Haven Reach · synthetic · day 7
Home Research Rapid Epidemic Growth
Research · modeled study · synthetic metapopulation
A seed-locked ensemble on a fictional 48-county commuting graph. Rapid growth onset defined as a ≥2× rise in 7-day incidence with a nowcasted reproduction number remaining ≥1.3 — a threshold that separates local flicker from regional acceleration.
48
Counties
Haven Reach metro
≥2×
RGO definition
per 7 days
1 d
Cadence
incidence nowcast
200
Seasons
seed-locked ensemble
The question
Hospital occupancy, school-closure timing, and staffing models all depend on a growth signal that is still local. When incidence doubles in a week and stays supercritical, every bed model, every absentee forecast, and every interruption rider priced on last week’s curve goes stale at once. The goal here is methodological: define a rapid-growth onset (RGO) that is the epidemiological analog of a ≥30 kt / 24 h wind jump, then test whether a nowcast on a commuting graph can flag it before occupancy moves.
Haven Reach is fictional. Populations, origin–destination flows, and linelists are constructed. Nothing on this page is a claim about a real outbreak, a real metro, or a published result. It is a modeled study — the same pipeline shape as the hurricane note, pointed at a different field.
This is the jump the pipeline is built to flag. A university-county seed is still a local cluster on day 0. Seven days later the downtown, airport, and Eastgate hubs are lit — a ≥2× seven-day incidence gain with Rê remaining above 1.3, visible on the graph as a corridor, not a single patch.
7-day incidence ratio · nowcast vs occupancy
TanStack Charts · dashed rule is the ≥2× RGO threshold. Ensemble draw, not observations.
Nodes are synthetic counties; edges are gravity-model commuting flows. Rapid-growth onsets in the ensemble concentrate on hub counties — downtown Haven, the airport, the university, Eastgate — where between-patch mixing is high enough to turn a local cluster into a regional wave.
01
Forty-eight counties given constructed populations and a gravity origin–destination matrix. Hub weights (downtown, airport, university, port, Eastgate) set mixing; weekend and holiday schedules thin the same matrix. No census tract, no real metro.
02
Each county is an SEIR compartment with between-patch force of infection from commuting. Transmission, latent, and infectious periods drawn once per season. Tau-leaping updates at daily cadence; hospital occupancy lagged from incidence by a fitted delay.
03
For each day, compute the 7-day incidence ratio and a nowcasted Rê. Observations where the ratio ≥ 2.0 and Rê remains ≥ 1.3 tagged as rapid-growth onset. Consecutive flags collapsed to a single event. Weekend reporting bias corrected before the ratio is taken.
04
Two hundred seasons, seed-locked. Pipeline is a single notebook: constructed OD → ensemble → figures. Environment pinned via conda-lock. Figures generated with matplotlib; any researcher can rerun end-to-end from the in-repo synthetic files.
~61%
of first RGO flags on hub counties
Downtown Haven, the airport, the university, and Eastgate account for most first onsets. Peripheral counties rarely lead; they follow the commuting corridors.
6–9 d
median nowcast lead vs occupancy
The RGO flag precedes the hospital occupancy upturn by about a week in the ensemble. That is the operational window the threshold is meant to buy.
~11 d
peak delay if top 8% of edges close
A counterfactual that zeros the heaviest commuting edges delays the regional incidence peak. It is a sensitivity result, not a policy recommendation.
Weekend bias
inflates false RGO if unadjusted
Raw seven-day ratios fire on reporting artifacts. The pipeline debiases weekday completeness before the threshold is applied; without that step, precision collapses.
RGO events per season · 20-draw slice
Illustrative slice of a 200-season synthetic ensemble. Not observations.
Mean first RGO flags · three-dimensional
Each column is a five-season window × hub cell. Height is mean first RGO flags in the ensemble. Downtown Haven leads every window; later seasons lift as amber caps. TanStack Charts, isometric projection of constructed ensemble counts.
Occupancy models trained on last week’s incidence miss the week the curve bends. An RGO flag is a staffing trigger: the lead time is the difference between a planned surge and a scramble.
Closure and remote-work decisions priced on county case counts arrive after commuting has already mixed the patches. A graph-aware threshold sees the corridor, not just the seed county.
Interruption riders and absentee forecasts assume a smooth epidemic curve. Rapid growth is a regime change. Pricing that ignores onset understates the week that actually costs.
Identifying the mixing edges that reliably precede RGO gives nowcasting a target: resolve those corridors, and growth forecasts improve where occupancy is about to move.
Stack
Data sources
Reproducibility
Pipeline is a single notebook from constructed OD to ensemble figures. No external outbreak feed.
Environment locked with conda-lock. All random seeds fixed. Re-runnable from the in-repo synthetic files.
Next project
Decoding hurricane rapid intensification →