as.ctd: Coerce data into ctd dataset

Description

Coerces a dataset into a ctd dataset.

Usage

as.ctd(salinity, temperature, pressure, conductivity,
       SA, CT,
       oxygen, nitrate, nitrite, phosphate, silicate,
       scan, other,
       missingValue,
       quality, 
       filename="", type="", model="", serialNumber="",
       ship="", scientist="", institute="", address="", cruise="", station="", 
       date="", startTime="", recovery="",
       longitude=NA, latitude=NA,
       pressureAtmospheric=NA, waterDepth=NA,
       sampleInterval=NA, src="")

Arguments

salinity

Salinity through the water column, or a data frame containing columns named salinity, temperature, and pressure, in which case these values are extracted from the data frame, and the next two arguments ar

temperature

Temperature through the water column. (This is converted to a vector, if it is not one already.

pressure

pressure through the water column. (If just a single value is given, then it is repeated to match the length of the temperature and salinity.

conductivity

electrical conductivity ratio through the water column (optional). Some devices report raw conductivity in milliSeimens per centimeter, and that number should be divided by 42.914 to get conductivity for use here.

absolute salinity (as in TEOS-10). If given, the supplied absolute salinity is converted internally to UNESCO-defined practical salinity.

conservative temperature (as in TEOS-10). If given, the supplied conservative temperature is converted internally to UNESCO-defined in-situ temperature.

oxygen

optional oxygen concentration

nitrate

optional nitrate concentration [micromole/kg]

nitrite

optional nitrite concentration [micromole/kg]

phosphate

optional phosphate concentration [micromole/kg]

silicate

optional silicate concentration [micromole/kg]

scan

optional scan number. If not provided, this will be set to 1:length(salinity).

other

optional list of other data columns that are not in the standard list

missingValue

optional missing value, indicating data that should be taken as NA.

quality

quality flag, e.g. from the salinity quality flag in WOCE data. (In WOCE, quality=2 indicates good data, quality=3 means questionable data, and quality=4 means bad data.

filename

filename to be stored in the object

type

type of CTD, e.g. "SBE"

model

model of instrument

serialNumber

serial number of instrument

ship

optional string containing the ship from which the observations were made.

scientist

optional string containing the chief scientist on the cruise.

institute

optional string containing the institute behind the work.

address

optional string containing the address of the institute.

cruise

optional string containing a cruise identifier.

station

optional string containing a station identifier.

date

optional string containing the date at which the profile was started.

startTime

optional string containing the start time.

recovery

optional string indicating the recovery time.

longitude

optional numerical value containing longitude in decimal degrees, positive in the eastern hemisphere.

latitude

optional numerical value containing the latitude in decimal degrees, positive in the northern hemisphere.

pressureAtmospheric

if provided, this value is subtracted from pressure data before storing them in the object.

waterDepth

optional numerical value indicating the water depth in metres.

sampleInterval

optional numerical value indicating the time between samples in the profile.

src

optional string indicating data source

Value

An object of class "ctd" (for details, see read.ctd).

Details

This function assembles vectors of salinity, temperature, and pressure, to create a ctd object, e.g. so that plot.ctd can be used to make a standard four-panel plot, or so that a section can be constructed with makeSection. Normally, the input vectors will be of the same length, but as.ctd can also handle cases in which one or two of these is of unit length. For example, if only a temperature profile is available, as.ctd(35, T, p) could be used to construct a ctd object with constant salinity.

Examples

Run this code

library(oce)
pressure <- 1:50
temperature <- 10 - tanh((pressure - 20) / 5) + 0.02*rnorm(50)
salinity <- 34 + 0.5*tanh((pressure - 20) / 5) + 0.01*rnorm(50)
ctd <- as.ctd(salinity, temperature, pressure)
summary(ctd)
plot(ctd)