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 coordinate. Time is usually encoded as an offset from an
origin. Using the
CFtimepackage these offsets can be turned into intelligible dates and times, for all defined calendars. - Bounds information. When present, bounds are read and used in analyses.
- Discrete coordinates, 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 also to scalar axes and auxiliary longitude-latitude grids. Auxiliary coordinates can be activated by the user and then used in display, selection and processing. Data on non-Cartesian grids can be automatically rectified to a longitude-latitude grid if an auxiliary grid is present in the resource.
- The cell measure variables are read and linked to any data variables referencing them. Cell measure variables that are external to the netCDF resource with the referring data variable can be linked to the data set and then they are immediately available to the referring data variables.
- Labels, as separate variables identified through the
coordinatesattribute of axes, are read, including when multiple sets of labels are defined for a single axis. Users can select which set of labels to make active for display, selection and processing. - 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/4.5-arm64/Resources/library/ncdfCF/extdata/ERA5land_Rwanda_20160101.nc
#> Format : offset64
#> Collection : 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
#>
#> Attributes:
#> name type length value
#> CDI NC_CHAR 64 Climate Data Interface version 2.4.1 (https://m...
#> Conventions NC_CHAR 6 CF-1.6
#> history NC_CHAR 482 Tue May 28 18:39:12 2024: cdo seldate,2016-01-0...
#> CDO NC_CHAR 64 Climate Data Operators version 2.4.1 (https://m...
# ...or very brief details
ds$var_names
#> [1] "t2m" "pev" "tp"
ds$axis_names
#> [1] "time" "longitude" "latitude"
# Variables and axes can be accessed through standard list-type extraction syntax
(t2m <- ds[["t2m"]])
#> <Variable> t2m
#> Long name: 2 metre temperature
#>
#> Axes:
#> axis name length unlim values
#> X longitude 31 [28 ... 31]
#> Y latitude 21 [-1 ... -3]
#> T time 24 U [2016-01-01T00:00:00 ... 2016-01-01T23:00:00]
#> unit
#> degrees_east
#> degrees_north
#> hours since 1900-01-01 00:00:00.0
#>
#> Attributes:
#> name type length value
#> long_name NC_CHAR 19 2 metre temperature
#> units NC_CHAR 1 K
ds[["longitude"]]
#> <Longitude axis> [1] longitude
#> Length : 31
#> Axis : X
#> Coordinates: 28, 28.1, 28.2 ... 30.8, 30.9, 31 (degrees_east)
#> Bounds : (not set)
#>
#> Attributes:
#> name type length value
#> standard_name NC_CHAR 9 longitude
#> long_name NC_CHAR 9 longitude
#> units NC_CHAR 12 degrees_east
#> axis NC_CHAR 1 X
#> actual_range NC_FLOAT 2 28, 31
# Regular base R operations simplify life further
dimnames(ds[["pev"]]) # A variable: list of axis names
#> [1] "longitude" "latitude" "time"
dimnames(ds[["longitude"]]) # An axis: vector of axis coordinates
#> [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:
peek_ncdf(fn)
#> $uri
#> [1] "/Library/Frameworks/R.framework/Versions/4.5-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 [2016-01-01T00:00:00 ... 2016-01-01T23:00:00] FALSE
#> longitude [28 ... 31] FALSE
#> latitude [-1 ... -3] FALSE
#> coordinate_sets
#> time 1
#> longitude 1
#> latitude 1
#>
#> $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 four ways to read data for a data variable from the resource:
data():Thedata()method returns all data of a variable, including its metadata, in aCFArrayinstance.[]: 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.profile(): Extract “profiles” from the data variable. This can take different forms, such as a temporal or depth profile for a single location, but it could also be a zonal field (such as a transect in latitude - atmospheric depth for a given longitude) or some other profile in the physical space of the data variable.
# 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
#> ..$ longitude: chr "28.4"
#> ..$ latitude : chr "-1.3"
#> ..$ time : chr [1:24] "2016-01-01T00:00:00" "2016-01-01T01:00:00" "2016-01-01T02:00:00" "2016-01-01T03:00:00" ...
