Analysis of Oceanographic data


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Documentation for package ‘oce’ version 0.9-14

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

-- A --

abbreviateTimeLabels Abbreviate a list of times by removing commonalities (e.g. year)
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
airRho Air density
angleRemap Convert angles from 0:360 to -180:180
applyMagneticDeclination Earth magnetic declination
approx3d Trilinear interpolation in a 3D array
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.gps Coerce data into a GPS dataset
as.lisst Coerce data into a lisst object
as.lobo Coerce data into lobo dataset
as.met Coerce data into met dataset
as.sealevel Coerce data into sea-level dataset
as.section Coerce ctd data into section dataset
as.tdr Create a TDR object
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 Change ADV or ADP coordinate systems
beamToXyzAdp Change ADP coordinate system
beamToXyzAdv Convert ADV from beam coordinates to xyz coordinates
beamUnspreadAdp Adjust ADP signal for spherical spreading
binApply Apply a function to binned matrix data
binApply1D Apply a function to binned matrix data
binApply2D Apply a function to binned matrix data
binAverage Bin-average a vector y, based on x values
binCount Bin-count or bin-average f=f(x) or f=f(x,y), based on x or (x,y) values
binCount1D Bin-count or bin-average f=f(x) or f=f(x,y), based on x or (x,y) values
binCount2D Bin-count or bin-average f=f(x) or f=f(x,y), based on x or (x,y) values
binmapAdp Bin-map an ADP object
binMean Bin-count or bin-average f=f(x) or f=f(x,y), based on x or (x,y) values
binMean1D Bin-count or bin-average f=f(x) or f=f(x,y), based on x or (x,y) values
binMean2D Bin-count or bin-average f=f(x) or f=f(x,y), based on x or (x,y) values
byteToBinary Format bytes as binary

-- C --

cm Current-meter record
cm-class Class to store current meter data
coastline-class Class to store coastline data
coastlineBest Find the name of the best coastline file
coastlineWorld World coastline
colormap Calculate color map
coordinate Determine coordinate system
coriolis Coriolis parameter on rotating earth
ctd A CTD profile in Halifax Harbour
ctd-class Class to store hydrographic data
ctdAddColumn Add a column to a CTD file
ctdDecimate Decimate a CTD profile
ctdFindProfiles Find profiles within a towyow CTD record
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
decodeHeaderNortek Decode a Nortek header
decodeTime Decode a time, similar to as.POSIXct()
despike Remove spikes from a time series
detrend Detrend a set of observations
distance Access or modify part of an Oce object
drawDirectionField Draw a direction field
drawIsopycnals Add isopycnal curves to TS plot
drawPalette Draw palette on RHS of plot device
drifter ARGO drifter dataset
drifter-class Class for drifter data

-- E --

echosounder echosounder dataset
echosounder-class Class to store echosounder data
eclipticalToEquatorial Convert ecliptical to equatorial coordinate
elevation Access or modify part of an Oce object
enuToOther Change ADV or ADP coordinate systems
enuToOtherAdp Convert east-north-up to other coordinate
enuToOtherAdv Convert east-north-up to other coordinate
equatorialToLocalHorizontal Convert equatorial to local horizontal coordinate
errorbars Draw error bars on an existing xy diagram
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 Confidence interval in parenthetic notation
formatPosition Geographical position in degrees and minutes
fullFilename full name of file, including path

-- G --

geodDist Geodesic distance on earth
geodGc Great-circle segments between points on earth
geodXy Convert lon/lat to x/y on earth
GMTOffsetFromTz Determine time offset from timezone
gps-class Class to store gps data
grad Gradient of a matrix
gravity Acceleration due to earth gravity

-- H --

head Ends of 'oce' objects.
head.adp Ends of 'oce' objects.
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 color palette
integerToAscii Decode integer to corresponding ASCII code
integrateTrapezoid Use trapezoidal integration
interpBarnes Grid data using Barnes algorithm
is.beam Determine coordinate system
is.enu Determine coordinate system
is.xyz Determine coordinate system

-- J --

julianCenturyAnomaly Julian-Day number to Julian century
julianDay Convert a POSIXt time to a Julian day

