R/mf_lag_trend.R

In PublicHealthEngland/hcaidcs: R functions for the mandatory surveillance of bacteraemia and C. difficile infection

#' lag mf trend data
#'
#' Creates twelve month lag, three month sum, lagged by twelve months, and
#' twelve month sum, lagged by 12 months.
#'
#' @param x A data frame with columns for "cdi", "ecoli", "mrsa", "mssa",
#'   "kleb", "paer" and "ecoli_ta".
#' @return The same dataframe, but with new lagged variables added
#'
#' @export
#' @examples
#' data(mf_trend_data)
#' library(dplyr)
#' mf_trend_data <- mf_trend_data %>% mf_lag_trend()
#' head(mf_trend_data)

mf_lag_trend <- function(x = trend){
  # RcppRoll::roll_sum <- suppressWarnings(RcppRoll::roll_sum())
  x <- x %>%
    dplyr::mutate(
      dplyr::across(c(cdi, ecoli, mrsa, mssa, kleb, paer ,ecoli_ta),
                    list(lag_12 = ~dplyr::lag(., n = 12)))
    ) %>%  # compares June 2016 to June 2015
    dplyr::mutate(
      dplyr::across(
        c(cdi, ecoli, mrsa, mssa, kleb, paer, ecoli_ta),
        list(sum_3 = ~suppressWarnings(RcppRoll::roll_sum(., 3,align = "right",
                                                              fill = "NA")))
      )
    ) %>%  # sum last three months
    dplyr::mutate(
      dplyr::across(
        c(cdi_sum_3, ecoli_sum_3, mrsa_sum_3, mssa_sum_3, kleb_sum_3, paer_sum_3,
          ecoli_ta_sum_3),
        list(lag_3 = ~dplyr::lag(., 12))
      )
    ) %>% # compares summed three months with summed three months, 12 months earlier
    dplyr::mutate(
      dplyr::across(
        c(cdi, ecoli, mrsa, mssa, kleb, paer, ecoli_ta),
        list(sum_12 = ~suppressWarnings(RcppRoll::roll_sum(., 12,
                                                               align = "right",
                                                               fill = "NA")))
      )
    ) %>% # rolling 12 month sum
    dplyr::mutate(
      dplyr::across(
        c(cdi_sum_12, ecoli_sum_12, mrsa_sum_12, mssa_sum_12, kleb_sum_12,
          paer_sum_12, ecoli_ta_sum_12),
        list(lag_12 = ~dplyr::lag(., 12))
      )
    )
}