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README.md

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Use this directory to erform the model inference (using the code in the Inference subdirectory). Specifically, estimate the rate of waning of heterosubtypic protection by constructing a likelihood profile. Please refer to the Introductory page for a step-by-step overview of the manuscript analysis. Briefly, the overview of the inference is as follows:

  1. Execute the make_host_data_list.R script to generate a list of host data objects

  2. Convert the host data list from step 1 to a POMP object using the data_to_pomp_object_structure.R file.

  3. Fixing the subtype-specific parameters from the single-strain models for H1N1pdm09 and H3N2, execute the experiment_profile_w_hetero.R to generate the likelihood profile for the rate of waning of heterosubtypic immunity.