ncdfCF 0.8.0

Conventions

• Ancillary variables are now associated with the data variables that reference them. They can be added with the CFVariable::add_ancillary_variable() method and the list of registered ancillary variables can be retrieved with the CFVariable$ancillary_variables field. Ancillary variables are CFVariable instances themselves and can have bounds and other data variable properties, and be processed like regular data variables.
• Vertical parametric coordinate "Atmosphere hybrid sigma pressure coordinate" added. This supports both the layer mid-point formulation of CF and the layer top and bottom formulation often found in satellite observations of the atmosphere.

API

• CFGroup is now the main hierarchy from the user perspective, maintaining all CF objects. The CFGroup$add_variable() method places a CFVariable somewhere in the hierarchy, with owned CF objects (like axes, boundary values, CRS, etc) automatically attached to the same group or some other specified group.
• All [] indexing and selection operations must include axes of length 1. This means that the indexing always has as many elements as there are axes in the CF variable. Reported dimensions include degenerate dimensions.
• The CFVariable::subset() method now has an optional .resolution argument that can be specified when interpolation with auxiliary latitude-longitude coordinates is requested; otherwise it has no effect. This change does not break any existing code.
• In CFVariable$subset() and $profile(), when selecting on auxiliary grid axes then both axes must be specified.
• Function create_ncdf() creates a new netCDF resource on disk, as a container for persisting CF objects, or in memory.
• Function as_CF() can now also convert a terra::SpatRaster to a CFDataset or a CFVariable, depending on the number of variables in the SpatRaster. This is a fragile process, mostly due to terra idiosyncrasies related to multi-dimensional data.
• Documentation updated, now available online.

Code

• Access to data values is now consistently using the public field values for "standard" objects. Only objects that require special values management use private fields and expose the data values in another, more appropriate form.
• CFGroup hierarchy maintains all CF objects. 1:1 alignment with the NCGroup hierarchy for NC objects backed by a netCDF resource.
• CFData class spawned from CFObject to act as a base class for CF objects that hold data, most notably CFVariable, CFAxis and CFBounds and descendant classes. The class manages the "shape" of the data, including degenerate dimensions, to maintain consistency with the owning object, principally the axes in a CFVariable instance.
• Stricter checking of data types versus netCDF types.
• Attributes are now considered when testing for axis equality.
• Support some edge cases in reading marginally-CF netCDF files, including lateral search.
• CFVariable S3 methods fixed.
• Multi-dimensional auxiliary lat-long grids are silently truncated to 2D.
• Improved speed of opening netCDF files with multiple data variables using the same auxiliary long-lat grid.
• CFResource has been renamed NCResource.
• Additional testing added.
• Bug fixes.