Package 'oce'

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'adp'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

Note that the entries within adp objects vary greatly, from instrument to instrument, and so are only sketched here, and in the output from ⁠[["?"]]⁠.

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items are not authoritative, because information provided by different instruments is so varied.

• If i is "u1" then the return value is v[,1]. The same holds for 2, etc., depending on the number of beams in the instrument.

• If i is "a1" then signal amplitude is returned, and similarly for other digits. The results can be in raw() or numeric form, as shown in the examples.

• If i is "q1" then signal quality is returned, and similarly for other digits. As with amplitude, the result can be in raw() or numeric form.

• If i is "coordinate", then the coordinate system is retrieved.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to adp data: [[<-,adp-method, ad2cpCodeToName(), ad2cpHeaderValue(), adp, adp-class, adpAd2cpFileTrim(), adpConvertRawToNumeric(), adpEnsembleAverage(), adpFlagPastBoundary(), adpRdiFileTrim(), adp_rdi.000, applyMagneticDeclination,adp-method, as.adp(), beamName(), beamToXyz(), beamToXyzAdp(), beamToXyzAdpAD2CP(), beamToXyzAdv(), beamUnspreadAdp(), binmapAdp(), enuToOther(), enuToOtherAdp(), handleFlags,adp-method, is.ad2cp(), plot,adp-method, read.adp(), read.adp.ad2cp(), read.adp.nortek(), read.adp.rdi(), read.adp.sontek(), read.adp.sontek.serial(), read.aquadopp(), read.aquadoppHR(), read.aquadoppProfiler(), rotateAboutZ(), setFlags,adp-method, subset,adp-method, subtractBottomVelocity(), summary,adp-method, toEnu(), toEnuAdp(), velocityStatistics(), xyzToEnu(), xyzToEnuAdp(), xyzToEnuAdpAD2CP()

Examples

data(adp)
# Tests for beam 1, distance bin 1, first 5 observation times
adp[["v"]][1:5, 1, 1]
adp[["a"]][1:5, 1, 1]
adp[["a", "numeric"]][1:5, 1, 1]
as.numeric(adp[["a"]][1:5, 1, 1]) # same as above

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'adv'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively, while dataDerived and metadataDerived hold the names of related things that can be derived from the object's contents.

• If i is "u1" then the return value is v[,1], and similarly for "u2" and "u3".

• If i is "a1" then signal amplitude is returned, and similarly for "a2" and "a3". The results can be in raw() or numeric form, as illustrated in the “Examples”.

• If i is "q1" then signal quality is returned, and similarly for "q2" and "q3". As with amplitude, the result can be in raw() or numeric form.

• If i is "heading", "pitch" or "roll", then these values are extracted from the "slow" form in the object (e.g. in headingSlow within the data slot). In that case, accessing by full name, e.g. x[["headingSlow"]] retrieves the item as expected, but x[["heading"]] interpolates to the faster timescale, using approx⁠(timeSlow,headingSlow,time)⁠.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to adv data: [[<-,adv-method, adv, adv-class, advSontekAdrFileTrim(), applyMagneticDeclination,adv-method, beamName(), beamToXyz(), enuToOther(), enuToOtherAdv(), plot,adv-method, read.adv(), read.adv.nortek(), read.adv.sontek.adr(), read.adv.sontek.serial(), read.adv.sontek.text(), rotateAboutZ(), subset,adv-method, summary,adv-method, toEnu(), toEnuAdv(), velocityStatistics(), xyzToEnu(), xyzToEnuAdv()

Examples

data(adv)
head(adv[["q"]]) # in raw form
head(adv[["q", "numeric"]]) # in numeric form

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'amsr'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Value

[[ returns numeric matrix data.

Details of the Specialized Method

The [[ method handles both old-format and new-format amsr objects. Old-format objects are read by read.amsr() from from gzipped files holding data in raw format, from which [[ computes numeric results with linear relationships provided at at ⁠http://www.remss.com/missions/amsre⁠. By contrast, new-format objects are read from NetCDF files that hold the data as 4-byte numeric values that are read directly, without applying a scaling transformation. The other difference is that old-format objects contain day and night values, e.g. SSTDay and SSTNight, whereas new-format objects contain single values that combine these, e.g. SST.

If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items are things that [[ can compute and then return.

