R/fortify-aggregate-data-frame.R

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

#' Takes in data from the R pomp package where the output is a data frame and
#' puts it in SIR format for EpiCompare
#'
#' @param data Output from a pomp simulation where the output is a data frame,
#'   \code{pomp::simulate()}
#' @param states vector of state names
#' @param package_source optional package name
#' @details The default variables that are retained are SIR, but can be modified
#'   with the \code{states} argument.  If code{states = NULL}, we will attempt
#'   to find all single letter names in POMP and output those.
#' @return data frame with the following columns
#' \describe{
#' \item{t}{the time}
#' \item{sim}{simulation number (factor variable) (optional column)}
#' \item{Xk}{where k = 0, ..., K}
#' }
#' @export
fortify_aggregate.data.frame <- function(data,
                                           states = NULL,
                                           package_source = NULL){

    if(!is.null(package_source) && package_source == "pomp"){
        out <- fortify_aggregate.pomp_df_inner(data, states = dplyr::enquo(states))
        return(out)
    }
    stop(paste("We currently do not support fortifying an object of class",
               "'data.frame' if 'package_source' is not 'pomp'"))

}