Calibrate a mixing model to a target reproduction number — calibrate_mixing

Uses the epiworldR::compute_reproduction_number() function to optimize the scaling factor of the contact matrix to match a target reproduction number.

Usage

calibrate_mixing_model(
  contact_matrix,
  target_rep_number,
  infectious_period_days,
  transmission_prob,
  ...
)

Arguments

contact_matrix: A contact matrix to be calibrated.
target_rep_number: The target reproduction number to calibrate to.
infectious_period_days: The average number of days an individual is infectious.
transmission_prob: The probability of transmission per contact.
...: Additional arguments to pass to stats::optimize().

Value

The scaling factor for the contact matrix that achieves the target reproduction number.

Examples

data(short_creek_matrix, package = "measles")

# Calibrating for a measles model with R0 of 10
# assuming agents are infectious during prodomal stage
# (isolated during rash stage)
calibrate_mixing_model(
  contact_matrix = short_creek_matrix,
  target_rep_number = 10,
  infectious_period_days = 4,
  transmission_prob = 0.2
)
#> [1] 0.4608991

# You can then use the scaling factor in a mixing
# model. Instead of using the original contact matrix,
# you would use:
#   contact_matrix * scaling_factor