ncdfCF
The ncdfCF package provides an easy to use interface to netCDF
resources in R, either in local files or remotely on a THREDDS server.
It is built on the RNetCDF package which, like package ncdf4,
provides a basic interface to the netcdf library, but which lacks an
intuitive user interface. Package ncdfCF provides a high-level
interface using functions and methods that are familiar to the R user.
It reads the structural metadata and also the attributes upon opening
the resource. In the process, the ncdfCF package also applies CF
Metadata Conventions to interpret the data. This currently applies to:
- The axis designation. The three mechanisms to identify the axis each dimension represents are applied until an axis is determined.
- The time dimension. Time is usually encoded as an offset from a
datum. Using the
CFtimepackage these offsets can be turned into intelligible dates and times, for all 9 defined calendars. - Bounds information. When present, bounds are read and used in analyses.
- Discrete dimensions, optionally with character labels. When labels
are provided, these will be used as
dimnamesfor the axis. (Note that this also applies to generic numeric axes with labels defined.) - Parametric vertical coordinates are read, including variables
listed in the
formula_termsattribute. - Auxiliary coordinates are identified and read. This applies to both scalar axes and auxiliary longitude-latitude grids. Data on non-Cartesian grids can be automatically rectified to a longitude-latitude grid if an auxiliary grid is present in the resource.
- The grid_mapping variables, providing the coordinate reference system (CRS) of the data, with support for all defined objects in the latest EPSG database as well as “manual” construction of CRSs.
Basic usage
Opening and inspecting the contents of a netCDF resource is very straightforward:
library(ncdfCF)
# Get any netCDF file
fn <- system.file("extdata", "ERA5land_Rwanda_20160101.nc", package = "ncdfCF")
# Open the file, all metadata is read
(ds <- open_ncdf(fn))
#> <Dataset> ERA5land_Rwanda_20160101
#> Resource : /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ncdfCF/extdata/ERA5land_Rwanda_20160101.nc
#> Format : offset64
#> Type : generic netCDF data
#> Conventions: CF-1.6
#> Keep open : FALSE
#>
#> Variables:
#> name long_name units data_type axes
#> t2m 2 metre temperature K NC_SHORT longitude, latitude, time
#> pev Potential evaporation m NC_SHORT longitude, latitude, time
#> tp Total precipitation m NC_SHORT longitude, latitude, time
#>
#> Axes:
#> id axis name length unlim values
#> 0 T time 24 U [2016-01-01 00:00:00 ... 2016-01-01 23:00:00]
#> 1 X longitude 31 [28 ... 31]
#> 2 Y latitude 21 [-1 ... -3]
#> unit
#> hours since 1900-01-01 00:00:00.0
#> degrees_east
#> degrees_north
#>
#> Attributes:
#> id name type length
#> 0 CDI NC_CHAR 64
#> 1 Conventions NC_CHAR 6
#> 2 history NC_CHAR 482
#> 3 CDO NC_CHAR 64
#> value
#> Climate Data Interface version 2.4.1 (https://m...
#> CF-1.6
#> Tue May 28 18:39:12 2024: cdo seldate,2016-01-0...
#> Climate Data Operators version 2.4.1 (https://m...