Data within the data slot may be found directly (for both new-format and old-format objects) or indirectly (only for old-style objects). For example, SST works by direct lookup for new-format objects, but it is computed using SSTNight and SSTDay for old-format objects. Use e.g. a[["?"]] for any given object, to see what can be retrieved.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to amsr data: [[<-,amsr-method, amsr, amsr-class, composite,amsr-method, download.amsr(), plot,amsr-method, read.amsr(), subset,amsr-method, summary,amsr-method

Examples

# Histogram of SST values (for an old-format dataset)
library(oce)
data(amsr)
hist(amsr[["SST"]])

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'argo'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

Note that argo data may contain both unadjusted data and adjusted data. By default, this extraction function refers to the former, but a preference for the latter may be set with preferAdjusted(), the documentation of which explains (fairly complex) details.

The results from argo[[i]] or argo[[i,j]] depend on the nature of i and (if provided) j. The details are as follows.

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items hold the names of things that can be inferred from the object's contents, e.g. "SA" is named in dataDerived, indicating that argo[["SA"]] is permitted (to compute Absolute Salinity).

• If i is "profile" and j is an integer vector, then an argo object is returned, as specified by j. For example, argo[["profile", 2:5]] is equivalent to subset(argo, profile %in% 2:5).

• If i is "CT", then Conservative Temperature is returned, as computed with gsw::gsw_CT_from_t⁠(SA,t,p)⁠, where first SA is computed as explained in the next item, t is in-situ temperature, and p is pressure.

• If i is "N2", then the square of buoyancy is returned, as computed with swN2().

• If i is "SA", then Absolute Salinity is returned, as computed with gsw::gsw_SA_from_SP().

• If i is "sigmaTheta", then potential density anomaly (referenced to zero pressure) is computed, with swSigmaTheta(), where the equation of state is taken to be getOption⁠("oceEOS", default="gsw")⁠.

• If i is "sigma0", "sigma1", "sigma2", "sigma3" or "sigma4", then the associated function in the gsw package. For example, "sigma0" uses gsw::gsw_sigma0(), which returns potential density anomaly referenced to 0 dbar, according to the gsw equation of state.

• If i is "theta", then potential temperature (referenced to zero pressure) is computed, with swTheta(), where the equation of state is taken to be getOption⁠("oceEOS", default="gsw")⁠.

• If i is "depth", then a matrix of depths is returned.

• If i is "id" or "ID", then the id element within the metadata slot is returned.

• If i is in the data slot of x, then it is returned, otherwise if it is in the metadata slot, then that is returned, otherwise NULL is returned.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to argo data: [[<-,argo-method, argo, argo-class, argoGrid(), argoNames2oceNames(), as.argo(), handleFlags,argo-method, plot,argo-method, read.argo(), read.argo.copernicus(), subset,argo-method, summary,argo-method

Examples

data(argo)
# 1. show that dataset has 223 profiles, each with 56 levels
dim(argo[["temperature"]])

# 2. show importance of focussing on data flagged 'good'
fivenum(argo[["salinity"]], na.rm = TRUE)
fivenum(argo[["salinity"]][argo[["salinityFlag"]] == 1], na.rm = TRUE)

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'bremen'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items are each NULL, because no derived values are defined by bremen objects.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to bremen data: [[<-,bremen-method, bremen-class, plot,bremen-method, read.bremen(), summary,bremen-method

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'cm'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items are each NULL, because no derived values are defined by cm objects.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to cm data: [[<-,cm-method, applyMagneticDeclination,cm-method, as.cm(), cm, cm-class, plot,cm-method, read.cm(), rotateAboutZ(), subset,cm-method, summary,cm-method

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'coastline'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items are each NULL, because no derived values are defined for coastline objects.

• In many cases, the focus will be on the coastline trace in longitude-latitude space, so x[["longitude"]] and x[["latitude"]] are commonly used.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to coastline data: [[<-,coastline-method, as.coastline(), coastline-class, coastlineBest(), coastlineCut(), coastlineWorld, download.coastline(), plot,coastline-method, read.coastline.openstreetmap(), read.coastline.shapefile(), subset,coastline-method, summary,coastline-method

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'ctd'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

Some uses of [[,ctd-method involve direct retrieval of items within the data slot of the ctd object, while other uses involve calculations based on items in that data slot. For example, all ctd objects should hold an item named temperature in the data slot, so for example x[["temperature"]] will retrieve that item. By contrast, x[["sigmaTheta"]] is taken to be a request to compute $\sigma_\theta$, and so it yields a call to swTheta(x) even if the data slot of x might happen to contain an item named theta. This can be confusing at first, but it tends to lead to fewer surprises in everyday work, for otherwise the user would be forced to check the contents of any ctd object under analysis, to determine whether that item will be looked up or computed. Nothing is lost in this scheme, since the data within the object are always accessible with oceGetData().

