R/lf.demean.R

In HaikunXu/RegressionTree: IATTC's regression tree R package for analyzing size frequency data

#' Aggregate length counts data
#'
#' \code{lf.demean} aggregates counts data by year, quarter, lat, lon, and user-sepcified length bins
#'
#' @param LF The length frequency data frame input; must include four columns: lat, lon, year, and quarter
#' @param fcol The first column in the data frame with length frequency info
#' @param lcol The last column in the data frame with length frequency info
#' @param bins Names of all bins included in LF
#'
#' @export

lf.demean <- function(LF,fcol,lcol,bins) {
  # check data first
  if ((lcol - fcol + 1) != length(bins))
    stop("Error! The number of bins does not match the number of LF columns specified")
  else
    names(LF)[fcol:lcol] <- bins

  if (is.null(LF[["ID"]]) == TRUE) {
      LF$ID <- seq(1, nrow(LF))
      fcol = fcol + 1 # add a ID column
      lcol = lcol + 1 # add a ID column
  }

  LF_select <-
    LF[, c("ID", "year", "quarter", "lat", "lon", paste0(bins))]
  LF_long <-
    data.frame(tidyr::gather(LF_select, fcol:lcol, key = "Length", value = "LF"))
  LF_long <- dplyr::mutate(LF_long, Length = as.numeric(Length))

  LF_mean <-
    dplyr::mutate(dplyr::group_by(LF_long, year, quarter, Length),
                  LF_mean = sum(LF))
  LF_mean$LF_demean <-
    ifelse(LF_mean$LF_mean == 0, 0, LF_mean$LF / LF_mean$LF_mean)

  LF_mean_scale <-
    dplyr::mutate(dplyr::group_by(LF_mean, ID),
                  LF_demean = LF_demean / sum(LF_demean))

  LF_demean <-
    tidyr::spread(
      dplyr::select(LF_mean_scale, ID, year, quarter, lat, lon, Length, LF_demean),
      Length,
      LF_demean,
      fill = 0
    )

  return(LF_demean)
}