# ...or very brief details
names(ds)
#> [1] "t2m" "pev" "tp"
dimnames(ds)
#> [1] "time" "longitude" "latitude"
# Variables and dimensions can be accessed through standard list-type extraction syntax
(t2m <- ds[["t2m"]])
#> <Variable> t2m
#> Long name: 2 metre temperature
#>
#> Axes:
#> id axis name length unlim values
#> 1 X longitude 31 [28 ... 31]
#> 2 Y latitude 21 [-1 ... -3]
#> 0 T time 24 U [2016-01-01 00:00:00 ... 2016-01-01 23:00:00]
#> unit
#> degrees_east
#> degrees_north
#> hours since 1900-01-01 00:00:00.0
#>
#> Attributes:
#> id name type length value
#> 0 long_name NC_CHAR 19 2 metre temperature
#> 1 units NC_CHAR 1 K
#> 2 add_offset NC_DOUBLE 1 292.664569285614
#> 3 scale_factor NC_DOUBLE 1 0.00045127252204996
#> 4 _FillValue NC_SHORT 1 -32767
#> 5 missing_value NC_SHORT 1 -32767
ds[["longitude"]]
#> <Longitude axis> [1] longitude
#> Length : 31
#> Axis : X
#> Values : 28, 28.1, 28.2 ... 30.8, 30.9, 31 degrees_east
#> Bounds : (not set)
#>
#> Attributes:
#> id name type length value
#> 0 standard_name NC_CHAR 9 longitude
#> 1 long_name NC_CHAR 9 longitude
#> 2 units NC_CHAR 12 degrees_east
#> 3 axis NC_CHAR 1 X
# Regular base R operations simplify life further
dimnames(ds[["pev"]]) # A variable: list of dimension names
#> [1] "longitude" "latitude" "time"
dimnames(ds[["longitude"]]) # A dimension: vector of dimension element values
#> [1] 28.0 28.1 28.2 28.3 28.4 28.5 28.6 28.7 28.8 28.9 29.0 29.1 29.2 29.3 29.4
#> [16] 29.5 29.6 29.7 29.8 29.9 30.0 30.1 30.2 30.3 30.4 30.5 30.6 30.7 30.8 30.9
#> [31] 31.0
# Access attributes
ds[["pev"]]$attribute("long_name")
#> [1] "Potential evaporation"If you just want to inspect what data is included in the netCDF
resource, use the peek_ncdf() function:
(ds <- peek_ncdf(fn))
#> $uri
#> [1] "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ncdfCF/extdata/ERA5land_Rwanda_20160101.nc"
#>
#> $type
#> [1] "generic netCDF data"
#>
#> $variables
#> id name long_name standard_name units axes
#> t2m 3 t2m 2 metre temperature NA K longitude, latitude, time
#> pev 4 pev Potential evaporation NA m longitude, latitude, time
#> tp 5 tp Total precipitation NA m longitude, latitude, time
#>
#> $axes
#> class id axis name long_name standard_name
#> time CFAxisTime 0 T time time time
#> longitude CFAxisLongitude 1 X longitude longitude longitude
#> latitude CFAxisLatitude 2 Y latitude latitude latitude
#> units length unlimited
#> time hours since 1900-01-01 00:00:00.0 24 TRUE
#> longitude degrees_east 31 FALSE
#> latitude degrees_north 21 FALSE
#> values has_bounds
#> time [2016-01-01 00:00:00 ... 2016-01-01 23:00:00] FALSE
#> longitude [28 ... 31] FALSE
#> latitude [-1 ... -3] FALSE
#>
#> $attributes
#> id name type length
#> 1 0 CDI NC_CHAR 64
#> 2 1 Conventions NC_CHAR 6
#> 3 2 history NC_CHAR 482
#> 4 3 CDO NC_CHAR 64
#> value
#> 1 Climate Data Interface version 2.4.1 (https://mpimet.mpg.de/cdi)
#> 2 CF-1.6
#> 3 Tue May 28 18:39:12 2024: cdo seldate,2016-01-01,2016-01-01 /Users/patrickvanlaake/CC/ERA5land/Rwanda/ERA5land_Rwanda_t2m-pev-tp_2016-2018.nc ERA5land_Rwanda_20160101.nc\n2021-12-22 07:00:24 GMT by grib_to_netcdf-2.23.0: /opt/ecmwf/mars-client/bin/grib_to_netcdf -S param -o /cache/data5/adaptor.mars.internal-1640155821.967082-25565-12-0b19757d-da4e-4ea4-b8aa-d08ec89caf2c.nc /cache/tmp/0b19757d-da4e-4ea4-b8aa-d08ec89caf2c-adaptor.mars.internal-1640142203.3196251-25565-10-tmp.grib
#> 4 Climate Data Operators version 2.4.1 (https://mpimet.mpg.de/cdo)Extracting data
There are three ways to read data for a variable from the resource:
data():Thedata()method returns all data of a variable, including its metadata, in aCFDatainstance.[]: The usual R array operator gives you access to the raw, non-interpreted data in the netCDF resource. This uses index values into the dimensions and requires you to know the order in which the dimensions are specified for the variable. With a bit of tinkering and some helper functions inncdfCFthis is still very easy to do.subset(): Thesubset()method lets you specify what you want to extract from each dimension in real-world coordinates and timestamps, in whichever order. This can also rectify non-Cartesian grids to regular longitude-latitude grids.