#> - attr(*, "axis")= Named chr [1:3] "X" "Y" "T"
#> ..- attr(*, "names")= chr [1:3] "longitude" "latitude" "time"
#> - attr(*, "time")=List of 1
#> ..$ time:CFTime with origin [hours since 1900-01-01 00:00:00.0] using calendar [standard] having 24 offset values
# 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
#> ..$ longitude: chr [1:31] "28" "28.1" "28.200001" "28.299999" ...
#> ..$ latitude : chr [1:21] "-1" "-1.1" "-1.2" "-1.3" ...
#> ..$ time : chr "2016-01-01T11:00:00"
#> - attr(*, "axis")= Named chr [1:3] "X" "Y" "T"
#> ..- attr(*, "names")= chr [1:3] "longitude" "latitude" "time"
#> - attr(*, "time")=List of 1
#> ..$ time:CFTime with origin [hours since 1900-01-01 00:00:00.0] using calendar [standard] having 1 offset valuesNote 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 CFArray, including axes and
attributes:
# Extract a specific region, full time dimension
(ts <- t2m$subset(list(X = 29:30, Y = -1:-2)))
#> <Data array> t2m
#> Long name: 2 metre temperature
#>
#> Values: [283.0182 ... 302.0447] K
#> NA: 0 (0.0%)
#>
#> Axes:
#> axis name length unlim values
#> X longitude 31 [28 ... 31]
#> Y latitude 21 [-1 ... -3]
#> T time 24 U [2016-01-01T00:00:00 ... 2016-01-01T23:00:00]
#> unit
#> degrees_east
#> degrees_north
#> hours since 1900-01-01 00:00:00.0
#>
#> Attributes:
#> name type length value
#> long_name NC_CHAR 19 2 metre temperature
#> units NC_CHAR 1 K
#> actual_range NC_DOUBLE 2 283.018168, 302.04472
# Extract specific time slices for a specific region
# Note that the dimensions are specified out of order and using alternative
# specifications: only the extreme values are used.
(ts <- t2m$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: [283.0182 ... 302.0447] K
#> NA: 0 (0.0%)
#>
#> Axes:
#> axis name length unlim values
#> X longitude 31 [28 ... 31]
#> Y latitude 21 [-1 ... -3]
#> T time 24 U [2016-01-01T00:00:00 ... 2016-01-01T23:00:00]
#> unit
#> degrees_east
#> degrees_north
#> hours since 1900-01-01 00:00:00.0
#>
#> Attributes:
#> name type length value
#> long_name NC_CHAR 19 2 metre temperature
#> units NC_CHAR 1 K
#> actual_range NC_DOUBLE 2 283.018168, 302.04472The latter two methods will read only as much data from the netCDF resource as is requested.
Summarising data over time
With the summarise() method, available for both CFVariable and
CFArray, you can apply a function over the data to generate summaries.
You could, for instance, summarise daily data to monthly means. These
methods use the specific calendar of the “time” axis. The return value
is a new CFArray object.
# Summarising hourly temperature data to calculate the daily maximum temperature
t2m$summarise("tmax", max, "day")
#> <Data array> tmax
#> Long name: 2 metre temperature
#>
#> Values: [290.0364 ... 302.0447] K
#> NA: 0 (0.0%)
#>
#> Axes:
#> axis name length values unit
#> X longitude 31 [28 ... 31] degrees_east
#> Y latitude 21 [-1 ... -3] degrees_north
#> T time 1 [2016-01-01T12:00:00] hours since 1900-01-01 00:00:00.0
#>
#> Attributes:
#> name type length value
#> long_name NC_CHAR 19 2 metre temperature
#> units NC_CHAR 1 K
#> actual_range NC_DOUBLE 2 290.036358, 302.04472A function may also return a vector of multiple values, in which case a
list is returned with a new CFArray object for each return value of
the function. This allows you to calculate multiple results with a
single call. You could write your own function to tailor the
calculations to your needs. Rather than just calculating the daily
maximum, you could get the daily maximum, minimum and diurnal range in
one go:
# Function to calculate multiple daily stats
# It is good practice to include a `na.rm` argument in all your functions
daily_stats <- function(x, na.rm = TRUE) {
# x is the vector of values for one day
minmax <- range(x, na.rm = na.rm)
diurnal <- minmax[2L] - minmax[1L]
c(minmax, diurnal)
}
