empirical_incubation_dist.RdThis function takes in a linelist data frame and extracts the empirical incubation period distribution and can take into account uncertain dates of exposure.
empirical_incubation_dist(x, date_of_onset, exposure, exposure_end = NULL)
| x | the linelist data (data.frame or linelist object) containing at least a column containing the exposure dates and one containing the onset dates. |
|---|---|
| date_of_onset | the name of the column containing the onset dates (bare variable name or in quotes) |
| exposure | the name of the column containing the exposure dates (bare variable name or in quotes) |
| exposure_end | the name of a column containing dates representing the end of the exposure period. This is `NULL` by default, indicating all exposures are known and in the `exposure` column. |
a data frame containing a column with the different incubation periods and a column containing their relative frequency
For exposure dates, each element can be a vector containing several possible exposure dates. Note that if the same exposure date appears twice in the list it is given twice as much weight.
x <- linelist::clean_data(linelist::messy_data()) # Linelist with a list column of potential exposure dates ------------------ mkexposures <- function(x) x - round(rgamma(sample.int(5, size = 1), shape = 12, rate = 3)) exposures <- sapply(x$date_of_onset, mkexposures) x$dates_exposure <- exposures incubation_period_dist <- empirical_incubation_dist(x, date_of_onset, dates_exposure) incubation_period_dist#> # A tibble: 8 x 2 #> incubation_period relative_frequency #> <dbl> <dbl> #> 1 0 0 #> 2 1 0.0125 #> 3 2 0.0867 #> 4 3 0.207 #> 5 4 0.393 #> 6 5 0.231 #> 7 6 0.045 #> 8 7 0.025# Linelist with exposure range --------------------------------------------- start_exposure <- round(rgamma(nrow(x), shape = 12, rate = 3)) end_exposure <- round(rgamma(nrow(x), shape = 12, rate = 7)) x$exposure_end <- x$date_of_onset - end_exposure x$exposure_start <- x$exposure_end - start_exposure incubation_period_dist <- empirical_incubation_dist(x, date_of_onset, exposure_start, exposure_end)