CFAxisVertical | R Documentation |
This class represents a vertical axis, which may be parametric. A regular vertical axis behaves like any other numeric axis. A parametric vertical axis, on the other hand, is defined through an index value that is contained in the axis coordinates, with additional data variables that hold ancillary "formula terms" with which to calculate dimensional axis coordinates. It is used in atmosphere and ocean data sets.
Parametric vertical axes can only be read from file, not created from scratch.
ncdfCF::CFObject
-> ncdfCF::CFAxis
-> ncdfCF::CFAxisNumeric
-> CFAxisVertical
friendlyClassName
(read-only) A nice description of the class.
formula_terms
(read-only) A data.frame
with the "formula_terms"
to calculate the parametric axis values.
is_parametric
(read-only) Logical flag that indicates if the coordinates of the axis are parametric.
parametric_coordinates
(read-only) Retrieve the parametric coordinates of this vertical axis as a CFVariable.
computed_name
(read-only) The name of the computed parameterised coordinates. If the parameterised coordinates have not been computed yet the computed name is an empty string.
computed_units
(read-only) Return the units of the computed
parameterised coordinates, if computed, otherwise return NULL
. This
will access the standard names table.
ncdfCF::CFObject$append_attribute()
ncdfCF::CFObject$attribute()
ncdfCF::CFObject$delete_attribute()
ncdfCF::CFObject$dim()
ncdfCF::CFObject$print_attributes()
ncdfCF::CFObject$set_attribute()
ncdfCF::CFObject$update_coordinates_attribute()
ncdfCF::CFObject$write_attributes()
ncdfCF::CFAxis$can_append()
ncdfCF::CFAxis$configure_terms()
ncdfCF::CFAxis$copy_terms()
ncdfCF::CFAxis$peek()
ncdfCF::CFAxis$shard()
ncdfCF::CFAxis$write()
ncdfCF::CFAxisNumeric$brief()
ncdfCF::CFAxisNumeric$identical()
ncdfCF::CFAxisNumeric$indexOf()
ncdfCF::CFAxisNumeric$print()
ncdfCF::CFAxisNumeric$range()
ncdfCF::CFAxisNumeric$slice()
new()
Create a new instance of this class.
CFAxisVertical$new( var, values, start = 1L, count = NA, attributes = data.frame() )
var
The name of the axis when creating a new axis. When reading an axis from file, the NCVariable object that describes this instance.
values
Optional. The values of the axis in a vector. The values
have to be numeric and monotonic. Ignored when argument var
is a
NCVariable
object.
start
Optional. Integer index where to start reading axis data
from file. The index may be NA
to start reading data from the start.
count
Optional. Number of elements to read from file. This may be
NA
to read to the end of the data.
attributes
Optional. A data.frame
with the attributes of the
axis. When an empty data.frame
(default) and argument var
is an
NCVariable
instance, attributes of the axis will be taken from the
netCDF resource.
detach()
Detach the parametric terms from an underlying netCDF resource.
CFAxisVertical$detach()
Self, invisibly.
copy()
Create a copy of this axis. The copy is completely separate from this instance, meaning that the copies of both this instance and all of its components are made as new instances.
CFAxisVertical$copy(name = "")
name
The name for the new axis. If an empty string is passed, will use the name of this axis.
The newly created axis.
copy_with_values()
Create a copy of this axis but using the supplied values. The attributes are copied to the new axis. Boundary values, parametric coordinates and auxiliary coordinates are not copied.
After this operation the attributes of the newly created axes may not be accurate, except for the "actual_range" attribute. The calling code should set, modify or delete attributes as appropriate.
CFAxisVertical$copy_with_values(name = "", values)
name
The name for the new axis. If an empty string is passed, will use the name of this axis.
values
The values to the used with the copy of this axis.
The newly created axis.
set_parametric_terms()
Set the parametric terms for this axis. The name and the terms have to fully describe a CF parametric vertical axis.
The terms must also agree with the other axes used by any data variable that refers to this axis. That is not checked here so the calling code must make that assertion.
CFAxisVertical$set_parametric_terms(sn, terms)
sn
The "standard_name" of the parametric formulation. See the CF documentation for details.
terms
A data.frame
with columns term
, variable
and
param
containing the terms of the formula to calculate the axis
values. Column param
has the references to the variables that
hold the data for each term.
append()
Append a vector of values at the end of the current values
of the axis. Boundary values are appended as well but if either this
axis or the from
axis does not have boundary values, neither will the
resulting axis.
This method is not recommended for parametric vertical axes. Any
parametric terms will be deleted. If appending of parametric axes is
required, the calling code should first read out the parametric terms
and merge them with the parametric terms of the from
axis before
setting them back for this axis.
CFAxisVertical$append(from)
from
An instance of CFAxisVertical
whose values to append to the
values of this axis.
A new CFAxisVertical
instance with values from this axis and
the from
axis appended.
subset()
Return an axis spanning a smaller coordinate range. This
method returns an axis which spans the range of indices given by the
rng
argument. If this axis has parametric terms, these are not subset
here - they should be separately treated once all associated axes in
the terms have been subset. That happens automatically in CFVariable
methods which call the subset_parametric_terms()
method.
CFAxisVertical$subset(name = "", rng = NULL)
name
The name for the new axis. If an empty string is passed (default), will use the name of this axis.
rng
The range of indices whose values from this axis to include in
the returned axis. If the value of the argument is NULL
, return a
copy of the axis.
A new CFAxisVertical
instance covering the indicated range of
indices. If the value of the argument rng
is NULL
, return a copy of
this axis as the new axis.
subset_parametric_terms()
Subset the parametric terms of this axis.
CFAxisVertical$subset_parametric_terms( original_axis_names, new_axes, start, count, aux = NULL, ZT_dim = NULL )
original_axis_names
Character vector of names of the axes prior to a modifying operation in the owning data variable
new_axes
List of CFAxis
instances to use for the subsetting.
start
The indices to start reading data from the file, as an integer vector at least as long as the number of axis for the term.
count
The number of values to read from the file, as an integer vector at least as long as the number of axis for the term.
aux
Optional. List with the parameters for an auxiliary grid
transformation. Default is NULL
.
ZT_dim
Optional. Dimensions of the non-grid axes when an auxiliary grid transformation is specified.
Self, invisibly. The parametric terms will have been subset in this axis.
https://cfconventions.org/Data/cf-conventions/cf-conventions.html#parametric-vertical-coordinate https://www.myroms.org/wiki/Vertical_S-coordinate
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