-- L --

landsat-class Class to store landsat data
landsatTrim Trim a landsat image to a lat-lon box
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
lisst LISST dataset
lisst-class Class to store LISST data
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 --

magneticField Earth magnetic declination, inclination, and intensity
makeFilter Make a digital filter
makeSection Bind CTD profiles together into a cross section
map2lonlat Find lon-lat coordinates of a point on a map
mapContour Plot contours on a existing map
mapImage Plot an image on a existing map
mapLines Plot lines on a existing map
mapLocator Locate points on a existing map
mapLongitudeLatitudeXY Convert from longitude and latitude to x and y
mapMeridians Plot meridians on an existing map
mapPlot Plot a map
mapPoints Plot points on a existing map
mapPolygon Plot a polygon on a existing map
mapScalebar Draw a scalebar on an existing map
mapText Plot text on a existing map
mapZones Plot zones on an existing map
matchBytes Locate byte sequences in a raw vector
matrixSmooth Smooth a matrix.
met Sample meteorological object
met-class Class to store meteorological data
moonAngle Lunar angle as function of space and time.

-- N --

nao North Atlantic Oscillation Index
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
numberAsHMS Convert a numeric time to hour, minute, and second
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.as.raw Version of as.raw() that clips data
oce.axis.POSIXct Modified version of axis.POSIXct
oce.plot.ts Plot a time-series, obeying the timezone
oce.write.table Write the data portion of object to a file
oceApprox Interpolate 1D data with Unesco or Reiniger-Ross algorithm
oceColors9A Create a palette of colours
oceColors9B Create a palette of colours
oceColorsGebco Create a palette of colours
oceColorsJet Create a palette of colours
oceColorsPalette Create a palette of colours
oceColorsTwo Create a palette of colours
oceContour Contour with ability to flip x and y
oceConvolve Convolve two time series
oceDebug Print a debugging message
oceEdit Edit an oce object
oceFilter Filter a time-series, possibly recursively
oceMagic Find the type of an oceanographic data file
ocePmatch Partial matching of strings or numbers
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 cm (current meter) 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 a gps object
plot-method Plot landsat data
plot-method Plot LISST data
plot-method Plot lobo data
plot-method Plot meteorological data
plot-method Plot sealevel data
plot-method Plot a CTD section
plot-method Plot tdr (temperature-depth recorder) data
plot-method Plot a tidal fit
plot-method Plot topography data
plot-method Plot a wind rose diagram
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.gps Plot a gps object
plot.landsat Plot landsat data
plot.lisst Plot LISST data
plot.lobo Plot lobo data
plot.met Plot meteorological data
plot.sealevel Plot sealevel data
plot.section Plot a CTD section
plot.tdr Plot tdr (temperature-depth recorder) data
plot.tidem Plot a tidal fit
plot.topo Plot topography data
plot.windrose Plot a wind rose diagram
plotInset Plot an inset diagram
plotPolar Draw a polar plot.
plotProfile Plot a CTD profile of various quantities
plotScan Plot seawater data in a low-level fashion
plotSticks Draw a stick-plot diagram
plotTaylor Plot a model-data comparison diagram.
plotTS Plot temperature-salinity diagram
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
prettyPosition Pretty lat/lon in deg, min, sec
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
pwelch Welch periodogram

-- R --

rangeExtended Calculate range, extended a little
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.aquadopp Read an ADP data file
read.aquadoppHR Read an ADP data file
read.aquadoppProfiler Read an ADP 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.openstreetmap Scan a coastline data file
read.coastline.shapefile Scan a coastline data file
read.ctd Read a CTD data file
read.ctd.itp 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.ctd.woce.other Read a CTD data file
read.drifter Read a drifter data file
read.echosounder Read an echosounder data file
read.gps Scan a gps data file
read.landsat Read a landsat data file
read.lisst Read a LISST data file
read.lobo Read a lobo data file
read.met Read a meteorological data file
read.observatory Read observatory data file
read.observatory.ctd Read observatory data file
read.oce Read an oceanographic data file
read.sealevel Read a sea-level data file
read.section Read a section containing multiple CTD profiles
read.tdr Read temperature-depth recorder file
read.topo Read an topography file
rescale Rescale values to lie in a given range
resizableLabel Provide axis names in adjustable sizes
retime Adjust the time within Oce object
roll Access or modify part of an Oce object
roll<- Access or modify part of an Oce object
runlm Calculate running linear models

