R/as_tibble_nc.R

In stineb/rbeni: Useful R functions for Beni.

#' Convert NetCDF contents to a data frame.
#'
#' Converts the output of \code{"read_nc_onefile()"} into a data frame (tibble)
#'
#' @param out An object returned by the function \link{read_nc_onefile}.
#' @return A tidy data frame with a row for each gridcell. Contains columns
#' \code{"lon"} (longitude), \code{"lat"} (latitude), and \code{"data"}
#' (containing all time steps' data for each gridcell.)
#' @export
#'
as_tibble_nc <- function(out){

  require(dplyr)
  require(tidyr)

  filn <- "/alphadata01/bstocker/sofun/output_nc_global/s1_fapar3g_v3_global.1983.d.wbal.nc"

  ## read nc file
  out <- read_nc_onefile(filn)
  varnams <- out[["varnams"]]

  if (length(out$lat)>1 && length(out$lat)>1){

    ## Output on a spatial grid
    df <- expand.grid(out$lon, out$lat) %>%
      as.matrix() %>%
      as_tibble() %>%
      setNames(c("lon", "lat"))

    ## Read only first time step of first variable to get a land mask
    ## get all data as columns in a data frame
    df_data <- purrr::map_dfc(as.list(varnams[1]), ~as_tibble_byvar_slice1(., out)) %>%
      setNames(varnams)

  } else {

    ## expand lon-lat-time grid -> produces flat data frame
    df <- expand.grid(out$lon, out$lat, out$time) %>%
      as.matrix() %>%
      as_tibble() %>%
      setNames(c("lon", "lat", "time"))

    ## get all data as columns in a data frame
    df_data <- purrr::map_dfc(as.list(varnams), ~as_tibble_byvar(., out)) %>%
      setNames(varnams)
  }

  ## combine lon, lat, time, and data columns
  df <- df %>%
    bind_cols(df_data) %>%
    tidyr::drop_na()

  ## nest time
  df <- df %>%
    dplyr::group_by(lon, lat) %>%
    tidyr::nest()


  return(df)
}

as_tibble_byvar <- function(varnam, out){
  data <- out$vars[[varnam]] %>% as.vector()
  df <- tibble( varnam = data )
  return(df)
}

as_tibble_byvar_slice1 <- function(varnam, out){
  data <- out$vars[[varnam]][,,1] %>% as.vector()
  df <- tibble( varnam = data )
  return(df)
}