Python library for infectious disease surveillance — EpiEstim / EpiNow2 / surveillance parity.
The canonical Python tools for infectious disease surveillance are incomplete relative to R's EpiEstim (Rt estimation), EpiNow2 (Rt + nowcasting + reporting delays), and surveillance (prospective/retrospective aberration detection). episurv closes this gap with direct feature parity, enabling Python-native public health workflows.
| Capability | R package | episurv |
Target |
|---|---|---|---|
| Instantaneous Rt (renewal equation) | EpiEstim |
episurv.rt.instant |
v0.1.0 |
| Rt with uncertain serial interval | EpiEstim |
episurv.rt.uncertain_si |
v0.2.0 |
| Rt + nowcasting + reporting delays | EpiNow2 |
episurv.rt.epinow |
v0.4.0 |
| Prospective aberration detection (CUSUM) | surveillance |
episurv.detect.cusum |
v0.3.0 |
| Prospective aberration detection (EARS) | surveillance |
episurv.detect.ears |
v0.3.0 |
| Retrospective outbreak detection (scan) | surveillance |
episurv.detect.scan |
v0.5.0 |
| SIR/SEIR compartmental models | EpiModel |
episurv.models.compartmental |
v0.2.0 |
| Age-stratified contact matrices | socialmixr |
episurv.contacts |
v0.6.0 |
| R parity validation suite | — | tests/test_vs_r/ |
v0.7.0 |
Apache-2.0 — see LICENSE.