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oce

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Oce is an R package for processing oceanographic data. Its webpage provides details, of which this README file is just a sketch.

Stable versions of the package are normally installed from within R, in the same way as other packages. However, this version is only updated a few times a year (pursuant to CRAN policy), so many users will want to install the develop branch instead. This branch may be updated several times per day, as the author fixes bugs or adds features that are motivated by day-to-day usage. This is the branch favoured by users who need new features or would like to contribute to Oce development.

The easy way to install the develop branch is to execute the following commands in R.

library(devtools)
install_github('dankelley/oce', ref='develop')

and most readers should also install Ocedata, with

install_github('dankelley/ocedata', ref='master')

Oce is emphatically an open-source system, and so the participation of users is very important. This is why Git is used for version control of the Oce source code, and why GitHub is the host for that code. All users are invited to take part in the development process, by suggesting features, by reporting bugs, or just by watching as others do such things. Oceanography is a collaborative discipline, so it makes sense that the evolution of Oce be similarly collaborative.

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Version

Install

install.packages('oce')

Monthly Downloads

2,573

Version

0.9-19

License

GPL (>= 2)

Maintainer

Dan Kelley

Last Published

July 8th, 2016

Functions in oce (0.9-19)

angleRemap

Convert angles from 0:360 to -180:180
adp

ADP (acoustic-doppler profiler) dataset
adv

ADV (acoustic-doppler velocimeter) dataset
amsr-class

Class to Hold amsr Data
applyMagneticDeclination

Earth magnetic declination
adv-class

Class to Hold adv Data
airRho

Air density
abbreviateTimeLabels

Abbreviate a vector of times by removing commonalities
addColumn

Add a Column to the Data Slot of an Oce object
adp-class

Class to Hold ADP (ADCP) Data
argo

ARGO float dataset
argoDataNames

Convert Data Names From the Argo Convention to the Oce Convention
as.coastline

Coerce Data into a Coastline Object
argoGrid

Grid Argo float data
as.ctd

Coerce data into CTD dataset
as.argo

Coerce Data Into an Argo Dataset
as.adp

Create an ADP Object
argShow

Show an argument to a function, e.g. for debugging
argo-class

Class to hold Argo data
approx3d

Trilinear interpolation in a 3D array
as.ladp

Coerce data into an ladp object
as.lisst

Coerce Data Into a LISST Object
as.echosounder

Coerce Data into an Echosounder Object
as.gps

Coerce data into a GPS dataset
as.lobo

Coerce Data into a Lobo Object
as.met

Coerce Data into Met Object
as.sealevel

Coerce Data Into a Sealevel Object
as.oce

Coerce Something Into an Oce Object
as.section

Create a Section
as.rsk

Coerce Data Into a Rsk Object
beamToXyzAdp

Convert ADP From Beam to XYZ Coordinates
beamToXyzAdv

Convert ADV from Beam to XYZ Coordinates
as.windrose

Create a Windrose Object
bcdToInteger

Decode BCD to integer
beamName

Get names of Acoustic-Doppler Beams
as.unit

Convert a String to a Unit
as.topo

Coerce Data into Topo Object
binMean2D

Bin-average f=f(x,y)
beamToXyz

Change ADV or ADP coordinate systems
bound125

Calculate a rounded bound, rounded up to matissa 1, 2, or 5
binmapAdp

Bin-map an ADP object
binMean1D

Bin-average f=f(x)
beamUnspreadAdp

Adjust ADP Signal for Spherical Spreading
binApply1D

Apply a function to vector data
binCount2D

Bin-count matrix data
binCount1D

Bin-count vector data
cm

A CM Record
cm-class

Class to Store Current Meter (CM) Data
colormap

Calculate colour map
colors

Data that define some colour palettes
coastlineCut

Cut a Coastline Object at Specified Longitude
ctdDecimate

Decimate a CTD profile
coastlineWorld

World Coastline
ctdFindProfiles

Find Profiles within a Tow-Yow CTD Record
dataLabel

Try to associate data names with units, for use by summary()
curl

Curl of 2D vector field
ctd

A CTD profile in Halifax Harbour
ctdAddColumn

Add a Column to the Data Slot of a CTD Object
decodeHeaderNortek

Decode a Nortek Header
decodeTime

Oce Version of as.POSIXct
despike

Remove spikes from a time series
enuToOther

Rotate acoustic-Doppler data to a new coordinate system
detrend

Detrend a set of observations
enuToOtherAdp

Convert ADP ENU to Rotated Coordinate
ctimeToSeconds

Interpret a character string as a time interval
ctdUpdateHeader

Update a CTD Header
errorbars

Draw error bars on an existing xy diagram
echosounder-class

Class to Store Echosounder Data
drawPalette

Draw a palette, leaving margins suitable for accompanying plot
fillGap

Fill a gap in an oce object
formatPosition

Format Geographical Position in Degrees and Minutes
fullFilename

Full name of file, including path
decimate

Smooth and Decimate, or Subsample, an Oce Object
decodeDataNames

Try to guess data names from hints found in file headers
firstFinite

Get first finite value in a vector or array, or NULL if none
equatorialToLocalHorizontal

