CFDataset: CF data set
In ncdfCF: Easy Access to NetCDF Files with CF Metadata Conventions
CFDataset R Documentation
CF data set
Description
This class represents a CF data set, the object that
encapsulates a netCDF resource. You should never have to instantiate this
class directly; instead, call open_ncdf() which will return an instance
that has all properties read from the netCDF resource. Class methods can then
be called, or the base R functions called with this instance.
The CF data set instance provides access to all the objects in the
netCDF resource, organized in groups.
Public fields
nameThe name of the netCDF resource. This is extracted from the
URI (file name or URL).
keep_openLogical flag to indicate if the netCDF resource has to
remain open after reading the metadata. This should be enabled
typically only for programmatic access or when a remote resource has an
expensive access protocol (i.e. 2FA). The resource has to be explicitly
closed with close() after use. Note that when a data set is opened
with keep_open = TRUE the resource may still be closed by the
operating system or the remote server.
rootRoot of the group hierarchy through which all elements of the
netCDF resource are accessed. It is strongly discouraged to
manipulate the objects in the group hierarchy directly. Use the provided
access methods instead.
file_typeThe type of data in the netCDF resource, if
identifiable. In terms of the CF Metadata Conventions, this includes
discrete sampling geometries (DSG). Other file types that can be
identified include L3b files used by NASA and NOAA for satellite
imagery (these data sets need special processing), and CMIP5, CMIP6 and
CORDEX climate projection data.
Active bindings
friendlyClassName(read-only) A nice description of the class.
resource(read-only) The connection details of the netCDF
resource. This is for internal use only.
uri(read-only) The connection string to the netCDF resource.
conventions(read-only) Returns the conventions that this netCDF
resource conforms to.
var_names(read-only) Vector of names of variables in this data set.
axis_names(read-only) Vector of names of axes in this data set.
Methods
Public methods
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Method new()
Create an instance of this class.
Usage
CFDataset$new(name, resource, keep_open, format)
Arguments
nameThe name that describes this instance.
resourceAn instance of CFResource that links to the netCDF
resource.
keep_openLogical. Should the netCDF resource be kept open for
further access?
formatCharacter string with the format of the netCDF resource as
reported by the call opening the resource.
Method print()
Summary of the data set printed to the console.
Usage
CFDataset$print(...)
Arguments
...Arguments passed on to other functions. Of particular interest
is width = to indicate a maximum width of attribute columns.
Method hierarchy()
Print the group hierarchy to the console.
Usage
CFDataset$hierarchy()
Method objects_by_standard_name()
Get objects by standard_name. Several conventions define
standard vocabularies for physical properties. The standard names from
those vocabularies are usually stored as the "standard_name" attribute
with variables or axes. This method retrieves all variables or axes
that list the specified "standard_name" in its attributes.
Usage
CFDataset$objects_by_standard_name(standard_name)
Arguments
standard_nameOptional, a character string to search for a
specific "standard_name" value in variables and axes.
Returns
If argument standard_name is provided, a character vector of
variable or axis names. If argument standard_name is missing or an
empty string, a named list with all "standard_name" attribute values in
the the netCDF resource; each list item is named for the variable or
axis.
Method has_subgroups()
Does the netCDF resource have subgroups? Newer versions of
the netcdf library, specifically netcdf4, can organize dimensions
and variables in groups. This method will report if the data set is
indeed organized with subgroups.
Usage
CFDataset$has_subgroups()
Returns
Logical to indicate that the netCDF resource uses subgroups.
Method find_by_name()
Find an object by its name. Given the name of a CF data
variable or axis, possibly preceded by an absolute group path, return
the object to the caller.
Usage
CFDataset$find_by_name(name, scope = "CF")
Arguments
nameThe name of a CF data variable or axis, with an optional
absolute group path.
scopeThe scope to look for the name. Either "CF" (default) to
search for CF variables or axes, or "NC" to look for groups or NC
variables.
Returns
The object with the provided name. If the object is not found,
returns NULL.
Method variables()
This method lists the CF data variables located in this
netCDF resource, including those in subgroups.
Usage
CFDataset$variables()
Returns
A list of CFVariable instances.
Method axes()
This method lists the axes located in this netCDF resource,
including axes in subgroups.
Usage
CFDataset$axes()
Returns
A list of CFAxis descendants.
Method attributes()
List all the attributes of a group. This method returns a
data.frame containing all the attributes of the indicated group.
Usage
CFDataset$attributes(group)
Arguments
groupThe name of the group whose attributes to return. If the
argument is missing, the global attributes will be returned.
Returns
A data.frame of attributes.
Method attribute()
Retrieve global attributes of the data set.
Usage
CFDataset$attribute(att, field = "value")
Arguments
attVector of character strings of attributes to return.
fieldThe field of the attribute to return values from. This must
be "value" (default) or "type".
Returns
If the field argument is "type", a character string. If field
is "value", a single value of the type of the attribute, or a vector
when the attribute has multiple values. If no attribute is named with a
value of argument att NA is returned.
Method clone()
The objects of this class are cloneable with this method.