It should be noted that the accessor is set up to retrieve quantities in conventional units. For example, read.ctd.sbe() is used on a .cnv file that stores pressure in psi, it will be stored in the same unit within the ctd object, but x[["pressure"]] will return a value that has been converted to decibars. (To get pressure in PSI, use x[["pressurePSI"]].) Similarly, temperature is returned in the ITS-90 scale, with a conversion having been performed with T90fromT68(), if the object holds temperature in IPTS-68. Again, temperature on the IPTS-68 scale is returned with x@data$temperature.

This preference for computed over stored quantities is accomplished by first checking for computed quantities, and then falling back to the general [[ method if no match is found.

Some quantities are optionally computed. For example, some data files (e.g. the one upon which the section() dataset is based) store nitrite along with the sum of nitrite and nitrate, the latter with name NO2+NO3. In this case, e.g. x[["nitrate"]] will detect the setup, and subtract nitrite from the sum to yield nitrate.

The list given below provides notes on some quantities that are available using e.g. ctd[[i]].

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items hold the names of things that can be inferred from the object's contents, e.g. "SA" is named in dataDerived, indicating that argo[["SA"]] is permitted (to compute Absolute Salinity).

• If i is "conductivity" without a second argument (e.g. a[["conductivity"]]) then the return value is the seawater electrical conductivity (if available or computable). However, if a second argument is given, and it is string specifying a unit, then conversion is made to that unit. The permitted units are: either "" or "ratio" (for ratio), "uS/cm", "mS/cm" and "S/m". The calculations are based on the definition of conductivity ratio as the ratio between measured conductivity and the standard value 4.2914 S/m.

• If i is "CT" or "Conservative Temperature" then Conservative Temperature, computed with gsw::gsw_CT_from_t(), is returned.

• If i is "density" then seawater density, computed with swRho(x), is returned. (Note that it may be better to call that function directly, to gain control of the choice of equation of state, etc.)

• If i is "depth" then the depth in metres below the surface, computed with swDepth(x), is returned.

• If i is "N2" then the square of Brunt-Vaisala frequency, computed with swN2(x), is returned.

• If i is "potential temperature" or "theta", then potential temperature in the UNESCO formulation, computed with swTheta(x), is returned.

• If i is "Rrho" then density ratio, computed with swRrho(x), is returned.

• If i is "SA" or "Absolute Salinity" then Absolute Salinity, computed with gsw::gsw_SA_from_SP(), is returned. The calculation involves location as well as measured water properties. If the object x does not containing information on the location, then 30N and 60W is used for the calculation, and a warning is generated.

• If i is "sigmaTheta" then a form of potential density anomaly, computed with swSigmaTheta(x), is returned.

• If i is "sigma0" then potential density anomaly referenced to a sea pressure of 0dbar (the surface), computed with swSigma0(x), is returned.

• If i is "sigma2" then potential density anomaly referenced to a sea pressure of 1000dbar, computed with swSigma1(x), is returned.

• If i is "sigma2" then potential density anomaly referenced to a sea pressure of 2000dbar, computed with swSigma2(x), is returned.

• If i is "sigma3" then potential density anomaly referenced to a sea pressure of 3000dbar, computed with swSigma3(x), is returned.

• If i is "sigma4" then potential density anomaly referenced to a sea pressure of 4000dbar, computed with swSigma4(x), is returned.

• If i is "SP" then salinity on the Practical Salinity Scale, which is salinity in the data slot, is returned.

• If i is "spice" then swSpice() is called to compute a quantity that is in some sense orthogonal to density on a T-S diagram. This is done by calling swSpice() with the eos argument set to "unesco". In an earlier version of oce, [[ could be provided with a second argument to yield a return value for "spiciness", a variable that is described in the next item. On 2024-02-14, this possibility was removed because it could lead to user confusion and non-reproducible code. To get spiciness, use ⁠[["spiciness0"]]⁠.

• If i is "spiciness0", "spiciness1" or "spiciness2", then the return value comes from the Gibbs SeaWater formulation of a variable that is in some sense orthogonal to density on a T-S diagram. The numbers refer to the reference pressure, in units of 1000 dbar. These results are computed with gsw::gsw_spiciness0(), etc.

• If i is "SR" then Reference Salinity, computed with gsw::gsw_SR_from_SP(), is returned.

• If i is "Sstar" then Preformed Salinity, computed with gsw::gsw_SR_from_SP(), is returned. See SA for a note on longitude and latitude.