Convert equatorial to local horizontal coordinate
enuToOtherAdv

Convert ENU to Other Coordinate
gravity

Acceleration due to earth gravity
formatCI

Confidence interval in parenthetic notation
handleFlags,argo-method

Handle Flags in ARGO Objects
landsatAdd

Add a Band to a landsat Object
landsatTrim

Trim a landsat Image to a Geographical Region
lobo-class

Class to Store LOBO Data
lobo

LOBO Dataset
grad

Calculate the grad of a matrix by first differences
gps-class

Class to Store GPS Data
GMTOffsetFromTz

Determine time offset from timezone
geodXyInverse

Inverse Geodesic Calculation
interpBarnes

Grid data using Barnes algorithm
julianCenturyAnomaly

Julian-Day number to Julian century
lisst-class

Class to Store LISST Data
lisst

LISST Dataset
makeSection

Make a Section (DEFUNCT)
findBottom

Find the Ocean Bottom in an Echosounder Object
integerToAscii

Decode integer to corresponding ASCII code
integrateTrapezoid

Use trapezoidal integration
geodGc

Great-circle Segments Between Points on Earth
findInOrdered

Find indices of times in an ordered vector
geodXy

Convert From Geographical to Geodesic Coordinates
magneticField

Earth magnetic declination, inclination, and intensity
makeFilter

Make a digital filter
numberAsPOSIXct

Convert a Numeric Time to a POSIXct Time
numberAsHMS

Convert a Numeric Time to Hour, Minute, and Second
map2lonlat

Convert X and Y to Longitude and Latitude
met

Sample Met Object
mapPolygon

Add a Polygon to a Map
mapPoints

Add Points to a Map
moonAngle

Lunar Angle as Function of Space and Time
oce.grid

Add a Grid to an Existing Oce Plot
oce

oce: A Package for Oceanographic Analysis
oceSetMetadata

Set something in the metadata slot of an oce object
oceSmooth

Smooth an Oce Object
binApply2D

Apply a function to matrix data
binAverage

Bin-average a vector y, based on x values
coastlineBest

Find the Name of the Best Coastline Object
ctdRaw

Seawater CTD Profile, Without Trimming of Extraneous Data
coastline-class

Class to Store Coastline Data
drawDirectionField

Draw a Direction Field
ctdTrim

Trim Beginning and Ending of a CTD cast
drawIsopycnals

Add Isopycnal Curves to TS Plot
eclipticalToEquatorial

Convert ecliptical to equatorial coordinate
echosounder

Echosounder Dataset
handleFlags,ctd-method

Handle Flags in CTD Objects
handleFlags,section-method

Handle flags in Section Objects
landsat-class

Class to Hold landsat Data
landsat

Sample landsat Dataset
lonlat2map

Convert Longitude and Latitude to X and Y
lonFormat

Format a longitude
mapArrows

Add Arrows to a Map
mapAxis

Add Axis Labels to an Existing Map
mapContour

Add Contours on a Existing map
mapDirectionField

Add a Direction Field to an Existing Map
mapLines

Add Lines to a Map
oce-deprecated

Deprecated and Defunct Elements of package ‘oce’
mapLocator

Locate Points on a Map
oce-class

Base Class for oce Objects
oce.as.raw

Version of as.raw() that clips data
oce.as.POSIXlt