Usage
CFDataset$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
ncdfCF documentation built on April 16, 2025, 9:08 a.m.
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| CFDataset | R Documentation |
CF data set
Description
This class represents a CF data set, the object that
encapsulates a netCDF resource. You should never have to instantiate this
class directly; instead, call open_ncdf() which will return an instance
that has all properties read from the netCDF resource. Class methods can then
be called, or the base R functions called with this instance.
The CF data set instance provides access to all the objects in the netCDF resource, organized in groups.
Public fields
nameThe name of the netCDF resource. This is extracted from the URI (file name or URL).
keep_openLogical flag to indicate if the netCDF resource has to remain open after reading the metadata. This should be enabled typically only for programmatic access or when a remote resource has an expensive access protocol (i.e. 2FA). The resource has to be explicitly closed with
close()after use. Note that when a data set is opened withkeep_open = TRUEthe resource may still be closed by the operating system or the remote server.rootRoot of the group hierarchy through which all elements of the netCDF resource are accessed. It is strongly discouraged to manipulate the objects in the group hierarchy directly. Use the provided access methods instead.
file_typeThe type of data in the netCDF resource, if identifiable. In terms of the CF Metadata Conventions, this includes discrete sampling geometries (DSG). Other file types that can be identified include L3b files used by NASA and NOAA for satellite imagery (these data sets need special processing), and CMIP5, CMIP6 and CORDEX climate projection data.
Active bindings
friendlyClassName(read-only) A nice description of the class.
resource(read-only) The connection details of the netCDF resource. This is for internal use only.
uri(read-only) The connection string to the netCDF resource.
conventions(read-only) Returns the conventions that this netCDF resource conforms to.
var_names(read-only) Vector of names of variables in this data set.
axis_names(read-only) Vector of names of axes in this data set.
Methods
Public methods
Method new()
Create an instance of this class.
Usage
CFDataset$new(name, resource, keep_open, format)
Arguments
nameThe name that describes this instance.
resourceAn instance of
CFResourcethat links to the netCDF resource.keep_openLogical. Should the netCDF resource be kept open for further access?
formatCharacter string with the format of the netCDF resource as reported by the call opening the resource.
Method print()
Summary of the data set printed to the console.
Usage
CFDataset$print(...)
Arguments
...Arguments passed on to other functions. Of particular interest is
width = to indicate a maximum width of attribute columns.
Method hierarchy()
Print the group hierarchy to the console.
Usage
CFDataset$hierarchy()
Method objects_by_standard_name()
Get objects by standard_name. Several conventions define standard vocabularies for physical properties. The standard names from those vocabularies are usually stored as the "standard_name" attribute with variables or axes. This method retrieves all variables or axes that list the specified "standard_name" in its attributes.
Usage
CFDataset$objects_by_standard_name(standard_name)
Arguments
standard_nameOptional, a character string to search for a specific "standard_name" value in variables and axes.
Returns
If argument standard_name is provided, a character vector of
variable or axis names. If argument standard_name is missing or an
empty string, a named list with all "standard_name" attribute values in
the the netCDF resource; each list item is named for the variable or
axis.
Method has_subgroups()
Does the netCDF resource have subgroups? Newer versions of
the netcdf library, specifically netcdf4, can organize dimensions
and variables in groups. This method will report if the data set is
indeed organized with subgroups.
Usage
CFDataset$has_subgroups()
Returns
Logical to indicate that the netCDF resource uses subgroups.
Method find_by_name()
Find an object by its name. Given the name of a CF data variable or axis, possibly preceded by an absolute group path, return the object to the caller.
Usage
CFDataset$find_by_name(name, scope = "CF")
Arguments
nameThe name of a CF data variable or axis, with an optional absolute group path.
scopeThe scope to look for the name. Either "CF" (default) to search for CF variables or axes, or "NC" to look for groups or NC variables.
Returns
The object with the provided name. If the object is not found,
returns NULL.
Method variables()
This method lists the CF data variables located in this netCDF resource, including those in subgroups.
Usage
CFDataset$variables()
Returns
A list of CFVariable instances.
Method axes()
This method lists the axes located in this netCDF resource, including axes in subgroups.
Usage
CFDataset$axes()
Returns
A list of CFAxis descendants.
Method attributes()
List all the attributes of a group. This method returns a
data.frame containing all the attributes of the indicated group.
Usage
CFDataset$attributes(group)
Arguments
groupThe name of the group whose attributes to return. If the argument is missing, the global attributes will be returned.
Returns
A data.frame of attributes.
Method attribute()
Retrieve global attributes of the data set.
Usage
CFDataset$attribute(att, field = "value")
Arguments
attVector of character strings of attributes to return.
fieldThe field of the attribute to return values from. This must be "value" (default) or "type".
Returns
If the field argument is "type", a character string. If field
is "value", a single value of the type of the attribute, or a vector
when the attribute has multiple values. If no attribute is named with a
value of argument att NA is returned.
Method clone()
The objects of this class are cloneable with this method.
Usage
CFDataset$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
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