# Call summarise() with your own function
# The `name` argument should have as many names as the function returns results
(stats <- t2m$summarise(c("tmin", "tmax", "diurnal_range"), daily_stats, "day"))
#> $tmin
#> <Data array> tmin
#> Long name: 2 metre temperature
#>
#> Values: [283.0182 ... 293.8659] K
#> NA: 0 (0.0%)
#>
#> Axes:
#> axis name length values unit
#> X longitude 31 [28 ... 31] degrees_east
#> Y latitude 21 [-1 ... -3] degrees_north
#> T time 1 [2016-01-01T12:00:00] hours since 1900-01-01 00:00:00.0
#>
#> Attributes:
#> name type length value
#> long_name NC_CHAR 19 2 metre temperature
#> units NC_CHAR 1 K
#> actual_range NC_DOUBLE 2 283.018168, 293.865857
#>
#> $tmax
#> <Data array> tmax
#> Long name: 2 metre temperature
#>
#> Values: [290.0364 ... 302.0447] K
#> NA: 0 (0.0%)
#>
#> Axes:
#> axis name length values unit
#> X longitude 31 [28 ... 31] degrees_east
#> Y latitude 21 [-1 ... -3] degrees_north
#> T time 1 [2016-01-01T12:00:00] hours since 1900-01-01 00:00:00.0
#>
#> Attributes:
#> name type length value
#> long_name NC_CHAR 19 2 metre temperature
#> units NC_CHAR 1 K
#> actual_range NC_DOUBLE 2 290.036358, 302.04472
#>
#> $diurnal_range
#> <Data array> diurnal_range
#> Long name: 2 metre temperature
#>
#> Values: [1.819982 ... 11.27369] K
#> NA: 0 (0.0%)
#>
#> Axes:
#> axis name length values unit
#> X longitude 31 [28 ... 31] degrees_east
#> Y latitude 21 [-1 ... -3] degrees_north
#> T time 1 [2016-01-01T12:00:00] hours since 1900-01-01 00:00:00.0
#>
#> Attributes:
#> name type length value
#> long_name NC_CHAR 19 2 metre temperature
#> units NC_CHAR 1 K
#> actual_range NC_DOUBLE 2 1.819982, 11.27369Note that you may have to update some attributes after calling
summarise(). You can use the set_attribute() method on the CFArray
objects to do that.
Exporting and saving data
A CFData object can be exported to a data.table or to a
terra::SpatRaster (3D) or terra::SpatRasterDataset (4D) for further
processing. Obviously, these packages need to be installed to utilise
these methods.
# install.packages("data.table")
library(data.table)
head(dt <- ts$data.table())
#> longitude latitude time t2m
#> <num> <num> <char> <num>
#> 1: 28.0 -1 2016-01-01T00:00:00 293.8875
#> 2: 28.1 -1 2016-01-01T00:00:00 294.4015
#> 3: 28.2 -1 2016-01-01T00:00:00 294.4972
#> 4: 28.3 -1 2016-01-01T00:00:00 293.9426
#> 5: 28.4 -1 2016-01-01T00:00:00 293.6339
#> 6: 28.5 -1 2016-01-01T00:00:00 293.0206
#install.packages("terra")
suppressMessages(library(terra))
(r <- stats[["diurnal_range"]]$terra())
#> class : SpatRaster
#> dimensions : 21, 31, 1 (nrow, ncol, nlyr)
#> resolution : 0.1, 0.1 (x, y)
#> extent : 27.95, 31.05, -3.05, -0.95 (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326)
#> source(s) : memory
#> name : 2016-01-01T12:00:00
#> min value : 1.819982
#> max value : 11.273690
terra::plot(r)A CFData object can also be written back to a netCDF file. The object
will have all its relevant attributes and properties written together
with the actual data: axes, bounds, attributes, CRS.
# Save a CFData instance to a netCDF file on disk
stats[["diurnal_range"]]$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 all data objects from netCDF resources in “classic” and
“netcdf4” formats; and can write single data arrays back to a netCDF
file. From the CF Metadata Conventions it supports identification of
axes, interpretation of the “time” axis, name resolution when using
groups, reading of “bounds” information, auxiliary coordinate variables,
labels, cell measures, attributes and grid mapping information.
Development plans for the near future focus on supporting the below features:
netCDF
- Support for writing of data sets (
CFArrayinstances can already be written to file).
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
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. The API may still change and although care is
taken not to make breaking changes, sometimes this is unavoidable.
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("R-CF/ncdfCF")