Oce Variant of as.POSIXlt
oceDebug

Print a debugging message
oceDeleteData

Delete data from an oce object
handleFlags,vector-method

Signal erroneous application to non-oce objects
handleFlags

Handle flags in oce objects
julianDay

Convert a POSIXt time to a Julian day
ladp-class

Class to store lowered-adp data
lookWithin

Look Within the First Element of a List for Replacement Values
lonlat2utm

Convert Longitude and Latitude to UTM
mapScalebar

Add a Scalebar to a Map
oce.colorsGebco

Gebco Colors
oce.axis.POSIXct

Oce Version of axis.POSIXct
mapText

Add Text to a Map
oceGetMetadata

Get metadata element from an oce object
oceMagic

Find the Type of an Oceanographic Data File
ocePmatch

Partial matching of strings or numbers
oceSetData

Set something in the data slot of an oce object
plot,cm-method

Plot CM data
plot,coastline-method

Plot a Coastline
plot,landsat-method

Plot a landsat Object
plot,windrose-method

Plot Windrose data
plot,lisst-method

Plot LISST data
oceDeleteMetadata

Delete metadata from an oce object
oceEdit

Edit an Oce Object
oceSpectrum

Wrapper to give normalized spectrum
odf-class

Class to Store ODF data
plot,argo-method

Plot Argo Data
plot,sealevel-method

Plot Sealevel Data
plot,bremen-method

Plot a Bremen Object
plot,tidem-method

Plot a Tidem Prediction
plot,section-method

Plot a Section
predict.tidem

Predict a Time Series from a Tidem Tidal Model
plot,topo-method

Plot a Topo Object
prettyPosition

Pretty lat/lon in deg, min, sec
read.adp.nortek

Read a Nortek ADP File
read.adp.rdi

Read a Teledyne/RDI ADP File
read.aquadopp

Read a Nortek Aquadopp File
read.lisst

Read a LISST File
read.echosounder

Read an Echosounder File
read.aquadoppHR

Read Nortek Aquadopp-HR File
plotInset

Plot an Inset Diagram
read.ctd.woce.other

Read a WOCE-type CTD file with First Word "EXPOCODE"
read.cm

Read a CM file
read.bremen

Read a Bremen File
read.ctd.sbe

Read an Seabird CTD File
read.ctd.woce

Read a WOCE-type CTD file with First Word "CTD"
read.met

Read a Met File
read.topo

Read a Topo File
read.netcdf

Read a NetCDF File
read.section

Read a Section File
secondsToCtime

Time interval as colon-separated string
read.lobo

Read a LOBO File
rskPatm

Estimate Atmospheric Pressure in Rsk Object
rsk2ctd

Create a ctd Object from an rsk Object
satellite-class

Class to hold satellite data
sealevel-class

Class to Store Sealevel Data
mapLongitudeLatitudeXY

Convert From Longitude and Latitude to X and Y
[[<-,coastline-method

Replace Parts of a Coastline Object
[[,g1sst-method

Extract Something From a G1SST Object
[[,echosounder-method

Extract Parts of an Echosounder Object
shiftLongitude

Shift Longitude to Range -180 to 180
sectionSort

Sort a Section
met-class

Class to Store Meteorological Data
matrixSmooth

Smooth a Matrix
oce.plot.ts

Oce Variant of plot.ts
mapMeridians

Add Meridians on a Map [DEPRECATED]
oceFilter

Filter a time-series
[[<-,ctd-method

