R/fortify-aggregate.R

In skgallagher/timeternR: A Pipeline to Analyze and Compare Infectious Disease Epidemics

## March 3, 2020
# Comments for Ben and Shannon
#
# This is the start of a reformat of fortify_epimodel and fortify_pomp into one
# function "fortify_aggregate".  This will take in aggregate level data from
# external sources (currently pomp and epimodel) and output, if possible,
# output a data.frame  with the columns t, X0, .., XK where Xk are the state
# names and the values in Xk are the numbers in state k at time t.



#'  Take external aggregate data and put it in a format used in this package
#'
#' @param data output from external source package.  See details
#' @param states names of states we want aggregate totals of at each time
#' @param package_source optional argument to include the package from which the
#'   output is derived from, which helps with the fortify function when outputs
#'   are of generic classes such as list or data.frame
#' @return a data frame with the following columns
#' \describe{
#' \item{t}{time}
#' \item{Xk}{columns X0, ..., X_K. which are numeric}
#' }
#' @details This function converts external data sources (we currently support
#'   output from the EpiModel and pomp R packages), which is already aggregated
#'   and puts it in a format that can be used by our exploring functions.
#' @export
#' @examples
#'    ## ICM
#'    out <- fortify_aggregate(EpiModel_icm)
#'    ## DCM
#'    out3 <- fortify_aggregate(EpiModel_det)
#'    ## POMP (POMP_LIST)
#'    out <- fortify_aggregate(pomp_pomp, states = NULL)
#'    ##
#'    out <- fortify_aggregate(pomp_pomp, states = c("S", "I", "R"))
#'    out <- fortify_aggregate(pomp_df, package_source = "pomp")
fortify_aggregate <- function(data,
                              states = NULL,
                              package_source = NULL){

    UseMethod("fortify_aggregate")
}