Apply a time-varying probability and delay function to linelist data

Usage

sim_delay(
  df = i_sim_linelist,
  p_fn,
  delay_fn,
  input = "time",
  output = "event",
  seed = Sys.time()
)

Arguments

df

a line list dataframe arising from e.g. sim_branching_process() - a dataframe with columns:

id (unique_id) - Patient level unique id
time (ggoutbreak::time_period) - Time of infection. A `time_period`

Any grouping allowed.

p_fn

Function that returns a probability between 0 and 1 for each row of the input dataframe. A purrr style lambda is OK (e.g. ~ 1 for always true) the first parameter of this will be time of infection. The function must be vectorised on its inputs (and consume additional inputs with ...)

delay_fn

A function that calculates the time to event onset from the input time. This will be called with a vector of infection times as the first parameter (time) but all other columns of df are also available as well as the symptomatic,died,and admitted flags. The function must be vectorised on its inputs (and consume additional inputs with ...). A purrr style lambda is OK e.g. ~ stats::rgamma(.x, shape = 3), and the first parameter will be infection time. if you have an discrete probability profile for this then you can use cfg_ip_sampler_rng(ip_symptoms) without the tilde.

input

a time column from which to calculate the delay from.

output

an output column set name (defaults to "event")

seed

RNG seed for reproducibility

Value

the line list with extra columns with prefix given by output, specifying whether the event was observed, the delay and the simulation time.

Examples


tmp = sim_branching_process(
  changes = dplyr::tibble(t = c(0,20,40,60,80,110), R = c(1.8,1.5,0.9,1.5,0.8,1.2)),
  max_time = 120,
  seed = 100
)
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tmp2 = tmp %>% sim_delay(
  p_fn = ~ rbern(.x, 0.8),
  delay_fn = ~ rgamma2(.x, mean = 5),
)
tmp2 %>% dplyr::glimpse()
#> Rows: 37,440
#> Columns: 8
#> $ time                <time_prd> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
#> $ id                  <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,…
#> $ generation_interval <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
#> $ infector            <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
#> $ generation          <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,…
#> $ event               <lgl> FALSE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, …
#> $ event_delay         <dbl> NA, 5.561777, 6.467923, 2.460097, NA, 5.893525, 2.…
#> $ event_time          <time_prd> NA, 5.561777, 6.467923, 2.460097, NA, 5.89352…