-- S --

salinity Access or modify part of an Oce object
salinity<- Access or modify part of an Oce object
sealevel Sea-level data set, from Halifax Harbour
sealevel-class Class to store sealevel data
sealevelTuktoyaktuk Sea-level data set acquired in 1975 at Tuktoyaktuk
secondsToCtime Time interval as colon-separated string
section Hydrographic section
section-class Class to store hydrographic section data
sectionGrid Grid a section
sectionSmooth Smooth a section
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 gps data
show-method Class to store landsat data
show-method Class to store LISST 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 sealevel data
show-method Class to store hydrographic section data
show-method Class to store temperature-depth recorder data
showMetadataItem Show metadata item
siderealTime Convert a POSIXt time to a sidereal time
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
standardDepths Standard oceanographic depths
subset-method Subset an adp object
subset-method Subset an adv object
subset-method Subset a cm object
subset-method Subset a coastline object
subset-method Subset a ctd object
subset-method Subset an echosounder object
subset-method Subset a lisst object
subset-method Subset an oce object
subset-method Subset a sealevel object
subset-method Subset a section object
subset-method Subset a tdr object
subset-method Subset a topo object
subset.adp Subset an adp object
subset.adv Subset an adv object
subset.cm Subset a cm object
subset.coastline Subset a coastline object
subset.ctd Subset a ctd object
subset.echosounder Subset an echosounder object
subset.lisst Subset a lisst object
subset.oce Subset an oce object
subset.sealevel Subset a sealevel object
subset.section Subset a section object
subset.tdr Subset a tdr object
subset.topo Subset a topo object
subtractBottomVelocity Subtract bottom velocity from ADP velocity
summary-method Summarize an ADP object
summary-method Summarize an ADV object
summary-method Summarize a cm (current meter) object
summary-method Summarize a coastline data object
summary-method Summarize a CTD object
summary-method Summarize a drifter object
summary-method Summarize an echosounder object
summary-method Summarize a gps object
summary-method Summarize a landsat object
summary-method Summarize a LISST object
summary-method Summarize a lobo data object
summary-method Summarize a met object
summary-method Summarize a sealevel object
summary-method Summarize a CTD section
summary-method Summarize a tdr object
summary-method Summarize a tide-model object
summary-method Summarize a topography data object
summary-method Summarize a windrose data 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.gps Summarize a gps object
summary.landsat Summarize a landsat object
summary.lisst Summarize a LISST object
summary.lobo Summarize a lobo data object
summary.met Summarize a met object
summary.sealevel Summarize a sealevel object
summary.section Summarize a CTD section
summary.tdr Summarize a tdr object
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.
swAbsoluteSalinity Seawater absolute salinity, in TEOS-10
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
swConservativeTemperature Seawater conservative temperature, in TEOS-10.
swDepth Water depth
swDynamicHeight Dynamic height of seawater profile
swLapseRate Seawater lapse rate
swN2 Squared buoyancy frequency for seawater
swPressure Water pressure
swRho Seawater density
swRrho Density ratio
swSCTp Salinity from electrical conductivity, temperature and pressure
swSigma Seawater density anomaly
swSigmaT Seawater quasi-potential density anomaly
swSigmaTheta Seawater potential density anomaly
swSoundAbsorption Seawater sound absorption in dB/m
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 Ends of 'oce' objects.
tail.adp Ends of 'oce' objects.
tdr tdr (temperature-data recorder) dataset
tdr-class Class to store temperature-depth recorder data
tdrPatm Estimate atmospheric pressure in tdr record
tdrTrim Trim start/end portions of a tdr cast
temperature Access or modify part of an Oce object
temperature<- Access or modify part of an Oce object
teos Interface to TEOS-10 library
teosSetLibrary Set location of TEOS-10 library
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 Change ADV or ADP coordinate systems
toEnuAdp Convert from ENU coordinates
toEnuAdv Convert from ENU coordinates
topo-class Class to store topographic data
topoInterpolate Interpolate within a topography dataset
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
ungrid Extract (x, y, z) from (x, y, grid)
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
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 Change ADV or ADP coordinate systems
xyzToEnuAdp Convert XYZ to ENU coordinates
xyzToEnuAdv Convert XYZ 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 for drifter data
[[-method Class to store echosounder data
[[-method Class to store gps data
[[-method Class to store landsat data
[[-method Class to store LISST data
[[-method Class to store LOBO data
[[-method Class to store meteorological data
[[-method base class of oce package
[[-method Class to store sealevel data
[[-method Class to store hydrographic section data
[[-method Class to store temperature-depth recorder 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 gps data
[[<--method Class to store landsat data
[[<--method Class to store LISST data
[[<--method Class to store LOBO data
[[<--method Class to store meteorological data
[[<--method base class of oce package
[[<--method Class to store sealevel data
[[<--method Class to store hydrographic section data
[[<--method Class to store temperature-depth recorder data