# Extract a timeseries for a specific location
ts <- t2m[5, 4, ]
str(ts)
#> num [1, 1, 1:24] 293 292 292 291 291 ...
#> - attr(*, "dimnames")=List of 3
#> ..$ : chr "28.4"
#> ..$ : chr "-1.3"
#> ..$ : chr [1:24] "2016-01-01 00:00:00" "2016-01-01 01:00:00" "2016-01-01 02:00:00" "2016-01-01 03:00:00" ...
#> - attr(*, "axis")= Named chr [1:3] "X" "Y" "T"
#> ..- attr(*, "names")= chr [1:3] "longitude" "latitude" "time"
#> - attr(*, "time")=List of 1
#> ..$ time:Classes 'CFTime', 'R6' 2016-01-01 00:00:00 2016-01-01 01:00:00 2016-01-01 02:00:00 2016-01-01 03:00:00 2016-01-01 04:00:00 2016-01-01 05:00:00 2016-01-01 06:00:00 2016-01-01 07:00:00 2016-01-01 08:00:00 2016-01-01 09:00:00 2016-01-01 10:00:00 2016-01-01 11:00:00 2016-01-01 12:00:00 2016-01-01 13:00:00 2016-01-01 14:00:00 2016-01-01 15:00:00 2016-01-01 16:00:00 2016-01-01 17:00:00 2016-01-01 18:00:00 2016-01-01 19:00:00 2016-01-01 20:00:00 2016-01-01 21:00:00 2016-01-01 22:00:00 2016-01-01 23:00:00
# Extract the full spatial extent for one time step
ts <- t2m[, , 12]
str(ts)
#> num [1:31, 1:21, 1] 300 300 300 300 300 ...
#> - attr(*, "dimnames")=List of 3
#> ..$ : chr [1:31] "28" "28.1" "28.2" "28.3" ...
#> ..$ : chr [1:21] "-1" "-1.1" "-1.2" "-1.3" ...
#> ..$ : chr "2016-01-01 11:00:00"
#> - attr(*, "axis")= Named chr [1:3] "X" "Y" "T"
#> ..- attr(*, "names")= chr [1:3] "longitude" "latitude" "time"
#> - attr(*, "time")=List of 1
#> ..$ time:Classes 'CFTime', 'R6' 2016-01-01 11:00:00Note that the results contain degenerate dimensions (of length 1). This
by design when using basic [] data access because it allows attributes
to be attached in a consistent manner. When using the subset() method,
the data is returned as an instance of CFData, including axes and
attributes:
# Extract a specific region, full time dimension
(ts <- t2m$subset(list(X = 29:30, Y = -1:-2)))
#> <Data array> t2m
#> Long name: 2 metre temperature
#>
#> Values: [283.0182 ... 299.917] K
#> NA: 0 (0.0%)
#>
#> Axes:
#> id axis name length unlim values
#> -1 X longitude 10 [29 ... 29.9]
#> -1 Y latitude 10 [-1.1 ... -2]
#> 0 T time 24 U [2016-01-01 00:00:00 ... 2016-01-01 23:00:00]
#> unit
#>
#>
#> hours since 1900-01-01 00:00:00.0
#>
#> Attributes:
#> id name type length value
#> 0 long_name NC_CHAR 19 2 metre temperature
#> 1 units NC_CHAR 1 K
#> 2 add_offset NC_DOUBLE 1 292.664569285614
#> 3 scale_factor NC_DOUBLE 1 0.00045127252204996
#> 4 _FillValue NC_SHORT 1 -32767
#> 5 missing_value NC_SHORT 1 -32767
# Extract specific time slices for a specific region
# Note that the dimensions are specified out of order and using alternative
# specifications: only the extreme values are used.
(ts <- t2m$subset(list(T = c("2016-01-01 09:00", "2016-01-01 15:00"),
X = c(29.6, 28.8),
Y = seq(-2, -1, by = 0.05))))
#> <Data array> t2m
#> Long name: 2 metre temperature
#>
#> Values: [288.2335 ... 299.917] K
#> NA: 0 (0.0%)
#>
#> Axes:
#> id axis name length values
#> -1 X longitude 8 [28.8 ... 29.5]
#> -1 Y latitude 10 [-1.1 ... -2]
#> -1 T time 6 [2016-01-01 09:00:00 ... 2016-01-01 14:00:00]
#>
#> Attributes:
#> id name type length value
#> 0 long_name NC_CHAR 19 2 metre temperature
#> 1 units NC_CHAR 1 K
#> 2 add_offset NC_DOUBLE 1 292.664569285614
#> 3 scale_factor NC_DOUBLE 1 0.00045127252204996
#> 4 _FillValue NC_SHORT 1 -32767
#> 5 missing_value NC_SHORT 1 -32767The latter two methods will read only as much data from the netCDF resource as is requested.
