Methods available for each module

Methods available for each module

Arguments

smoothing_method

string. Method used to smooth the original incidence data. Available options are:
deconvolution_method

string. Method used to infer timings of infection events from the original incidence data (aka deconvolution step). Available options are:
estimation_method

string. Method used to estimate reproductive number values through time from the reconstructed infection timings. Available options are:
uncertainty_summary_method

string. One of the following options:

  • 'NONE' if no summary of bootstrap estimates is required

  • 'original estimate - CI from bootstrap estimates'. The confidence interval is built using bootstrapped estimates and centered around the original estimates.

  • 'bagged mean - CI from bootstrap estimates'. The confidence interval is built using bootstrapped estimates and centered around the mean of bootstrapped estimates and original estimates.
bootstrapping_method

string. Method to perform bootstrapping of the original incidence data. Available options are: