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Initialize Storage for a ctd Object

Source: R/ctd.R
initialize-ctd-method.Rd

This function creates ctd objects. It is mainly used by oce functions such as read.ctd() and as.ctd(), and it is not intended for novice users, so it may change at any time, without following the usual rules for transitioning to deprecated and defunct status (see oce-deprecated).

Usage

# S4 method for class 'ctd'
initialize(
  .Object,
  pressure,
  salinity,
  temperature,
  conductivity,
  units,
  pressureType,
  deploymentType,
  ...
)

Arguments

.Object

the string "ctd"

pressure

optional numerical vector of pressures.

salinity

optional numerical vector of salinities.

temperature

optional numerical vector of temperatures.

conductivity

optional numerical vector of conductivities.

units

optional list indicating units for the quantities specified in the previous arguments. If this is not supplied, a default is set up, based on which of the pressure to conductivity arguments were specified. If all of those 4 arguments were specified, then units is set up as if the call included the following: units=list(temperature=list(unit=expression(degree*C), scale="ITS-90"), salinity=list(unit=expression(), scale="PSS-78"), conductivity=list(unit=expression(), scale=""), pressure=list(unit=expression(dbar), scale=""), depth=list(unit=expression(m), scale="")). This list is trimmed of any of the 4 items that were not specified in the previous arguments. Note that if units is specified, then it is just copied into the metadata slot of the returned object, so the user must be careful to set up values that will make sense to other oce functions.

pressureType

optional character string indicating the type of pressure; if not supplied, this defaults to "sea", which indicates the excess of pressure over the atmospheric value, in dbar.

deploymentType

optional character string indicating the type of deployment, which may be "unknown", "profile", "towyo", or "thermosalinograph". If this is not set, the value defaults to "unknown".

...

Ignored.

Details

To save storage, this function has arguments only for quantities that are often present in data files all cases. For example, not all data files will have oxygen, so that's not present here. Extra data may be added after the object is created, using oceSetData(). Similarly, oceSetMetadata() may be used to add metadata (station ID, etc), while bearing in mind that other functions look for such information in very particular places (e.g. the station ID is a string named station within the metadata slot). See ctd for more information on elements stored in ctd objects.

See also

Other things related to ctd data: CTD_BCD2014666_008_1_DN.ODF.gz, [[,ctd-method, [[<-,ctd-method, as.ctd(), as.ctd.argo(), 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, 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


# 1. empty
new("ctd")
#> ctd object has nothing in its data slot.

# 2. fake data with no location information, so can only
#    plot with the UNESCO equation of state.
#    NOTE: always name arguments, in case the default order gets changed
ctd <- new("ctd", salinity = 35 + 1:3 / 10, temperature = 10 - 1:3 / 10, pressure = 1:3)
summary(ctd)
#> CTD Summary
#> -----------
#> 
#> * Data Overview
#> 
#>                              Min. Mean Max. Dim. NAs
#>     pressure [dbar]          1    2    3    3    0  
#>     temperature [°C, ITS-90] 9.7  9.8  9.9  3    0  
#>     salinity [PSS-78]        35.1 35.2 35.3 3    0  
#> 
#> * Processing Log
#> 
#>     - 2024-12-21 18:02:49 UTC: `create 'ctd' object`
plot(ctd, eos = "unesco")


# 3. as 2, but insert location and plot with GSW equation of state.
ctd <- oceSetMetadata(ctd, "latitude", 44)
ctd <- oceSetMetadata(ctd, "longitude", -63)
plot(ctd, eos = "gsw")