Tycho Data - Level 1 National Incidence Rate

This repository contains data and code to reproduce national incidence rate results as in:

Panhuis, Willem G. van, John Grefenstette, Su Yon Jung, Nian Shong Chok, Anne Cross, Heather Eng, Bruce Y. Lee, et al. 2013. “Contagious Diseases in the United States from 1888 to the Present.” New England Journal of Medicine 369 (22): 2152–58. https://doi.org/10.1056/NEJMms1215400.

Infectious Disease - Data

Tycho Version 1 - Level 1

Data are downloadable from Zenodo

Version 1.0.0 of level 1 data includes counts at the state level for smallpox, polio, measles, mumps, rubella, hepatitis A, and whooping cough and at the city level for diphtheria. The time period of data varies per disease somewhere between 1916 and 2011. This version includes cases as well as incidence rates per 100,000 population based on historical population estimates. These data have been used by investigators at the University of Pittsburgh to estimate the impact of vaccination programs in the United States, published in the New England Journal of Medicine.

Raw data at the city/state level are mirrored at raw/tycho_level1/ProjectTycho_Level1_v1.0.0.csv.

Procesed data containing national rates can be found at process_data/national_incidence_rate_lvl1.csv. These ratese were calculated by adding all the state or city together per epi week and disease, and then calculating the incidence rate per 100,000 by applying: number of cases divided by the population size, multiplied by 100,000.

Additional Information

Measles

• Black, Francis L. 1959. “Measles Antibodies in the Population of New Haven, Connecticut1.” The Journal of Immunology 83 (1): 74–82. https://doi.org/10.4049/jimmunol.83.1.74.
• CDC. 2024. “Chapter 13: Measles.” Epidemiology and Prevention of Vaccine- Preventable Diseases. September 30, 2024. https://www.cdc.gov/pinkbook/hcp/table-of-contents/chapter-13-measles.html.
• CDC. 2024. “History of Measles.” Measles (Rubeola). May 20, 2024. https://www.cdc.gov/measles/about/history.html
• Collins, Selwyn D. 1929. “Age Incidence of the Common Communicable Diseases of Children: A Study of Case Rates among All Children and among Children Not Previously Attacked and of Death Rates and the Estimated Case Fatality.” Public Health Reports (1896-1970) 44 (14): 763–826. https://doi.org/10.2307/4579202.
• LANGMUIR, ALEXANDER D. 1962. “Medical Importance of Measles.” American Journal of Diseases of Children 103 (3): 224–26. https://doi.org/10.1001/archpedi.1962.02080020236005

Polio

• CDC. 2024. “Chapter 18: Poliomyelitis.” Epidemiology and Prevention of Vaccine-Preventable Diseases. September 30, 2024. https://www.cdc.gov/pinkbook/hcp/table-of-contents/chapter-18-poliomyelitis.html.

Census

Total population estimates per states and at national level per year from census.gov

• Data from 1910 to 1990
• Data from 1990 to 2000
• Data from 2000 to 2010
• Data from 2010 to 2020

Age Group

Additional age group information is available at national (and state, for specific years) level on the census.gov website:

• Data from 1900 to 1979
• Data from 1980 to 1990
• Data from 1990 to 2000
• Data from 2000 to 2010
• Data from 2010 to 2020

Data Processing Pipeline

Scripts in the src directory pull data from Zenodo and census and prepare data for processing. These data are also mirrored in the raw directory.

Output

Data

The output of the data processing pipeline is available in the process_data directory.

The directory contains 4 files:

• census.csv: population size per year and location (state, national) since 1900 to 2023.
• national_incidence_rate_lvl1.csv: case count ("value") and incidence rate per 100,000 ("incidence_rate") per disease and per week ("date"). For each disease, the vaccine introduction year (extracted from the NEJM article) is available and set to the first day of the year for visualization purposes ("vaccine")
• vaccine_year_introduction.csv: year of the vaccine introduction for each disease of interest (extracted from the NEJM article).
• sysdata.rda: internal location dictionary to help with standardizing location name in between different sources.

Visualization

The Visualization folder contains multiple outputs files and code in a quarto file to generate them. All the quarto files have at least one output format, to generate all the available formats, please use the quarto::quarto_render() function.

For example:

quarto::quarto_render("visualization/nat_incidence_level1.qmd", 
                      output_format = "all")