Analysis of Oceanographic data


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Documentation for package ‘oce’ version 0.8-6

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A B C D E F G H I L M N O P R S T U V W X misc

-- A --

a03 WOCE section a03
addColumn Add a column to an oce object
adp ADP (acoustic-doppler profiler) dataset
adp-class Class to store acoustic Doppler profiler data
adv ADV (acoustic-doppler velocimeter) dataset
adv-class Class to store acoustic Doppler velocimeter data
airHalifax Time-series of wind and temperature at Halifax, Canada.
airRho Air density
angleRemap Convert an angle from the 0:360 range to -180:180
applyMagneticDeclination Earth magnetic declination
argo ARGO drifter dataset
as.coastline Coerce data into coastline dataset
as.ctd Coerce data into ctd dataset
as.drifter Coerce data into drifter dataset
as.echosounder Coerce data into echosounder dataset
as.lobo Coerce data into lobo dataset
as.met Coerce data into met dataset
as.pt Create an TDR temperature-depth recorder data file
as.sealevel Coerce data into sea-level dataset
as.topo Coerce data into topo dataset
as.windrose Create a windrose object

-- B --

bcdToInteger Decode BCD to integer
beamName Name an acoustic-doppler beam.
beamToXyz Convert ADV or ADP data between various coordinate systems
beamToXyzAdp Convert ADP from beam coordinates to xyz coordinates
beamToXyzAdv Convert ADV from beam coordinates to xyz coordinates
beamUnattenuateAdp Unattenuate ADP beam signal strength
binAverage Bin-average a vector y, based on x values
byteToBinary Format bytes as binary

-- C --

cm-class Class to store current meter data
coastline-class Class to store coastline data
coastlineHalifax Coastline data set, showing Halifax Harbour
coastlineMaritimes Coastline data set, showing Maritime provinces of Canada
coastlineSLE Coastline of St Lawrence Estuary
coastlineWorld World coastline
coordinate Determine coordinate system for acoustic-doppler device
coriolis Coriolis parameter on rotating earth
ctd Seawater CTD profile
ctd-class Class to store hydrographic data
ctdAddColumn Add a column to a CTD file
ctdDecimate Decimate a CTD profile
ctdRaw Seawater CTD profile, without trimming of extraneous data
ctdTrim Trim start/end portions of a CTD cast
ctdUpdateHeader Update a CTD header
ctimeToSeconds Interpret a character string as a time interval

-- D --

decimate Smooth and decimate an oce object
despike Remove spikes from a time series
detrend Detrend a set of observations
distance Access or modify part of an Oce object
drag Wind drag coefficient
drawIsopycnals Draw isopycnal curves on an existing temperature-salinity plot
drawPalette Draw a palette on the right-hand side of plot device
drifter-class Class to store drifter data, e.g. from an ARGOS float

-- E --

echosounder-class Class to store echosounder data
elevation Access or modify part of an Oce object
enuToOther Convert ADV or ADP data between various coordinate systems
enuToOtherAdp Convert ADP from east-north-up coordinates to other coordinates
enuToOtherAdv Convert ADV from east-north-up coordinates to other coordinates
extract Extract data from an oce object

-- F --

fillGap Fill a gap in an oce object
findBottom Find the ocean bottom in an echosounder object
findInOrdered Find indices of tiems in an ordered vector
formatCI Format a confidence interval in parenthetic notation
fullFilename full name of file, including path

-- G --

geodDist Geodesic distance on earth
geodXy Convert lat/lon to x/y on earth
geosecs235 GEOSECS station 235 data
GMTOffsetFromTz Determine time offset from timezone
gravity Acceleration due to earth gravity

-- H --

head Returns the first or last parts of an 'oce' object.
head.adp Returns the first or last parts of an 'oce' object.
header Return the header for an Oce data object
heading Access or modify part of an Oce object
heading<- Access or modify part of an Oce object