• If i is "time" then either vector of times or a single time, is returned, if available. A vector is returned if time is present in the data slot, or if a time can be inferred from other entries in the data slot (some of which, such as the common timeS, also employ startTime within the metadata slot). A single value is returned if the dataset only has information on the start time (which is stored as startTime within the metadata slot. If it is impossible to determine the sampling time, then NULL is returned. These time variants occur, in the present version of oce, only for data read by read.ctd.sbe(), the documentation of which explains how times are computed.

• If i is "z" then vertical coordinate in metres above the surface, computed with swZ(x), is returned.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to ctd data: CTD_BCD2014666_008_1_DN.ODF.gz, [[<-,ctd-method, as.ctd(), cnvName2oceName(), ctd, ctd-class, ctd.cnv.gz, ctdDecimate(), ctdFindProfiles(), ctdFindProfilesRBR(), ctdRaw, ctdRepair(), ctdTrim(), ctd_aml_type1.csv.gz, ctd_aml_type3.csv.gz, d200321-001.ctd.gz, d201211_0011.cnv.gz, handleFlags,ctd-method, initialize,ctd-method, initializeFlagScheme,ctd-method, oceNames2whpNames(), oceUnits2whpUnits(), plot,ctd-method, plotProfile(), plotScan(), plotTS(), read.ctd(), read.ctd.aml(), read.ctd.itp(), read.ctd.odf(), read.ctd.odv(), read.ctd.saiv(), read.ctd.sbe(), read.ctd.ssda(), read.ctd.woce(), read.ctd.woce.other(), setFlags,ctd-method, subset,ctd-method, summary,ctd-method, woceNames2oceNames(), woceUnit2oceUnit(), write.ctd()

Examples

data(ctd)
head(ctd[["temperature"]])

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'echosounder'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The metadataDerived item is NULL, while the dataDerived item holds "Sv" and "TS" (see next).

• If i is "Sv", then the following is returned.

  20*log10(a) -
    (x@metadata$sourceLevel+x@metadata$receiverSensitivity+x@metadata$transmitPower) +
    20*log10(r) +
    2*absorption*r -
    x@metadata$correction +
    10*log10(soundSpeed*x@metadata$pulseDuration/1e6*psi/2)
  

• If i is "TS", then the following is returned.

  20*log10(a) -
    (x@metadata$sourceLevel+x@metadata$receiverSensitivity+x@metadata$transmitPower) +
    40*log10(r) +
    2*absorption*r +
    x@metadata$correction
  

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to echosounder data: [[<-,echosounder-method, as.echosounder(), echosounder, echosounder-class, findBottom(), plot,echosounder-method, read.echosounder(), subset,echosounder-method, summary,echosounder-method

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'g1sst'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items are each NULL, because no derived values are defined by g1sst objects.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to g1sst data: [[<-,g1sst-method, g1sst-class, read.g1sst()

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'gps'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items are each NULL, because no derived values are defined by gps objects.

• If i is "longitude" or "latitude", then the corresponding vector is returned.

• If i is "filename" then a filename is returned, if known (i.e. if the object was created with read.gps() or with as.gps() with the filename argument specified).

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to gps data: [[<-,gps-method, as.gps(), gps-class, plot,gps-method, read.gps(), summary,gps-method

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'ladp'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The metadataDerived item is NULL, and the dataDerived item holds the following synonyms: "p" for "pressure", "t" for "temperature" and "S" for "salinity".

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to ladp data: [[<-,ladp-method, as.ladp(), ladp-class, plot,ladp-method, summary,ladp-method

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'landsat'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The data entries are difficult to deal with directly, and so users are advised to use dataDerived instead.

Accessing band data. The data may be accessed with e.g. landsat[["panchromatic"]], for the panchromatic band. If a new “band” is added with landsatAdd(), it may be referred by name. In all cases, a second argument can be provided, to govern decimation. If this is missing, all the relevant data are returned. If this is present and equal to TRUE, then the data will be automatically decimated (subsampled) to give approximately 800 elements in the longest side of the matrix. If this is present and numerical, then its value governs decimation. For example, landsat[["panchromatic",TRUE]] will auto-decimate, typically reducing the grid width and height from 16000 to about 800. Similarly, landsat[["panchromatic",10]] will reduce width and height to about 1600. On machines with limited RAM (e.g. under about 6GB), decimation is a good idea in almost all processing steps. It also makes sense for plotting, and in fact is done through the 'decimate' argument of plot,landsat-method().

