wrapper for literature/known incubation periods for other infections

[smwindecker]

Currently incubation period distributions are created by make_cdf. We want to allow for other diseases with other strains/covariants.

[smwindecker]

make_cdf / make_ecdf duplication. make_cdf should be split to a few levels of function.

base function to make distributions from empirical data
hard code distribution
from parameters for given dist.
these can all be called for ones which are prebaked from other functions.
combine two pmfs

[smwindecker]

old make_cdf which we can reference for th different variant wrappers:

#' Make cumulative density function
#'
#' @description Define cumulative density function. Used especially for
#'  calculation of incubation period. Parameters for Omicron and Delta
#'  SARS-CoV-2 strains estimated from
#'  https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2022.27.6.2200042.
#'  This is not a time-varying biological quantity - any changes in the
#'  dominant variant should be modelled separately.
#'
#' @param option SARS-CoV-2 covariant or NULL model
#'
#' @importFrom stats approxfun pweibull
#'
#' @return cumulative density function for incubation period
#' @export
make_cdf <- function (option = c('Omicron',
                                 'Delta',
                                 'None'),
                      weibull_shape = NULL,
                      weibull_scale = NULL) {

  days <- 0:28

  f <- function (option) {
    switch (option,
            Delta = stats::pweibull(days, shape = 1.83, scale = 4.93),
            Omicron = stats::pweibull(days, shape = 1.5, scale = 3.6),
            None = stats::pweibull(days,
                                   shape = weibull_shape,
                                   scale = weibull_scale))
  }


  cum_density <- f(option)
  cdf <- stats::approxfun(days, cum_density)

  return(cdf)
}