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Calculate the total infectiousness at each observed time point.

Source: R/delay_calculator.R
delay_calculator.Rd

The total infectiousness at each observed time point is calculated by \(\sum_{s=1}^t I_{t-s}w_s\), where \(I\) denotes the vector containing observed incidence, and \(w\) denotes the generation interval distribution. Typically, the generation interval is challenging to estimate from data, so the serial interval is used instead. The serial interval distribution expresses the probability of a secondary infection caused by a primary infection which occurred \(s\) days earlier.

Usage

delay_calculator(
  observed_counts,
  x = NULL,
  dist_gamma = c(2.5, 2.5),
  delay_distn = NULL,
  delay_distn_periodicity = NULL,
  xout = x
)

Arguments

observed_counts

vector of the observed daily infection counts

x

a vector of positions at which the counts have been observed. In an ideal case, we would observe data at regular intervals (e.g. daily or weekly) but this may not always be the case. May be numeric or Date.

dist_gamma

Vector of length 2. These are the shape and scale for the assumed serial interval distribution. Roughly, this distribution describes the probability of an infectious individual infecting someone else after some period of time after having become infectious. As in most literature, we assume that this interval follows a gamma distribution with some shape and scale.

delay_distn

in the case of a non-gamma delay distribution, a vector or matrix (or Matrix::Matrix()) of delay probabilities may be passed here. For a vector, these will be coerced to sum to 1, and padded with 0 in the right tail if necessary. If a time-varying delay matrix, it must be lower-triangular. Each row will be silently coerced to sum to 1. See also vignette("delay-distributions").

delay_distn_periodicity

Controls the relationship between the spacing of the computed delay distribution and the spacing of x. In the default case, x would be regular on the sequence 1:length(observed_cases), and this would be 1. But if x is a Date object or spaced irregularly, the relationship becomes more complicated. For example, weekly data when x is a date in the form YYYY-MM-DD requires specifying delay_distn_periodicity = "1 week". Or if observed_cases were reported on Monday, Wednesday, and Friday, then delay_distn_periodicity = "1 day" would be most appropriate.

xout

a vector of positions at which the results should be returned. By default, this will be the same as x, but in the case that observations are unequally spaced, alternatives may be desired. Note that xout must satisfy min(x) <= min(xout) and max(x) >= max(xout).

Value

A vector containing the total infectiousness at each point xout.

Examples

delay_calculator(c(3, 2, 5, 3, 1), dist_gamma = c(2.5, 2.5))
#> [1] 0.000000 3.000000 2.767428 2.856849 3.126332