Accessing derived data. One may retrieve several derived quantities that are calculated from data stored in the object: landsat[["longitude"]] and landsat[["latitude"]] give pixel locations. Accessing landsat[["temperature"]] creates an estimate of ground temperature as follows (see reference 4). First, the “count value” in band 10, denoted $b_{10}$ say, is scaled with coefficients stored in the image metadata using $\lambda_L=b_{10}M_L+A_L$ where $M_L$ and $A_L$ are values stored in the metadata (e.g. the first in landsat@metadata$header$radiance_mult_band_10) Then the result is used, again with coefficients in the metadata, to compute Celcius temperature $T=K_2/ln(\epsilon K_1/\lambda_L+1)-273.15$. The value of the emissivity $\epsilon$ is set to unity by read.landsat(), although it can be changed easily later, by assigning a new value to 'landsat@metadata$emissivity'. The default emissivity value set by read.landsat() is from reference 11, and is within the oceanic range suggested by reference 5. Adjustment is as simple as altering 'landsat@metadata$emissivity'. This value can be a single number meant to apply for the whole image, or a matrix with dimensions matching those of band 10. The matrix case is probably more useful for images of land, where one might wish to account for the different emissivities of soil and vegetation, etc.; for example, Table 4 of reference 9 lists 0.9668 for soil and 0.9863 for vegetation, while Table 5 of reference 10 lists 0.971 and 0.987 for the same quantities.

Accessing metadata. Anything in the metadata can be accessed by name, e.g. landsat[["time"]]. Note that some items are simply copied over from the source data file and are not altered by e.g. decimation. An exception is the lat-lon box, which is altered by landsatTrim().

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to landsat data: [[<-,landsat-method, landsat, landsat-class, landsatAdd(), landsatTrim(), plot,landsat-method, read.landsat(), summary,landsat-method

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'lisst'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items are each NULL, because no derived values are defined by lisst objects.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to lisst data: [[<-,lisst-method, as.lisst(), lisst-class, plot,lisst-method, read.lisst(), summary,lisst-method

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'lobo'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items are each NULL, because no derived values are defined by cm objects.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to lobo data: [[<-,lobo-method, as.lobo(), lobo, lobo-class, plot,lobo-method, read.lobo(), subset,lobo-method, summary,lobo-method

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'met'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items are each NULL, because no derived values are defined by met objects.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to met data: [[<-,met-method, as.met(), download.met(), met, met-class, plot,met-method, read.met(), subset,met-method, summary,met-method

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'oce'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Many oce object classes have specialized versions of [[ that handle the details in specialized way.

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'odf'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items are each NULL, because no derived values are defined by odf objects.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to odf data: CTD_BCD2014666_008_1_DN.ODF.gz, ODF2oce(), ODFListFromHeader(), ODFNames2oceNames(), [[<-,odf-method, odf-class, plot,odf-method, read.ctd.odf(), read.odf(), subset,odf-method, summary,odf-method

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'rsk'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items are each NULL, because no derived values are defined by rsk objects.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to rsk data: [[<-,rsk-method, as.rsk(), ctdFindProfilesRBR(), plot,rsk-method, read.rsk(), rsk, rsk-class, rskPatm(), rskToc(), subset,rsk-method, summary,rsk-method

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'sealevel'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items are each NULL, because no derived values are defined by sealevel objects.

• In many cases, the focus will be on variations of sealevel elevation over time, so it is common to use e.g. x[["time"]] and x[["elevation"]] to retrieve vectors of these quantities. Another common task is to retrieve the location of the observations, using e.g. x[["longitude"]] and x[["latitude"]].

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to sealevel data: [[<-,sealevel-method, as.sealevel(), plot,sealevel-method, read.sealevel(), sealevel, sealevel-class, sealevelTuktoyaktuk, subset,sealevel-method, summary,sealevel-method

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'section'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

There are several possibilities, depending on the nature of i.

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. This list is compiled by examining all the stations in the object, and reporting an entry if it is found in any one of them. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items hold data-like and metadata-like things that can be derived from these.

• If i is "station", then [[ will return a list() of ctd objects holding the station data. If j is also given, it specifies a station (or set of stations) to be returned. if j contains just a single value, then that station is returned, but otherwise a list is returned. If j is an integer, then the stations are specified by index, but if it is character, then stations are specified by the names stored within their metadata. (Missing stations yield NULL in the return value.)

• If i is "station ID", then the IDs of the stations in the section are returned.

