Estimating the number of children at risk for measles in North Carolina. Note that elementary schools are generally between kindergarten and 5th grade (6 total grades).
Data from NCDHHS were downloaded for each year from the following url
Data were then aggregated and manually cleaned to ensure that school names year over year were consistent.
Note that there were some changes in naming convention (e.g., Elem vs Elementary), but these were addressed manually and programatically in the
data-raw/vaccinations.R script.
Rurality/non-rural designations were retrieved and saved in the data-raw/designations-county.xlsx file.
The outbreak model was created and turned into an R package called measlesrisk (located in this directory as well).
We ran the model over each county and elementary school with sufficient data as shown in the src/seir.R script.
The data were run using the HPC with 20 cores and a limit of 14 hours.
Estimates were saved in the data directory
Outputs were summarized into figures using the src/results-figures.R scripts.
All outputs are available in either the data folder or the figures directory.
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