R package not installed | Run the dependency check command above |
Error in library(X) : there is no package called 'X' |
Same | Same |
quarto: command not found |
Quarto CLI not installed or not in PATH | brew install quarto or download from quarto.org; restart terminal |
object 'X' not found in R |
Column renamed or missing in master CSV | Check column names in data/processed/master_combined_counts.csv; compare against what sitrep_report.qmd expects |
Error in dmy(count_end_date) |
Malformed date in master CSV | Inspect count_end_date column for non-DD/MM/YYYY values; trace to the offending sitrep's combined_counts.csv |
Quarto render error: ... execution halted |
R code chunk error | Read the full R traceback printed above it; fix the specific data issue |
git push rejected (non-fast-forward) |
Remote has new commits | Run git pull --rebase then git push again |
git push authentication failure |
HTTPS/SSH credentials expired | Run gh auth login (GitHub CLI) or re-add SSH key |
| GitHub Pages not updating after push | CI workflow not triggered or failed | Check Actions tab: github.com/bquilty25/bvd_sitrep_extractor/actions |
| Report renders but plots are empty | Master CSV has no rows for the expected date range | Verify data/processed/master_combined_counts.csv has data with head data/processed/master_combined_counts.csv |
Key Files
| File | Description |
|---|---|
sitrep_report.qmd |
Quarto source document |
_quarto.yml |
Project config — sets output-dir: outputs |
outputs/sitrep_report.html |
Rendered output (git-tracked, deployed to GitHub Pages) |
data/processed/master_combined_counts.csv |
Primary data source for the report |
data/processed/master_response_counts.csv |
Patient movement data for the report |
data/processed/master_poe_counts.csv |
Points d'Entrée data for the report |
.github/workflows/deploy-report-pages.yml |
CI/CD deploy workflow |