Calculate Serial Interval Probability Matrix — calculate_si_probability

Computes a matrix of transmission probabilities between all pairs of cases based on their time differences and the specified serial interval distribution. Only considers epidemiologically plausible transmission pairs (earlier to later cases).

Usage

calculate_si_probability_matrix(day_diffs, si_mean, si_sd, si_dist)

Arguments

day_diffs: numeric matrix; matrix of day differences between each pair of cases, where element [i,j] represents days between case i and case j
si_mean: numeric; mean of the serial interval distribution in days
si_sd: numeric; standard deviation of the serial interval distribution in days
si_dist: character; distribution type, either "gamma" or "normal"

Value

numeric matrix; matrix of transmission probabilities where element [i,j] represents the probability that case j infected case i based on their time difference and the serial interval distribution

Examples

# Create sample day differences matrix
dates <- as.Date(c("2023-01-01", "2023-01-03", "2023-01-05"))
day_diffs <- create_day_diff_matrix(dates)

# Calculate probability matrix
prob_matrix <- calculate_si_probability_matrix(day_diffs, si_mean = 7, si_sd = 3, si_dist = "gamma")