Replace Parts of a CTD Object
oce.write.table

Write the Data Portion of Object to a File
oceGetData

Get data from an oce object
ODFNames2oceNames

Translate from ODF Names to Oce Names
ODF2oce

Create ODF object from the output of ODF::read_ODF()
[[<-,odf-method

Replace Parts of an ODF Object
[[<-,oce-method

Replace Parts of an Oce Object
subset,adv-method

Subset an ADV Object
subset,adp-method

Subset an ADP Object
subset,section-method

Subset a Section Object
subset,sealevel-method

Subset a Sealevel Object
plot,amsr-method

Plot an amsr Object
plot,lobo-method

Plot LOBO data
summary,met-method

Summarize a Met Object
summary,gps-method

Summarize a GPS Object
plot,adv-method

Plot ADV data
summary,echosounder-method

Summarize an Echosounder Object
processingLogItem

Create an item that can be inserted into a processing log
plot,met-method

Plot Met Data
read.adv.nortek

Read an ADV data file
read.adv

Read an ADV data file
processingLogShow

Show the processing log of an oce object
byteToBinary

Format bytes as binary
read.coastline.openstreetmap

Read a Coastline File in Openstreetmap Format
bremen-class

Class for data stored in a format used at Bremen
read.coastline

Read a Coastline File
g1sst-class

Class to Hold G1SST Satellite-model Data
coriolis

Coriolis parameter on rotating earth
ctd-class

Class to Store CTD (or general hydrographic) Data
geodDist

Compute Geodesic Distance on Surface of Earth
imagep

Plot an Image with a Color Palette
latFormat

Format a latitude
latlonFormat

Format a latitude-longitude pair
head.oce

Extract The Start of an Oce Object
plot,rsk-method

Plot Rsk Data
plot,echosounder-method

Plot Echosounder Data
plot,ctd-method

Plot CTD Data
plot,satellite-method

Plot a satellite object
plotPolar

Draw a Polar Plot
plotProfile

Plot a CTD Profile
pwelch

Welch periodogram
rangeExtended

Calculate Range, Extended a Little, as is Done for Axes
read.adv.sontek.adr

Read an ADV data file
read.adv.sontek.serial

Read an ADV data file
section-class

Class to Store Hydrographic Section Data
sectionSmooth

Smooth a Section
sectionGrid

Grid a Section
[[,coastline-method

Extract Something From a Coastline Object
[[,ctd-method

Extract Parts of a CTD Object
[[,landsat-method

Extract Something From a landsat Object
[[<-,lobo-method

Replace Parts of a LOBO Object
[[<-,adv-method

Replace Parts of an ADV Object
[[<-,adp-method

Replace Parts of an ADP Object
[[,lisst-method

Extract Something From a LISST Object
[[<-,met-method

Replace Parts of a Met Object
subset,argo-method

Subset an Argo Object
summary,satellite-method

Summarize a satellite object
subset,cm-method

Subset a CM Object
summary,sealevel-method

Summarize a Sealevel Object
swAlpha

Seawater thermal expansion coefficient
swRrho

Density ratio
swRho

Seawater density
swAlphaOverBeta

Ratio of seawater thermal expansion coefficient to haline contraction coefficient
plot,odf-method

