R/prep_curve_params_for_array.R

In serocalculator: Estimating Infection Rates from Serological Data

# note: this function outputs "value" on the log scale;
# this gets undone in `par.pred.n()`
prep_curve_params_for_array <- function(data) {
  data %>%
    mutate(y1 = .data$y1 - .data$y0) %>%
    mutate(d = .data$r - 1) %>% # DM: issue here?
    tidyr::pivot_longer(
      names_to = "parameter",
      cols = c("y0", "y1", "t1", "alpha", "d")
    ) %>%
    mutate(
      parameter =
        .data$parameter %>%
          factor(
            levels = c("y0", "y1", "t1", "alpha", "d")
          )
    ) %>%
    select(-any_of(c("Country", "ageCat"))) %>%
    mutate(value = log(.data$value)) %>%
    droplevels()
}