R/cummulative_rate.R

In alrobles/PNASSubmit-Wildlife-susceptibility-to-infectious-diseases-at-global-scales: Set of tools for ecological interaction geospatial analysis

#' cummulative_rate
#' @importFrom dplyr mutate lag
#' @importFrom rlang enquo :=
#' @param data A \code{data.frame} object with interaction information
#' @param id Row id of incidence
#' @param incidence The incidence of interaction in the data \code{data.frame}
#' @param cummulativesum cummulative counted incidences
#' @param accuracy of the derivate of the rate
#' @return A \code{data.frame} with the rate of change from fractional cuumlative incidence
#' and the first and second derivates of the rate
#' @export
#'
#' @examples
#' library(ecointeraction)
#' data <-  acummulate_incidence(mammalvirus, mammal_species, incidence)
#' cumrateData <- cummulative_rate(data, id, incidence, cummulativesum)
cummulative_rate <- function(data, id = id, incidence = incidence, cummulativesum = cummulativesum, accuracy = 4){
  id <- rlang::enquo(id)
  incidence <- rlang::enquo(incidence)
  cummulativesum <- rlang::enquo(cummulativesum)
  cummulativesum_frac <- "cummulativesum_frac"
  rate <- "rate"
  id_fraction <- "id_fraction"
  ratediff <- "ratediff"
  ratediffdiff <- "ratediffdiff"

  data %>%
    dplyr::mutate(!! cummulativesum_frac := !! cummulativesum/sum(!! incidence)) %>%
    dplyr::mutate(!! id_fraction := !! id/max(!! id) ) %>%
    dplyr::mutate(!! rate := id_fraction/cummulativesum_frac ) %>%
    dplyr::mutate(!! ratediff := log(rate - dplyr::lag(rate)))  %>%
    dplyr::mutate(!! ratediffdiff := round( round(ratediff - dplyr::lag(ratediff), 3)^2, accuracy ))
}