Straightforward 'NetCDF' Metadata

Extract metadata from 'NetCDF' data sources, these can be files, file handles or servers. This package leverages and extends the lower level functions of the 'RNetCDF' package providing a consistent set of functions that all return data frames. We introduce named concepts of 'grid', 'axis' and 'source' which are all meaningful entities without formal definition in the 'NetCDF' library < https://www.unidata.ucar.edu/software/netcdf/>. 'RNetCDF' matches the library itself with only the named concepts of 'variables', 'dimensions' and 'attributes'. 'ncmeta' provides a required framework for the in-development 'tidync' project < https://github.com/hypertidy/tidync>.


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The ncmeta package provides straightforward NetCDF metadata, with a set of consistent entity-based functions for extracting metadata from a file or online source. We aim to fill a gap in between the generality and power of the NetCDF framework and the availability of easy to use modern software tools.

There are two main packages for using NetCDF in R, RNetCDF and ncdf4 and ncmeta use both of them, for subtle situations. Both packages are very close the native API of NetCDF itself, and ncmeta simply provides an easier high-level interpretation.

About NetCDF

NetCDF is both a data model and an API, and provides a very general framework for expressing data formats. The explicit entities in NetCDF are variables, dimensions and attributes and ncmeta provides functions nc_vars, nc_dims, and nc_atts to extract their names, order and other metadata. There are matching functions nc_var, nc_dim, and nc_att with an extra identifier argument that extract specific information about individual an variable, dimension, or attribute.

Ncmeta includes functions for implicit entities, these are grids and axes. These don’t exist in the NetCDF specification explicitly, but are meaningful and we think worth making explicit.

A grid is an ordered set of dimensions, and the Unidata site refers informally to this concept as shape. Many NetCDF tools don’t explicitly present these shapes, or grids so we are a little tentative in our definitions.

An axis is an instance of a dimension, the use of that dimension within a particular variable.

Together these entities provide a more developer-friendly scheme for working with the range of formats provided by the NetCDF ecosystem.

Installation

Install ncmeta from CRAN with:

install.packages("ncmeta")

You can install the development version of ncmeta from github with:

# install.packages("devtools")
devtools::install_github("hypertidy/ncmeta")

Example

This example shows some of the functions for extracting information from a NetCDF source.

library(ncmeta)
filename <- system.file("extdata", "S2008001.L3m_DAY_CHL_chlor_a_9km.nc", package = "ncmeta")
nc_inq(filename) # one-row summary of file
 
nc_dim(filename, 0)  ## first dimension
nc_dims(filename)  ## all dimensions

Get involved!

Please let us know if you have any feedback, see the Issues tab if you found a bug or have a question. Feel free to email the maintainer directly for other questions.

Community

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

News

ncmeta 0.0.4

  • nc_grids() now normal form, with nested variables so we can easily link grids to variables.

  • New functions nc_coord_var to find coordinate variables (if any), gm_to_prj to determine PROJ string in use, and nc_grid_mapping_atts to determine grid mapping parameters; #19, #14, #12, #9.

ncmeta 0.0.3

  • Fix for grid organization providing variables out of native order.

  • Added 'variable' argument to 'nc_atts', per #8.

ncmeta 0.0.2

  • added some extra checks for bad source strings, particularly the empty string to prevent crashing (this happens with system.file() where the file does not exist)
  • fix attribute types problem

ncmeta 0.0.1

*updates from CRAN feedback

  • ncmeta now provides support for dimensions that do not have explicit coordinates: dimension and variable tables now have information about "dimvals", in the form of "dim_coord" and "coord_dim" i.e. if a variable is 1D and its name corresponds to a dimension name, then it is a rectlinear coordinate vector of that dimension. (The coordinates can be of type "char", and that must be dealt with down stream as it now is in tidync).

  • new function nc_grids, the spaces available to variables

  • new function nc_axes, nc_axis for the instances of dimensions

  • nc_vars now returns only variables

  • First working version.

Reference manual

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install.packages("ncmeta")

0.0.4 by Michael Sumner, 4 months ago


https://github.com/hypertidy/ncmeta


Report a bug at https://github.com/hypertidy/ncmeta/issues


Browse source code at https://github.com/cran/ncmeta


Authors: Michael Sumner [aut, cre] , Tomas Remenyi [ctb] , Ben Raymond [ctb] , David Blodgett [ctb]


Documentation:   PDF Manual  


GPL-3 license


Imports dplyr, rlang, RNetCDF, tibble, stats, tidyr

Suggests testthat, covr


Imported by ncdfgeom, tidync.

Suggested by stars.


See at CRAN