In stineb/rbeni: Useful R functions for Beni.

The rbeni package contains a set of functions that let you do standard tasks working with NetCDF files on one line and let you quickly convert the contents of a NetCDF file into a tidy data frame (tibble).

Here is a demonstration example.

Read

Load the package and read the contents of one NetCDF file.

library(rbeni)
library(tidyverse)  # depends
nc <- read_nc_onefile("~/data/stocker20gmd_outputs/global/global_FULL_fAPAR3g_v2_2000_2016.a.gpp.nc")

The returned object nc is a list with:

print(ls(nc))

• lon: vector of longitudes of gridcell mid-points
• lat: vector of latitudes of gridcell mid-points
• time: vector of dates created by lubridate::ymd dates
• varnams: vector of all variable names as strings,
• vars: named list of the data arrays (lon x lat [x time]) for each variable. The names of that list correspond to varnams.

## available variable names
print(nc$varnams)

## available variable arrays (names thereof)
print(ls(nc$vars))

## dimension of variable array number one
print(dim(nc$vars[[1]]))

Make tidy

The object nc can be converted into a tidy dataframe.

df <- nc_to_df(nc, varnam = "gpp")
head(df)

The data frame is organised by gridcells along rows. Since the NetCDF contains multiple time steps, the time series are nested inside the column data for each gridcell.

head(df$data[[1]])

Note that df contains rows for all gridcells, also those that have no data (here, non-land gridcells). That's why the above time series data frame is empty.

Since object nc contains data for multiple time steps, we can select a single time step and get an object that has only lon and lat.

nc_2d <- slice_nc(nc, 1)

This 2D data frame can be converted back into a grid:

gridded <- df_to_grid(nc_2d, varnam = "data")
gridded

(This makes sense only if df is not a nested data frame and contains only data for one time step.)

Plot

This can now be used to create a nice map.

gg <- plot_map3(nc_2d, varnam = "gpp", plot_title = "GPP", latmin = -65, latmax = 85)
gg

Write

Very useful also to quickly write the nc object into a new NetCDF file.

write_nc2(nc, path = "./test.nc")

stineb/rbeni documentation built on Feb. 24, 2023, 5:40 a.m.