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improve handling of seeding time in simulate_infections() #627

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Merged
merged 9 commits into from
Mar 28, 2024
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improve handling of seeding time in simulate_infections() #627

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c71fb78
add `seeding_time` arg to `simulate_inections()`
sbfnk Mar 25, 2024
5aa839f
adjust initial infections to exp growth
sbfnk Mar 25, 2024
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add news item
sbfnk Mar 25, 2024
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update snapshot
sbfnk Mar 25, 2024
ead3e9a
update other snapshot
sbfnk Mar 26, 2024
c9e709d
test seeding time setting
sbfnk Mar 26, 2024
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sbfnk Mar 26, 2024
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sbfnk Mar 27, 2024
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sbfnk Mar 27, 2024
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adjust initial infections to exp growth
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@sbfnk
sbfnk committed Mar 27, 2024
commit 5aa839fc8f1e729214c1d19f774bc248030e9cbe
11 changes: 9 additions & 2 deletions R/simulate_infections.R
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,10 @@
#' `date`). Column `R` must be numeric and `date` must be in date format. If
#' not all days between the first and last day in the `date` are present,
#' it will be assumed that R stays the same until the next given date.
#' @param initial_infections numeric; the initial number of infections.
#' @param initial_infections numeric; the initial number of infections (i.e.
#' before `R` applies). Note that results returned start the day after, i.e.
#' the initial number of infections is not reported again. See also
#' `seeding_time`
#' @param day_of_week_effect either `NULL` (no day of the week effect) or a
#' numerical vector of length specified in [obs_opts()] as `week_length`
#' (default: 7) if `week_effect` is set to TRUE. Each element of the vector
Expand Down Expand Up @@ -115,16 +118,20 @@ simulate_infections <- function(estimates, R, initial_infections,
## estimate initial growth from initial reproduction number if seeding time
## is greater than 1
initial_growth <- (R$R[1] - 1) / mean(generation_time)
## adjust initial infections for initial exponential growth
log_initial_infections <- log(initial_infections) -
(seeding_time - 1) * initial_growth
} else {
initial_growth <- numeric(0)
log_initial_infections <- log(initial_infections)
}

data <- list(
n = 1,
t = nrow(R) + seeding_time,
seeding_time = seeding_time,
future_time = 0,
initial_infections = array(log(initial_infections), dim = c(1, 1)),
initial_infections = array(log_initial_infections, dim = c(1, 1)),
initial_growth = array(initial_growth, dim = c(1, length(initial_growth))),
R = array(R$R, dim = c(1, nrow(R))),
pop = pop
Expand Down
5 changes: 4 additions & 1 deletion man/simulate_infections.Rd
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