-- I --

imagep Plot an image with a colour palette
integerToAscii Decode integer to corresponding ASCII code
interpBarnes Grid data using Barnes algorithm
is.beam Determine coordinate system for acoustic-doppler device
is.enu Determine coordinate system for acoustic-doppler device
is.xyz Determine coordinate system for acoustic-doppler device

-- L --

latFormat Format a latitude
latitude Access or modify part of an Oce object
latitude<- Access or modify part of an Oce object
latlonFormat Format a latitude-longitude pair
lobo lobo dataset
lobo-class Class to store LOBO data
loggerToc Decode table-of-contents file from a datalogger
lonFormat Format a longitude
longitude Access or modify part of an Oce object
longitude<- Access or modify part of an Oce object

-- M --

magic Find the type of an oceanographic data file
magneticDeclination Earth magneticDeclination
makeFilter Make a digital filter
makeSection Bind CTD profiles together into a cross section
matchBytes Find spots in a raw vector that match a given byte sequence.
matrixSmooth Smooth a matrix.
met Sample meteorological object
met-class Class to store meteorological data
munk Munk's (1966) temperature profile

-- N --

nitrate Access or modify part of an Oce object
nitrate<- Access or modify part of an Oce object
nitrite Access or modify part of an Oce object
nitrite<- Access or modify part of an Oce object
numberAsPOSIXct Convert a numeric time to a POSIXct time

-- O --

oce base class of oce package
oce-class base class of oce package
oce.as.POSIXlt More general form of as.POSIXlt
oce.axis.POSIXct Modified version of axis.POSIXct
oce.plot.sticks Draw a stick-plot diagram
oce.plot.ts Plot a time-series, obeying the timezone
oce.write.table Write the data portion of object to a file
oceApprox Interpolate with Reiniger-Ross algorithm
oceBisect Find the root of a function by bisection
oceColorsGebco Create a palette of colours
oceColorsJet Create a palette of colours
oceColorsPalette Create a palette of colours
oceColorsTwo Create a palette of colours
oceDebug Print a debugging message
oceEdit Edit an oce object
oceFilter Filter a time-series, possibly recursively
oceSmooth Smooth an oce object
oceSpectrum Wrapper to give normalized spectrum
oxygen Access or modify part of an Oce object
oxygen<- Access or modify part of an Oce object

-- P --

parseLatLon Parse a latitude or longitude string
phosphate Access or modify part of an Oce object
phosphate<- Access or modify part of an Oce object
pitch Access or modify part of an Oce object
pitch<- Access or modify part of an Oce object
plot-method Plot ADP data
plot-method Plot ADV data
plot-method Plot a coastline
plot-method Plot seawater CTD data
plot-method Plot drifter data
plot-method Plot echosounder data
plot-method Plot meteorological data
plot-method Plot pt (pressure-temperature) recorder data
plot-method Plot a CTD section
plot.adp Plot ADP data
plot.adv Plot ADV data
plot.cm Plot cm (current meter) data
plot.coastline Plot a coastline
plot.ctd Plot seawater CTD data
plot.drifter Plot drifter data
plot.echosounder Plot echosounder data
plot.lobo Plot lobo data
plot.met Plot meteorological data
plot.pt Plot pt (pressure-temperature) recorder data
plot.sealevel Plot sealevel data
plot.section Plot a CTD section
plot.tidem Plot a tidal fit
plot.topo Plot topography data
plot.windrose Plot a wind rose diagram
plotInset Plot an inset diagram
plotProfile Plot a CTD profile of various quantities
plotScan Plot seawater data in a low-level fashion
plotTS Plot temperature-salinity diagram for seawater (CTD) data
predict.tidem Predict a time series from a tidal model
pressure Access or modify part of an Oce object
pressure<- Access or modify part of an Oce object
print.summary.tidem Summarize a tide-model object
processingLog Add an item to object processingLog
processingLog<- Add an item to object processingLog
processingLogItem Add an item to object processingLog
processingLogShow Add an item to object processingLog
pt-class Class to store pressure-temperature recorder data
ptPatm Estimate atmospheric pressure in pt record
ptr ptr (pressure-temperature) dataset
ptTrim Trim start/end portions of a pt cast
pwelch Welch periodogram

