R/ag.R

In serocalculator: Estimating Infection Rates from Serological Data

# kinetics of the bacteria (ag: antigen) response
ag <- function(t, par) {
  t1 <- t1func(par)
  y0 <- par[1, ]
  b0 <- par[2, ]
  mu0 <- par[3, ]
  mu1 <- par[4, ]
  c1 <- par[5, ]
  bt <- array(0, dim = c(length(t), ncol(par)))
  for (k in 1:ncol(par)) {
    u <- (t <= t1[k])
    bt[u, k] <- b0[k] * exp(mu0[k] * t[u]) -
      c1[k] * y0[k] * (exp(mu0[k] * t[u]) - exp(mu1[k] * t[u])) /
        (mu0[k] - mu1[k])
  }
  return(bt)
}