Plot an ODF Object
plot,oce-method

Plot an oce Object
topoWorld

Global Topographic Dataset at Half-degree Resolution
plotTaylor

Plot a Model-data Comparison Diagram
processingLog<-

Add an item to a processing log (in place)
plotTS

Plot Temperature-Salinity Diagram
processingLogAppend

Append an item to a processing log
read.aquadoppProfiler

Read a Nortek Aquadopp-Profiler File
read.amsr

Read an amsr File
read.adv.sontek.text

Read an ADV data file
read.ctd.odf

Read a CTD file in ODF format
read.ctd

Read a General CTD File
read.argo

Read an Argo Data File
read.observatory.ctd

Read observatory data CTD file
sealevel

Sealevel data for Halifax Harbour
read.observatory

Read observatory data file
sealevelTuktoyaktuk

Sea-level data set acquired in 1975 at Tuktoyaktuk
standardDepths

Standard Oceanographic Depths
standardizeLongitude

Put longitude in the range from -180 to 180
[[,amsr-method

Extract Something From an amsr Object
[[,met-method

Extract Something From a Met Object
[[,lobo-method

Extract Something From a LOBO Object
[[,argo-method

Extract Something From an Argo Object
[[,windrose-method

Extract Something From a Windrose Object
[[,topo-method

Extract Something From a Topo Object
[[<-,gps-method

Replace Parts of a GPS Object
[[<-,lisst-method

Replace Parts of a LISST Object
[[<-,topo-method

Replace Parts of a Topo Object
subset,met-method

Subset a Met Object
[[<-,windrose-method

Replace Parts of a Windrose Object
read.g1sst

Read a G1SST file
read.gps

Read a GPS File
read.rsk

Read a Rsk file
read.sealevel

Read a Sealevel File
rsk

Sample Rsk Dataset
rsk-class

Class to Store Rsk Data
rskToc

Decode table-of-contents File from a Rsk File
showMetadataItem

Show metadata item
runlm

Calculate running linear models
siderealTime

Convert a POSIXt time to a sidereal time
read.odf

Read an ODF file
renameData

Rename items in the data slot of an oce object
read.oce

Read an Oceanographic Data File
rescale

Rescale values to lie in a given range
[[,gps-method

Extract Something From a GPS Object
[[,ladp-method

Extract Something From an ladp Object
[[,section-method

Extract Something From a Section Object
subset,ctd-method

Subset a CTD Object
subset,coastline-method

Subset a Coastline Object
[[,tidem-method

Extract Something From a Tidem Object
summary,oce-method

Summarize an oce Object
swBeta

Seawater haline contraction coefficient
swConservativeTemperature

Seawater conservative temperature, in GSW formulation
swSCTp

Salinity from electrical conductivity, temperature and pressure
swSigma2

Seawater potential density anomaly referenced to 2000db pressure
swSigma

Seawater density anomaly
swSigma3

Seawater potential density anomaly referenced to 3000db pressure
T68fromT90

Convert from ITS-90 to IPTS-68 temperature
mapImage

Add an Image to a Map
mapGrid

Add a Longitude and Latitude Grid to a Map
T90fromT48

Convert from ITS-48 to ITS-90 temperature
mapZones

Add Zones to a Map [DEPRECATED]
mapTissot

Add Tissot Indicatrices to a Map
matchBytes

Locate byte sequences in a raw vector
matrixShiftLongitude

Rearrange areal matrix so Greenwich is near the centre
oce.colorsTwo

Create a Palette of Colours
oce.contour

Oce Variant of contour
oceApprox

Interpolate 1D Data with Unesco or Reiniger-Ross Algorithm
summary,amsr-method

Summarize an AMSR Object
subset,oce-method

Subset an oce Object
summary,argo-method

Summarize an Argo Object
summary,rsk-method

Summarize a Rsk Object
summary,odf-method

Summarize an ODF Object
summary,topo-method

Summarize A Topo Object
summary,windrose-method

Summarize a windrose object
swN2

Squared buoyancy frequency for seawater
swPressure

Water pressure
swSigma0

Seawater potential density anomaly referenced to surface pressure
useHeading

Replace the Heading for One Instrument With That of Another
unwrapAngle

Unwrap an angle that suffers modulo-360 problems
trimString

Remove leading and trailing whitespace from strings
subset,odf-method

Subset an ODF object
summary,bremen-method

Summarize a Bremen Object
subset,rsk-method

Subset a Rsk Object
summary,cm-method

Summarize a CM Object
summary,lisst-method

Summarize a LISST Object
summary,lobo-method

Summarize a LOBO Object
