R interface

The R interface consists of an R package that provides the import, export and version functions.

Products are represented in R as lists which can be manipulated freely from within R. A product structure contains a sub-list field for each variable contained in the product.

Products can be exported as HARP compliant products in any of the file formats supported by the HARP C library (netCDF/HDF4/HDF5). Such exported products can subsequently be processed further using the HARP command line tools.

Dimension types

The HARP C library defines several dimension types (time, vertical, latitude etc.). This information is stored in the dimension field of each variable in R. If a variable is a scalar (which has no dimensions), the dimension field is NULL.

Because of a mismatch in storage between the C and R side (row-major versus column-major), the dimension order is reversed on the R side.

Data types

The HARP R interface takes care of the conversion of product and variables from the C domain to the R domain and back. This section describes the relation between types in the C domain and types in the R domain.

The table below shows the type map that is used when importing or ingesting a product, i.e. when translating from the C domain to the R domain.

Variable data arrays are converted to arrays in the product structure. The data type used for the converted array is determined from the HARP data type of the variable according to the type map shown below. Zero-dimensional arrays of length 1 are converted to R arrays of 1x1. The resulting R type is also shown in the type map.

HARP data type

R type

harp_type_int8

integer

harp_type_int16

integer

harp_type_int32

integer

harp_type_float

real

harp_type_double

real

harp_type_string

string

Unicode

Zero-terminated C strings received from the HARP C library are always converted to arrays of mxCHAR in R which is a unicode string.

Examples

# Ingest a file and convert it to a HARP product (the
# file that is used in this example is an S5P L2 HCHO product).
hcho_product = harp::import("S5P_NRTI_L2__HCHO___20080808T224727_20080808T234211_21635_01_021797_00000000T000000.nc",
                            "solar_zenith_angle < 60 [degree]; latitude > 30 [degree_north]; latitude < 60 [degree_north]")

# Print product
print(hcho_product)

# Print variable 'tropospheric_HCHO_column_number_density'.
print(hcho_product$tropospheric_HCHO_column_number_density)

# Export the updated product as an HDF5 file (the format must be
# HDF4, HDF5 or netCDF, if no format is specified netCDF is used).
harp::export(hcho_product, "product.h5", "hdf5")

# Import the HDF5 file and perform an operation to exclude the variable
# solar_azimuth_angle.
hcho_product2 = harp::import("product.h5", "exclude(solar_azimuth_angle)");

API reference

This section describes the functions defined by the HARP R interface.

import(filename, operations='', options='')

Import a product from a file.

This will first try to import the file as an HDF4, HDF5, or netCDF file that complies to the HARP Data Format. If the file is not stored using the HARP format then it will try to import it using one of the available ingestion modules.

Parameters:

  • filename (str) – Filename of the product to ingest

  • operations (str) – Actions to apply as part of the import; should be specified as a semi-colon separated string of operations.

  • options (str) – Ingestion module specific options; should be specified as a semi-colon separated string of key=value pairs; only used if the file is not in HARP format.

Returns:

Ingested product.

export(product, filename, file_format='netcdf')

Export a HARP compliant product.

Parameters:

  • product – Product to export.

  • filename (str) – Filename of the exported product.

  • file_format (str) – File format to use; one of ‘netcdf’, ‘hdf4’, or ‘hdf5’. If no format is specified, netcdf is used.

version()

Returns the version number of HARP.