R/flux_gep.R

In fluxible: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup

#' Calculates GEP
#' @description
#' `r lifecycle::badge("deprecated")`
#'
#' `flux_gep` was renamed `flux_gpp` out of consistancy with the litterature.
#'
#' Calculate gross ecosystem production (GEP) from net ecosystem
#' (NEE) exchange and ecosystem respiration (ER) as GEP = NEE - ER.
#' Datetime and other variables to keep will be taken from the NEE measurement.
#' Fluxes presents in the dataset that are neither NEE nor ER
#' (soilR, LRC or other) are not lost.
#' @param fluxes_df a dataframe containing NEE and ER
#' @param id_cols columns used to identify each pair of ER and NEE
#' @param f_flux column containing flux values
#' @param type_col column containing type of flux (NEE or ER)
#' @param f_datetime column containing start of measurement as datetime
#' @param nee_arg argument designating NEE fluxes in type column
#' @param er_arg argument designating ER fluxes in type column
#' @param cols_keep columns to keep from `fluxes_df`. Values from NEE row will
#' be filled in GEP row. `none` (default) keeps only the columns in `id_cols`,
#' flux, type and datetime columns; `all` keeps all the columns;
#' can also be a vector of column names.
#' @return a dataframe with $GEP = NEE - ER$ in long format with GEP, NEE, and
#' ER as flux type, datetime, and any column specified in `cols_keep`.
#' Values of datetime and columns in `cols_keep` for GEP row are taken from
#' NEE measurements.
#' @importFrom dplyr rename select mutate case_when filter full_join
#' cur_group_id bind_rows
#' @importFrom tidyr pivot_wider fill
#' @importFrom purrrlyr slice_rows unslice
#' @importFrom lifecycle deprecate_warn
#' @examples
#' data(co2_fluxes)
#' flux_gep(co2_fluxes, type, f_start, id_cols = "turfID",
#' cols_keep = c("temp_soil"))
#' @export

flux_gep <- function(fluxes_df,
                     type_col,
                     f_datetime,
                     f_flux = f_flux,
                     id_cols,
                     nee_arg = "NEE",
                     er_arg = "ER",
                     cols_keep = "none") {

  deprecate_warn("1.1.1", "flux_gep()", "flux_gpp()")
  flux_gpp(
    fluxes_df = fluxes_df,
    type_col = {{type_col}},
    f_datetime = {{f_datetime}},
    f_flux = {{f_flux}},
    id_cols = id_cols,
    nee_arg = nee_arg,
    er_arg = er_arg,
    cols_keep = cols_keep
  )
}