-- R --

rangeLimit Substitute NA for data outside a range
read.adp Read an ADP data file
read.adp.nortek Read an ADP data file
read.adp.rdi Read an ADP data file
read.adp.sontek Read an ADP data file
read.adp.sontek.serial Read an ADP data file
read.adv Read an ADV data file
read.adv.nortek Read an ADV data file
read.adv.sontek.adr Read an ADV data file
read.adv.sontek.serial Read an ADV data file
read.adv.sontek.text Read an ADV data file
read.cm Read a current-meter data file
read.cm.s4 Read a current-meter data file
read.coastline Scan a coastline data file
read.coastline.shapefile Scan a coastline data file
read.ctd Read a CTD data file
read.ctd.odf Read a CTD data file
read.ctd.sbe Read a CTD data file
read.ctd.woce Read a CTD data file
read.drifter Read a drifter data file
read.echosounder Read an echosounder data file
read.lobo Read a lobo data file
read.met Read a meteorological data file
read.oce Read an oceanographic data file
read.pt Read an TDR temperature-depth recorder data file
read.sealevel Read a sea-level data file
read.section Read a section containing multiple CTD profiles
read.topo Read an topography file
redfieldNC Redfield's (1934) NO3 and total CO2 data
redfieldNP Redfield's (1934) NO3 and PO4 data
redfieldPlankton Redfield's (1934) Table II
rescale Rescale values to lie in a given range
resizableLabel Provide axis names in adjustable sizes
retime Adjust the time within Oce object
riley Riley's (1946) observation and theory of phytoplankton concentration
roll Access or modify part of an Oce object
roll<- Access or modify part of an Oce object
RRprofile Seawater profile used by Reiniger and Ross (1968)

-- S --

salinity Access or modify part of an Oce object
salinity<- Access or modify part of an Oce object
schmitt Schmitt's (1981) NACW temperature-salinity data
sealevel-class Class to store sealevel data
sealevelHalifax Sea-level data set, from Halifax Harbour
sealevelTuktoyaktuk Sea-level data set acquired in 1975 at Tuktoyaktuk
secondsToCtime Convert a time interval to a colon-separated string
section Seawater CTD section
section-class Class to store hydrographic section data
sectionGrid Grid a section
sectionSmooth Smooth a section (preliminary version that may change)
sectionSort Sort a section
show-method Class to store acoustic Doppler profiler data
show-method Class to store acoustic Doppler velocimeter data
show-method Class to store current meter data
show-method Class to store coastline data
show-method Class to store hydrographic data
show-method Class to store echosounder data
show-method Class to store LOBO data
show-method Class to store meteorological data
show-method base class of oce package
show-method Class to store pressure-temperature recorder data
show-method Class to store sealevel data
show-method Class to store hydrographic section data
showMetadataItem Show metadata item
sigmaTheta Access or modify part of an Oce object
sigmaTheta<- Access or modify part of an Oce object
silicate Access or modify part of an Oce object
silicate<- Access or modify part of an Oce object
soi Southern Oscillation Index
spice Access or modify part of an Oce object
stickplot Draw a stick-plot diagram
subset.oce Subset an oce object
summary.adp Summarize an ADP object
summary.adv Summarize an ADV object
summary.cm Summarize a cm (current meter) object
summary.coastline Summarize a coastline data object
summary.ctd Summarize a CTD object
summary.drifter Summarize a drifter object
summary.echosounder Summarize an echosounder object
summary.lobo Summarize a lobo data object
summary.met Summarize a met object
summary.pt Summarize a pt object
summary.sealevel Summarize a sealevel object
summary.section Summarize a CTD section
summary.tidem Summarize a tide-model object
summary.topo Summarize a topography data object
summary.windrose Summarize a windrose data object
sunAngle Solar angle as function of space and time.
swAlpha Seawater thermal expansion coefficient
swAlphaOverBeta Ratio of seawater thermal expansion coefficient to haline contraction coefficient
swBeta Seawater haline contraction coefficient
swConductivity Seawater thermal conductivity
swDepth Water depth
swDynamicHeight Dynamic height of seawater profile
swLapseRate Seawater lapse rate
swN2 Squared buoyancy frequency for seawater
swRho Seawater density
swSCTp Seawater salinity from conductivity ratio, temperature and pressure
swSigma Seawater density anomaly
swSigmaT Seawater quasi-potential density anomaly
swSigmaTheta Seawater potential density anomaly
swSoundSpeed Seawater sound speed
swSpecificHeat Seawater specific heat
swSpice Seawater spiciness
swSTrho Seawater salinity from temperature and density
swTFreeze Seawater freezing temperature
swTheta Seawater potential temperature
swTSrho Seawater temperature from salinity and density
swViscosity Seawater viscosity
swZ Water depth

