By name: sitrep-validation description: "Update and validate against the INRB-UMIE Ebola DRC 2026 reference dataset. Use when: updating the INRB-UMIE submodule before rendering; the cross-source validation section is missing or stale; git submodule errors; understanding which INRB-UMIE files feed the report; interpreting discrepancies between automated extraction and the INRB-UMIE manually-coded data."
INRB-UMIE Validation Data
The Ebola_DRC_2026 git submodule (kraemer-lab/Ebola_DRC_2026) provides a manually-coded reference dataset that the report compares against automated extraction outputs in the "Cross-source validation" section.
When to Use
- Before rendering — to pull the latest INRB-UMIE data so the validation section reflects current numbers
- Diagnosing why the cross-source validation plots are stale or empty
- Understanding a discrepancy flagged in the rendered report
Update Command
cd /Users/billyquilty/Documents/Work/bvd_sitrep_extractor
git submodule update --remote Ebola_DRC_2026
This pulls the latest commit from https://github.com/kraemer-lab/Ebola_DRC_2026 into the pinned Ebola_DRC_2026/ directory.
After updating, confirm new data arrived:
git submodule status Ebola_DRC_2026
# Shows: <new_commit_hash> Ebola_DRC_2026 (build-YYYY-MM-DD-...)
git -C Ebola_DRC_2026 log --oneline -3
Files Used by the Report
All under Ebola_DRC_2026/build/long/:
| File | Used for |
|---|---|
insp_sitrep__cumulative_confirmed_cases.csv |
Confirmed case counts by zone |
insp_sitrep__cumulative_suspected_cases.csv |
Suspected case counts by zone |
insp_sitrep__cumulative_suspected_deaths.csv |
Suspected deaths by zone |
insp_sitrep__cumulative_confirmed_deaths.csv |
Confirmed deaths by zone |
insp_sitrep__hospitalised.csv |
Hospitalised patients |
insp_sitrep__in_bed_previous_day.csv |
Response indicators |
insp_sitrep__new_hosp_admissions.csv |
New admissions |
insp_sitrep__new_hosp_detainees.csv |
New detainees |
insp_sitrep__new_hosp_other.csv |
Other new admissions |
insp_sitrep__cumulative_contacts_traced.csv |
Contact tracing totals |
Zone name differences are harmonised in the report via KRAEMER_NAME_MAP:
"Mongbalu"→"Mongbwalu""Nyakunde"→"Nyankunde"
Interpreting the Cross-Source Comparison
The validation section overlays this extraction's values against INRB-UMIE values on the same chart. Expected behaviour:
| Observation | Meaning |
|---|---|
| Lines overlap closely | Extraction and INRB-UMIE agree — good |
| INRB-UMIE lags by 1–2 sitreps | INRB-UMIE dataset not yet updated; re-run submodule update later |
| Systematic offset for one zone | Possible zone name mismatch or aggregation difference; check KRAEMER_NAME_MAP |
| Extraction higher than INRB-UMIE | Extraction may be capturing aggregate rows that INRB-UMIE excludes; check is_aggregate column in master CSV |
| Large isolated spike | Likely a table parsing error in one sitrep; inspect data/raw/<name>/raw_extraction.json for the outlier date |
Committing the Submodule Pin
After updating, the new commit hash should be committed with the rest of the pipeline output:
git add Ebola_DRC_2026
git commit -m "Update INRB-UMIE submodule to YYYY-MM-DD build"
# This can be combined with the report commit:
# git commit -m "Add SitRep NNN, update INRB-UMIE submodule, rebuild report"
Error Table
| Error | Cause | Fix |
|---|---|---|
fatal: no submodule mapping found in .gitmodules |
Submodule not initialised | Run git submodule init && git submodule update |
fatal: repository 'https://github.com/kraemer-lab/Ebola_DRC_2026' not found |
Network or GitHub auth issue | Check internet; re-authenticate with gh auth login if using HTTPS |
Error in read_csv(...) : cannot open the connection |
CSV file missing from submodule | Submodule may be partially initialised; run git submodule update --init --recursive |
| Cross-source section renders blank | INRB-UMIE files exist but all rows filtered out | Check that zone values in INRB-UMIE data match ZONE_LEVELS defined in sitrep_report.qmd |
| Submodule is already up to date | INRB-UMIE has not pushed a new build | Check https://github.com/kraemer-lab/Ebola_DRC_2026/commits for the latest build date |