• If i is "dynamic height", then an estimate of dynamic height is returned, as calculated with swDynamicHeight(x).

• If i is "distance", then the distance along the section is returned, using geodDist().

• If i is "depth", then a vector containing the depths of the stations is returned.

• If i is "z", then a vector containing the z coordinates is returned.

• If i is "theta" or "potential temperature", then the potential temperatures of all the stations are returned in one vector. Similarly, "spice" returns the property known as spice, using swSpice().

• If i is a string ending with "Flag", then the characters prior to that ending are taken to be the name of a variable contained within the stations in the section. If this flag is available in the first station of the section, then the flag values are looked up for every station.

If j is "byStation", then a list is returned, with one (unnamed) item per station.

If j is "grid:distance-pressure" or "grid:time-pressure", then a gridded representation of i is returned, as a list with elements: distance (in km) or time (in POSIXct); pressure (in dbar) and field (in whatever unit is used for i). See the examples in the documentation for plot,section-method().

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to section data: [[<-,section-method, as.section(), handleFlags,section-method, initializeFlagScheme,section-method, plot,section-method, read.section(), section, section-class, sectionAddStation(), sectionGrid(), sectionSmooth(), sectionSort(), subset,section-method, summary,section-method

Examples

data(section)
length(section[["latitude"]])
length(section[["latitude", "byStation"]])
# Vector of all salinities, for all stations
Sv <- section[["salinity"]]
# List of salinities, grouped by station
Sl <- section[["salinity", "byStation"]]
# First station salinities
Sl[[1]]

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'tidem'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. Note that metadataDerived holds only "", because no derived metadata values are defined for tidem objects.

• If i is "frequency" or "freq", then a vector of constituent frequencies is returned.

• If i is "amplitude" then a vector of constituent amplitudes is returned.

• If i is "phase" then a vector of constituent phases is returned.

• If i is "constituents" then a data frame holding constituent name, frequency, amplitude and phase is returned.

• If i is a vector of constituent names, then the return value is as for "constituents", except that only the named those constituents are returned.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,topo-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to tides: [[<-,tidem-method, as.tidem(), plot,tidem-method, predict.tidem(), summary,tidem-method, tidalCurrent, tidedata, tidem, tidem-class, tidemAstron(), tidemVuf(), webtide()

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'topo'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items are each NULL, because no derived values are available for topo objects.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,windrose-method, [[,xbt-method, [[<-,adv-method

Other things related to topo data: [[<-,topo-method, as.topo(), download.topo(), plot,topo-method, read.topo(), subset,topo-method, summary,topo-method, topo-class, topoInterpolate(), topoWorld

Examples

data(topoWorld)
dim(topoWorld[["z"]])

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'windrose'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The metadataDerived and dataDerived items are both NULL.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,xbt-method, [[<-,adv-method

Other things related to windrose data: [[<-,windrose-method, as.windrose(), plot,windrose-method, summary,windrose-method, windrose-class

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 method for signature 'xbt'
x[[i, j, ...]]

Arguments

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

• If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items are each NULL, because no derived values are defined by cm objects.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[<-,adv-method

Other things related to xbt data: [[<-,xbt-method, as.xbt(), plot,xbt-method, read.xbt(), read.xbt.noaa1(), subset,xbt-method, summary,xbt-method, xbt, xbt-class, xbt.edf

Description

In addition to the usual insertion of elements by name, note that e.g. pitch gets stored into pitchSlow.

The [[<- method works for all oce objects. The purpose, as with the related extraction method, [[, is to insulate users from the internal details of oce objects, by looking for items within the various storage slots of the object. Items not actually stored can also be replaced, including units and data-quality flags.

Usage

## S4 replacement method for signature 'adp'
x[[i, j, ...]] <- value

Arguments

Details

As with [[ method, the procedure works in steps.

First, the metadata slot of x is checked to see whether it contains something named with i. If so, then the named item is replaced with value.

Otherwise, if the string value of i ends in Unit, then the characters preceding that are taken as the name of a variable, and the metadata slot of x is updated to store that unit, e.g.

x[["temperatureUnits"]] <- list(unit=expression(degree*F),scale="")

Similarly, if i ends in Flag, then quality-control flags are set up as defined by result, e.g.

o[["temperatureFlags"]] <- c(2,4,2,2)

Otherwise, pmatch() is used for a partial-string match with the names of the items that are in the data slot of x. The first item found (if any) is then updated to hold the value result.

If none of these conditions is met, a warning is issued.

