flexible antibody titre output

[slwu89]

Needs:

• population-level protection from infection, and subsequently R_effective (i.e. reproduction number with impact of vaccine- and infection-acquired immunity) at each day

Requirements:

• output antibody titre stratified by infection/vaccine/age status.

[slwu89]

One way to do it is this. Because the number of rows will vary as more people become infected/vaccinated this doesn't sit well with the standard Render method of generating output.

nat_inf <- list('age' = NULL, 'inf' = NULL, 'NAT' = NULL)
nat_vaxx <- list('age' = NULL, 'vaccine' = NULL, 'NAT' = NULL)

for (i in seq_len(length.out = parameters$N_age)) {

  # age/infection
  bset_i <- variables$discrete_age$get_index_of(set = i)
  inf_i <- variables$inf_num$get_values(index = bset_i)
  ab_i <- exp(variables$ab_titre$get_values(index = bset_i))
  nat_i <- vapply(X = unique(inf_i), FUN = function(inf) {
    mean(ab_i[which(inf_i == inf)])
  }, FUN.VALUE = numeric(1), USE.NAMES = FALSE)
  nat_inf$inf <- c(nat_inf$inf, unique(inf_i))
  nat_inf$age <- c(nat_inf$age, rep(i, times = length(nat_i)))
  nat_inf$NAT <- c(nat_inf$NAT, nat_i)

  # age/vaccine
  vaxx_i <- variables$dose_num$get_values(index = bset_i)
  nat_i <- vapply(X = unique(vaxx_i), FUN = function(vaxx) {
    mean(ab_i[which(vaxx_i == vaxx)])
  }, FUN.VALUE = numeric(1), USE.NAMES = FALSE)

  nat_vaxx$vaccine <- c(nat_vaxx$vaccine, unique(vaxx_i))
  nat_vaxx$age <- c(nat_vaxx$age, rep(i, times = length(nat_i)))
  nat_vaxx$NAT <- c(nat_vaxx$NAT, nat_i)
}

nat_inf <- do.call(cbind, nat_inf)
nat_vaxx <- do.call(cbind, nat_vaxx)