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C++ code for inferring the time of infection from serological data, as presented in the Handbook for Infectious Disease Data Analysis Chapter 17 (2019 Edition)
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README.md

2019-HIDDA-Time-Of-Infection

[[ WORK IN PROGRESS ]]

C++ code for inferring the time of infection from serological data, as presented in

Inferring the time of infection from serological data. Boni MF, Mølbak K, Krogfelt KA. In L. Held, N. Hens, P O'Neill, J. Wallinga, editors, Handbook of Infectious Disease Data Analysis, 2019.

STEP 1:

Compile the code and run

./mlesearch_and_profile

from the command line. This will give you the MLE estimates for the slope (antibody waning rate) as well as the estimates of mean and variance of peak antibody titer. Note, that the search is not inferring the time of infection at this moment.

If you run

./mlesearch_and_profile -profile

the slope parameter will be profiled and a confidence interval will be reported.

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