adjust_infection_to_report {EpiNow2} | R Documentation |
Adjust from Case Counts by Infection Date to Date of Report
Description
Maps from cases by date of infection to date of report via date of onset.
Usage
adjust_infection_to_report(
infections,
delay_defs,
reporting_model,
reporting_effect,
type = "sample",
truncate_future = TRUE
)
Arguments
infections |
|
delay_defs |
A list of single row data.tables that each defines a
delay distribution (model, parameters and maximum delay for each model).
See |
reporting_model |
A function that takes a single numeric vector as an argument and returns a single numeric vector. Can be used to apply stochastic reporting effects. See the examples for details. |
reporting_effect |
A numeric vector of length 7 that allows the scaling of reported cases by the day on which they report (1 = Monday, 7 = Sunday). By default no scaling occurs. |
type |
Character string indicating the method to use to transform counts. Supports either "sample" which approximates sampling or "median" would shift by the median of the distribution. |
truncate_future |
Logical, should cases be truncated if they occur
after the first date reported in the data. Defaults to |
Value
A data.table
containing a date
variable (date of report) and a
cases
variable. If return_onset = TRUE
there will be a third variable
reference
which indicates what the date variable refers to.
Author(s)
Sam Abbott
Examples
# define example cases
cases <- data.table::copy(example_confirmed)[, cases := as.integer(confirm)]
# define a single report delay distribution
delay_def <- lognorm_dist_def(
mean = 5, mean_sd = 1, sd = 3, sd_sd = 1,
max_value = 30, samples = 1, to_log = TRUE
)
# define a single incubation period
incubation_def <- lognorm_dist_def(
mean = incubation_periods[1, ]$mean,
mean_sd = incubation_periods[1, ]$mean_sd,
sd = incubation_periods[1, ]$sd,
sd_sd = incubation_periods[1, ]$sd_sd,
max_value = 30, samples = 1
)
# simple mapping
report <- adjust_infection_to_report(
cases, delay_defs = list(incubation_def, delay_def)
)
print(report)
# mapping with a weekly reporting effect
report_weekly <- adjust_infection_to_report(
cases,
delay_defs = list(incubation_def, delay_def),
reporting_effect = c(1.1, rep(1, 4), 0.95, 0.95)
)
print(report_weekly)
# map using a deterministic median shift for both delays
report_median <- adjust_infection_to_report(cases,
delay_defs = list(incubation_def, delay_def),
type = "median"
)
print(report_median)
# map with a weekly reporting effect and stochastic reporting model
report_stochastic <- adjust_infection_to_report(
cases,
delay_defs = list(incubation_def, delay_def),
reporting_effect = c(1.1, rep(1, 4), 0.95, 0.95),
reporting_model = function(n) {
out <- suppressWarnings(rnbinom(length(n), as.integer(n), 0.5))
out <- ifelse(is.na(out), 0, out)
}
)
print(report_stochastic)