Exporting and saving data
A CFData object can be exported to a data.table or to a
terra::SpatRaster (3D) or terra::SpatRasterDataset (4D) for further
processing. Obviously, these packages need to be installed to utilise
these methods.
# install.packages("data.table")
library(data.table)
head(dt <- ts$data.table())
#> longitude latitude time t2m
#> <num> <num> <char> <num>
#> 1: 28.8 -1.1 2016-01-01 09:00:00 296.0753
#> 2: 28.9 -1.1 2016-01-01 09:00:00 294.9227
#> 3: 29.0 -1.1 2016-01-01 09:00:00 295.8135
#> 4: 29.1 -1.1 2016-01-01 09:00:00 297.0929
#> 5: 29.2 -1.1 2016-01-01 09:00:00 297.4697
#> 6: 29.3 -1.1 2016-01-01 09:00:00 298.5419
#install.packages("terra")
suppressMessages(library(terra))
(r <- ts$terra())
#> class : SpatRaster
#> dimensions : 10, 8, 6 (nrow, ncol, nlyr)
#> resolution : 0.1, 0.1 (x, y)
#> extent : 28.75, 29.55, -2.05, -1.05 (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326)
#> source(s) : memory
#> names : 2016-~00:00, 2016-~00:00, 2016-~00:00, 2016-~00:00, 2016-~00:00, 2016-~00:00
#> min values : 290.0364, 288.9316, 288.7990, 288.3621, 288.3680, 288.2335
#> max values : 299.8894, 299.8691, 299.9066, 299.9170, 299.7626, 299.5948
terra::plot(r[names(r)[1]])A CFData object can also be written back to a netCDF file. The object
will have all its relevant attributes and properties written together
with the actual data: axes, bounds, attributes, CRS.
# Save a CFData instance to a netCDF file on disk
ts$save("~/path/file.nc")A note on Discrete Sampling Geometries
Discrete Sampling Geometries (DSG) map almost directly to the venerable
data.frame in R (with several exceptions). In that sense, they are
rather distinct from array-based data sets. At the moment there is no
specific code for DSG, but the simplest layouts can currently already be
read (without any warranty). Various methods, such as
CFVariable::subset() or CFData::array() will fail miserably, and you
are well-advised to try no more than the empty array indexing operator
CFVariable::[] which will yield the full data variable
with column and row names set as an array, of CFVariable::data() to
get the whole data variable as a CFData object for further processing.
You can identify a DSG data set by the featureType attribute of the
CFDataset.
More comprehensive support for DSG is in the development plan.
Development plan
Package ncdfCF is in the early phases of development. It supports
reading of groups, variables, dimensions, user-defined data types,
attributes and data from netCDF resources in “classic” and “netcdf4”
formats; and can write single data variables back to a netCDF file. From
the CF Metadata Conventions it supports identification of dimension
axes, interpretation of the “time” dimension, name resolution when using
groups, reading of “bounds” information, parametric vertical
coordinates, auxiliary coordinate variables, labels, and grid mapping
information.
Development plans for the near future focus on supporting the below features:
netCDF
- Support for writing of data sets.
CF Metadata Conventions
- Calculate parametric vertical coordinates.
- Aggregation, using the CFA convention.
- Support for discrete sampling geometries.
- Interface to “standard_name” libraries and other “defined vocabularies”.
- Compliance with CMIP5 / CMIP6 requirements.
Installation
CAUTION: Package ncdfCF is still
in the early phases of development. While extensively tested on multiple
well-structured datasets, errors may still occur, particularly in
datasets that do not adhere to the CF Metadata Conventions.
Installation from CRAN of the latest release:
install.packages("ncdfCF")You can install the development version of ncdfCF from
GitHub with:
# install.packages("devtools")
devtools::install_github("pvanlaake/ncdfCF")