PHIDO is a statistical algorithm that determines whether a sequence of weekly case counts is unusual compared to any trends shown over the previous years. More specifically, it estimates the expected value ("expected count") for each epi-week based on counts from the previous epi-weeks from the past five years. When an expected count disagrees with the actual value ("observed count") substantially in a statistical sense, an alert is generated. Different thresholds may be set for different diseases to give rise to different alerting schemes. Note that rare diseases will always lead to an alert.
In Spring of 2024, PHIDO-App was developed to allow users to interactively analyze the PHIDO outputs and understand the alerts generated by the PHIDO algorithm, and to...
- Explore counts and alerts by geography
- Examine the trendtimes for a particular disease-region combination
- Visualize aggregated counts based on a given sex-gender-disease-region combination with a map
- Interact with the menu to explore the effects of the thresholds on the alerts
- ...
Purpose of this repo
This repo provides links to key documents and step-by-step instructions for different tasks required for maintaining the PHIDO-App.
Diseases reflected by the app
List of rare diseases
Anthrax
Botulism
Brucella Infection
Chlamydia (neonatal)
Congenital Rubella Syndrome
Creutzfeldt-Jakob Disease: Classic/Unspecified
Creutzfeldt-Jakob Disease: Variant
Crimean Congo Fever
Cyclospora Infection
Diphtheria: Carrier
Diphtheria: Case
Ebola
Gonorrhea (neonatal)
Haemophilus Influenzae (invasive type b)
Hantavirus Infection
Hepatitis B: Acute
Hepatitis D
Hepatitis E
Herpes (congenital)
Human Immunodeficiency Virus (HIV) Infection (congenital/neonatal)
Lassa Fever
Legionella Infection
Listeria Infection (invasive)
Marburg Fever
Measles
Meningococcal Disease (invasive)
Middle East Respiratory Syndrome Coronavirus (MERS-CoV)
Mpox
Plague
Poliomyelitis
Q fever
Rabies
Rubella (non-congenital)
Subacute Sclerosing Panencephalitis
Syphilis (congenital)
Tetanus
Toxoplasma Infection
Tularemia Infection
Varicella (congenital)
Viral Hemorrhagic Fever: Other
West Nile Virus
Yellow Fever
Important links
More data?
Below are links to the diseases not currently reported on the PHIDO-App:
- Weekly PDF reports report latest data on SARS-CoV-2, RSV, ERV, influenza
- Shellfish harvesting status map
- ...
Maintaining the app
- Standard Operating Procedure for use by data analysts
Details on the algorithm
Terms
- Case counts: counts of case records pulled from the Panorama system
- Types: Confirmed, confirmed Epi-Linked, Clinical, Probable (exclude suspected cases)
- Expected count: the count estimated by PHIDO algorithm using time-series of historical counts
Revision history
- v1.0, 2024-08-09
- v1.2, 2024-10-07
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. 