Author(s)

Dan Kelley

See Also

Other functions that replace parts of oce objects: [[<-,amsr-method, [[<-,argo-method, [[<-,bremen-method, [[<-,cm-method, [[<-,coastline-method, [[<-,ctd-method, [[<-,echosounder-method, [[<-,g1sst-method, [[<-,gps-method, [[<-,ladp-method, [[<-,landsat-method, [[<-,lisst-method, [[<-,lobo-method, [[<-,met-method, [[<-,oce-method, [[<-,odf-method, [[<-,rsk-method, [[<-,sealevel-method, [[<-,section-method, [[<-,tidem-method, [[<-,topo-method, [[<-,windrose-method, [[<-,xbt-method

Other things related to adp data: [[,adp-method, ad2cpCodeToName(), ad2cpHeaderValue(), adp, adp-class, adpAd2cpFileTrim(), adpConvertRawToNumeric(), adpEnsembleAverage(), adpFlagPastBoundary(), adpRdiFileTrim(), adp_rdi.000, applyMagneticDeclination,adp-method, as.adp(), beamName(), beamToXyz(), beamToXyzAdp(), beamToXyzAdpAD2CP(), beamToXyzAdv(), beamUnspreadAdp(), binmapAdp(), enuToOther(), enuToOtherAdp(), handleFlags,adp-method, is.ad2cp(), plot,adp-method, read.adp(), read.adp.ad2cp(), read.adp.nortek(), read.adp.rdi(), read.adp.sontek(), read.adp.sontek.serial(), read.aquadopp(), read.aquadoppHR(), read.aquadoppProfiler(), rotateAboutZ(), setFlags,adp-method, subset,adp-method, subtractBottomVelocity(), summary,adp-method, toEnu(), toEnuAdp(), velocityStatistics(), xyzToEnu(), xyzToEnuAdp(), xyzToEnuAdpAD2CP()

Description

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

## S4 replacement method for signature 'adv'
x[[i, j, ...]] <- value

Arguments

Details

If the adv object holds slow variables (i.e. if timeSlow is in the data slot), then assigning to .e.g. heading will not actually assign to a variable of that name, but instead assigns to headingSlow. To catch misapplication of this rule, an error message will be issued if the assigned value is not of the same length as timeSlow.

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the values of i and, optionally, j. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. A check is made as to whether i names one of the standard oce slots. If so, [[ returns the slot contents of that slot. Thus, x[["metadata"]] will retrieve the metadata slot, while x[["data"]] and x[["processingLog"]] return those slots.

2. If i is a string ending in the "Unit", then the characters preceding that string are taken to be the name of an item in the data object, and a list containing the unit is returned (or NULL if there is no such unit). This list consists of an item named unit, which is an expression(), and an item named scale, which is a string describing the measurement scale. If the string ends in " unit", e.g. x[["temperature unit"]] (note the space), then just the expression is returned, and if it ends in " scale", then just the scale is returned.

3. If i is a string ending in "Flag", then the corresponding data-quality flag is returned (or NULL if there is no such flag).

4. If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. If i is "sigmaTheta", then the value of swSigmaTheta() is called with x as the sole argument, and the results are returned. Similarly, swSigma0() is used if i="sigma0", and swSpice() is used if i="spice". Of course, these actions only make sense for objects that contain the relevant items within their data slot.

5. After these possibilities are eliminated, the action depends on whether j has been provided. If j is not provided, or is the string "", then i is sought in the metadata slot, and then in the data slot, returning whichever is found first. In other words, if j is not provided, the metadata slot takes preference over the data slot. However, if j is provided, then it must be either the string "metadata" or "data", and it directs where to look.

6. If none of the above-listed conditions holds, then NULL is returned.

Author(s)

Dan Kelley

See Also

Other functions that extract parts of oce objects: [[,adp-method, [[,adv-method, [[,amsr-method, [[,argo-method, [[,bremen-method, [[,cm-method, [[,coastline-method, [[,ctd-method, [[,echosounder-method, [[,g1sst-method, [[,gps-method, [[,ladp-method, [[,landsat-method, [[,lisst-method, [[,lobo-method, [[,met-method, [[,oce-method, [[,odf-method, [[,rsk-method, [[,sealevel-method, [[,section-method, [[,tidem-method, [[,topo-method, [[,windrose-method, [[,xbt-method

Other things related to adv data: [[,adv-method, adv, adv-class, advSontekAdrFileTrim(), applyMagneticDeclination,adv-method, beamName(), beamToXyz(), enuToOther(), enuToOtherAdv(), plot,adv-method, read.adv(), read.adv.nortek(), read.adv.sontek.adr(), read.adv.sontek.serial(), read.adv.sontek.text(), rotateAboutZ(), subset,adv-method, summary,adv-method, toEnu(), toEnuAdv(), velocityStatistics(), xyzToEnu(), xyzToEnuAdv()

Description

The [[<- method works for all oce objects. The purpose, as with the related extraction method, [[, is to insulate users from the internal details of oce objects, by looking for items within the various storage slots of the object. Items not actually stored can also be replaced, including units and data-quality flags.

