R/get_obs_bysite_gpp_gepisat.R

In stineb/ingestr: Environmental point data ingest

#' The GePiSaT method flux decomposition.
#'
#' Function for reading observational GPP data from GePiSaT (Tyler's 
#' alternative flux decomposition) for FLUXNET 2015 stations.
#'
#' @param sitename A character string specifying the site name for which FLUXNET
#'  2015 data is searched (based on the site name appearing as part of the
#'  respective file name). Defaults to NA.
#' @param path_gepisat A character string specifying the local path of 
#'  FLUXNET 2015 data.
#' @param timescale A character specifying the time scale of FLUXNET 2015 data.
#'  Only available: \code{c("d")} for daily.
#'
#' @return A data frame (tibble) containint observational data.
#' @export
#'
#' @examples 
#' \dontrun{
#' df <- get_obs_bysite_gpp_gepisat
#' }
 
get_obs_bysite_gpp_gepisat <- function(
  sitename,
  path_gepisat,
  timescale = "d"
  ) {

  # define variables
  GPP_mol.m2 <- GPP_err_mol.m2 <- gpp_obs <- cols <- 
    ymd <- Timestamp <- NULL
    
# Take only file for this site
  if (timescale == "d") {

  # Daily
    filn <- list.files( path_gepisat, 
      pattern = paste0( sitename, ".*_daily_GPP.txt" ), 
      recursive = TRUE 
      )

  } else {

    warning("Aborting. GePiSaT data only available for daily time step.")

  }

  if (length(filn) > 0) {

  # This returns a data frame with columns 
  # (date, temp, prec, nrad, ppfd, vpd, ccov)
    df <- get_obs_gepisat_raw( 
      sitename = sitename, 
      path = paste0(path_gepisat, filn), 
      freq = timescale 
      ) %>%
      
    # Convert units
    # given in molCO2 m-2 d-1, converted to gC m-2 d-1
      mutate_at( vars(starts_with("GPP_")), funs(convert_gpp_gepisat) ) %>%
      
    # rename so that it is like in FLUXNET 2015
      rename( gpp_obs = GPP_mol.m2, gpp_err_obs = GPP_err_mol.m2 ) %>%
      
    # some are NaN
      mutate( gpp_obs = ifelse( is.nan(gpp_obs), NA, gpp_obs ) )
  
  } else {
    df <- NULL
  }
  
  return(df)
}


get_obs_gepisat_raw <- function(
  sitename,
  path,
  freq = "d"
) {
  

# Function returns a dataframe containing all the data of the GePiSaT
# data file of respective temporal resolution.
# Returns data in units given in the fluxnet 2015 dataset

  
  # define variables
  cols <- ymd <- Timestamp <- NULL
  
# get data
  df <-  readr::read_csv( path, na = "-9999", col_types = cols() )

# get dates, their format differs slightly between temporal resolution
  if ( freq == "d" ){

    df <- df %>%
      mutate( Timestamp = ymd( Timestamp ) ) %>%
      rename( date = Timestamp )

  } else {
    warning("get_obs_gepisat_raw() implemented only for daily time step.")
  }

  return( df )
}

# Converts units of GPP variables from GePiSaT to SOFUN standard
# in GePiSaT given in molCO2 m-2 d-1, converted to gC m-2 d-1

convert_gpp_gepisat <- function( gpp ){
  c_molmass <- 12.0107  # molar mass of C
  gpp_coverted <- gpp * c_molmass
  return(gpp_coverted)
}