Contact likelihood affected by contact directionality

[CyGei]

Description:

The contact likelihood function does not consider directed contacts (link to code & article) despite the outbreaker_config() function allowing specification of whether contacts are directed. If the user specifies that ctd_directed = TRUE in outbreaker_config(), the resulting contact matrix will not be pairwise.

Proposed Solution:

Simplify the internal handling of the contact matrix to always make it pairwise, regardless of user input. Alternatively, remove the option for directed contacts.

Illustration Code:

n = 10
ids = LETTERS[1:n]
i = LETTERS[1:(n / 2)]
j = LETTERS[(n / 2 + 1):n]
ctd_dup <- data.frame("i" = c(i, j), "j" = c(j, i))
ctd <- data.frame("i" = i, "j" = j)

data <- lapply(list(ctd_dup = ctd_dup, ctd = ctd), function(x) {
  data <- outbreaker_data(
    ids = ids,
    dates = sample(1:40, n, replace = TRUE),
    ctd = x,
    w_dens = fake_outbreak$w
  )
  data$contacts
})
data
all.equal(data$ctd, data$ctd_dup)

#/// from internals.R line 291
make_ctd_pairwise <- function(contacts) {
  contacts[] <- as.integer(contacts == 1 | t(contacts) == 1)
  return(contacts)
}
all.equal(make_ctd_pairwise(data$ctd), make_ctd_pairwise(data$ctd_dup))

[finlaycampbell]

Hi Cy! Thanks for raising the issue :)

It's true that the original paper states we use only non-directed contacts, but we made a later addition to the package itself to accommodate directed contacts too. As far as I can tell, when ctd_directed=TRUE and the matrix is not symmetrical, cpp_ll_contact will only count a "true positive" (i.e. a transmission pair aligns with a reported contact) if the directionality is also aligned (i.e. A contacted B and A infected B). The likelihood code refers to a pairwise matrix but by that I don't mean symmetrical, I just mean it contains information on all infector-infectee pairs.

Not sure if that makes sense, let me know. It shouldn't be too difficult to run some tests to check whether the implementation actually works, I am on leave for all of August though and so don't have capacity to do that now.