Usage

## S4 replacement method for signature 'amsr'
x[[i, j, ...]] <- value

Arguments

Details

As with [[ method, the procedure works in steps.

First, the metadata slot of x is checked to see whether it contains something named with i. If so, then the named item is replaced with value.

Otherwise, if the string value of i ends in Unit, then the characters preceding that are taken as the name of a variable, and the metadata slot of x is updated to store that unit, e.g.

x[["temperatureUnits"]] <- list(unit=expression(degree*F),scale="")

Similarly, if i ends in Flag, then quality-control flags are set up as defined by result, e.g.

o[["temperatureFlags"]] <- c(2,4,2,2)

Otherwise, pmatch() is used for a partial-string match with the names of the items that are in the data slot of x. The first item found (if any) is then updated to hold the value result.

If none of these conditions is met, a warning is issued.

See Also

Other functions that replace parts of oce objects: [[<-,adp-method, [[<-,argo-method, [[<-,bremen-method, [[<-,cm-method, [[<-,coastline-method, [[<-,ctd-method, [[<-,echosounder-method, [[<-,g1sst-method, [[<-,gps-method, [[<-,ladp-method, [[<-,landsat-method, [[<-,lisst-method, [[<-,lobo-method, [[<-,met-method, [[<-,oce-method, [[<-,odf-method, [[<-,rsk-method, [[<-,sealevel-method, [[<-,section-method, [[<-,tidem-method, [[<-,topo-method, [[<-,windrose-method, [[<-,xbt-method

Other things related to amsr data: [[,amsr-method, amsr, amsr-class, composite,amsr-method, download.amsr(), plot,amsr-method, read.amsr(), subset,amsr-method, summary,amsr-method

Description

The [[<- method works for all oce objects. The purpose, as with the related extraction method, [[, is to insulate users from the internal details of oce objects, by looking for items within the various storage slots of the object. Items not actually stored can also be replaced, including units and data-quality flags.

Usage

## S4 replacement method for signature 'argo'
x[[i, j, ...]] <- value

Arguments

Details

As with [[ method, the procedure works in steps.

First, the metadata slot of x is checked to see whether it contains something named with i. If so, then the named item is replaced with value.

Otherwise, if the string value of i ends in Unit, then the characters preceding that are taken as the name of a variable, and the metadata slot of x is updated to store that unit, e.g.

x[["temperatureUnits"]] <- list(unit=expression(degree*F),scale="")

Similarly, if i ends in Flag, then quality-control flags are set up as defined by result, e.g.

o[["temperatureFlags"]] <- c(2,4,2,2)

Otherwise, pmatch() is used for a partial-string match with the names of the items that are in the data slot of x. The first item found (if any) is then updated to hold the value result.

If none of these conditions is met, a warning is issued.

See Also

Other functions that replace parts of oce objects: [[<-,adp-method, [[<-,amsr-method, [[<-,bremen-method, [[<-,cm-method, [[<-,coastline-method, [[<-,ctd-method, [[<-,echosounder-method, [[<-,g1sst-method, [[<-,gps-method, [[<-,ladp-method, [[<-,landsat-method, [[<-,lisst-method, [[<-,lobo-method, [[<-,met-method, [[<-,oce-method, [[<-,odf-method, [[<-,rsk-method, [[<-,sealevel-method, [[<-,section-method, [[<-,tidem-method, [[<-,topo-method, [[<-,windrose-method, [[<-,xbt-method

Other things related to argo data: [[,argo-method, argo, argo-class, argoGrid(), argoNames2oceNames(), as.argo(), handleFlags,argo-method, plot,argo-method, read.argo(), read.argo.copernicus(), subset,argo-method, summary,argo-method

Description

The [[<- method works for all oce objects. The purpose, as with the related extraction method, [[, is to insulate users from the internal details of oce objects, by looking for items within the various storage slots of the object. Items not actually stored can also be replaced, including units and data-quality flags.

Usage

## S4 replacement method for signature 'bremen'
x[[i, j, ...]] <- value