-- T --

tail Returns the first or last parts of an 'oce' object.
tail.adp Returns the first or last parts of an 'oce' object.
temperature Access or modify part of an Oce object
temperature<- Access or modify part of an Oce object
threenum Calculate min, mean, and max values
tidedata Tidal constituent information
tidem Fit a tidal model to a timeseries
tidem-class Class to store tidal-constituent models
tidemAstron Do ephemeris calculations for tidem
tidemVuf Do ephemeris calculations for tidem
time Access or modify part of an Oce object
time.oce Extract time from an oce object
toEnu Convert ADV or ADP data between various coordinate systems
toEnuAdp Convert ADP to enu coordinates, from any other coordinates
toEnuAdv Convert ADV to enu coordinates, from any other coordinates
topo-class Class to store topographic data
topoInterpolate Interpolate within a topography dataset
topoMaritimes Topographic dataset, showing Maritime region of Canada
topoWorld Global topographic dataset at half-degree resolution
tritium Access or modify part of an Oce object

-- U --

unabbreviateYear Determine year from various abbreviations
undriftTime Correct for drift in instrument clock
unwrapAngle Unwrap an angle that suffers modulo-360 problems
useHeading Replace the heading for one instrument with the heading for another

-- V --

vectorShow Show some values from a vector
velocity Access or modify part of an Oce object
velocityStatistics Report statistics of ADP or ADV velocities.

-- W --

webtide Get a tidal prediction from a WebTide database
wilson Wilson's (1963) table of seafloor spreading
wind Wind dataset
window.oce Window an oce object by time or distance
windrose-class Class to store windrose data
write.ctd Write a CTD data object as a .csv file

-- X --

xyzToEnu Convert ADV or ADP data between various coordinate systems
xyzToEnuAdp Convert ADP or ADV from xyz coordinates to enu coordinates
xyzToEnuAdv Convert ADP or ADV from xyz coordinates to enu coordinates

-- misc --

+.section Bind CTD profiles together into a cross section
[[-method Access or modify part of an Oce object
[[-method Class to store acoustic Doppler profiler data
[[-method Class to store acoustic Doppler velocimeter data
[[-method Class to store current meter data
[[-method Class to store coastline data
[[-method Class to store hydrographic data
[[-method Class to store drifter data, e.g. from an ARGOS float
[[-method Class to store echosounder data
[[-method Class to store LOBO data
[[-method Class to store meteorological data
[[-method base class of oce package
[[-method Class to store pressure-temperature recorder data
[[-method Class to store sealevel data
[[-method Class to store hydrographic section data
[[-method Class to store tidal-constituent models
[[-method Class to store topographic data
[[-method Class to store windrose data
[[<--method Class to store acoustic Doppler profiler data
[[<--method Class to store acoustic Doppler velocimeter data
[[<--method Class to store current meter data
[[<--method Class to store coastline data
[[<--method Class to store hydrographic data
[[<--method Class to store echosounder data
[[<--method Class to store LOBO data
[[<--method Class to store meteorological data
[[<--method base class of oce package
[[<--method Class to store pressure-temperature recorder data
[[<--method Class to store sealevel data
[[<--method Class to store hydrographic section data