summary,section-method

Summarize a Section Object
summary,tidem-method

Summarize a Tidem Object
swDynamicHeight

Dynamic height of seawater profile
T90fromT68

Convert from IPTS-68 to ITS-90 temperature
swLapseRate

Seawater lapse rate
unabbreviateYear

Determine year from various abbreviations
tail.oce

Extract the End of an Oce Object
undriftTime

Correct for drift in instrument clock
xyzToEnuAdp

Convert ADP From XYZ to ENU Coordinates
xyzToEnuAdv

Convert an ADP from XYZ to ENU Coordinates
plot,adp-method

Plot ADP Data
oceConvolve

Convolve two time series
parseLatLon

Parse a Latitude or Longitude String
plotSticks

Draw a Stick Plot
plot,gps-method

Plot a GPS Object
plot,ladp-method

Plot an ladp object
plotScan

Plot CTD data in a Low-Level Fashion
rangeLimit

Substitute NA for data outside a range
read.adp

Read an ADP File
[[,sealevel-method

Extract Something From a Sealevel Object
[[<-,cm-method

Replace Parts of a CM Object
[[,cm-method

Extract Something From a CM Object
[[,rsk-method

Extract Something From a Rsk Object
[[<-,bremen-method

Replace Parts of a Bremen Object
[[,bremen-method

Extract Something From a Bremen Object
[[<-,g1sst-method

Replace Parts of a G1SST Object
[[<-,echosounder-method

Replace Parts of an Echosounder Object
swSoundSpeed

Seawater sound speed
subset,echosounder-method

Subset an Echosounder Object
swSpecificHeat

Seawater specific heat Source= http://sam.ucsd.edu/sio210/propseawater/ppsw_fortran/ppsw.f check value: cpsw = 3849.500 j/(kg deg. c) for s = 40 (ipss-78),
swViscosity

Seawater viscosity
swZ

Vertical coordinate
tidem-class

Class to Store Tidal Models
wind

Wind dataset
toEnuAdv

Convert an ADV Object to ENU Coordinates
tidem

Fit a Tidem (Tidal Model) to a Timeseries
toEnuAdp

Convert an ADP Object to ENU Coordinates
write.ctd

Write a CTD Data Object as a CSV File
window.oce

Window an Oce Object by Time or Distance
read.adp.sontek

Read a Sontek ADP File
xyzToEnu

Convert acoustic-Doppler data from xyz coordinates to enu coordinates
read.ctd.itp

Read an ITP-type CTD File
read.adp.sontek.serial

Read a serial Sontek ADP file
read.index

Read a NOAA ocean index file
read.coastline.shapefile

Read a Coastline File in Shapefile Format
resizableLabel

Provide axis names in adjustable sizes
retime

Adjust the time within Oce object
read.landsat

Read a landsat File Directory
section

Hydrographic section
sectionAddStation

Add a CTD Station to a Section
[[,adp-method

[[,oce-method

Extract Something From an oce Object
[[,adv-method

Extract Parts of an ADV Object
[[<-,sealevel-method

Replace Parts of a Sealevel Object
[[<-,amsr-method

Replace Parts of an AMSR Object
[[,odf-method

Extract Something From an ODF Object
[[<-,rsk-method

Replace Parts of a Rsk Object
[[<-,argo-method

Replace Parts of an Argo Object
[[<-,section-method

Replace Parts of a Section Object
subset,topo-method

Subset a Topo Object
[[<-,tidem-method

Replace Parts of a Tidem Object
subtractBottomVelocity

Subtract Bottom Velocity from ADP
swSigmaTheta

Seawater potential density anomaly
summary,adp-method

Summarize an ADP Object
swTSrho

Seawater temperature from salinity and density
swTheta

Seawater potential temperature
summary,adv-method

Summarize an ADV object
swSoundAbsorption

Seawater sound absorption in dB/m
titleCase

Capitalize first letter of each of a vector of words
toEnu

Rotate acoustic-Doppler data to the enu coordinate system
unduplicateNames

Rename duplicated items (used in reading CTD files)
ungrid

Extract (x, y, z) from (x, y, grid)
utm2lonlat

Convert UTM to Longitude and Latitude
swSigma1

Seawater potential density anomaly referenced to 1000db pressure
swSpice

Seawater spiciness
vectorShow

Show some values from a vector
swSTrho

Seawater salinity from temperature and density
tidedata

Tidal Constituent Information
threenum

Calculate min, mean, and max values
unitFromStringRsk

Infer Rsk units from a vector of strings
subset,lobo-method

Subset a LOBO Object
unitFromString

Decode units, from strings
summary,ladp-method

Summarize an ladp object
summary,landsat-method

Summarize a landsat Object
summary,coastline-method

Summarize a Coastline Object
summary,ctd-method

Summarize a CTD Object
swAbsoluteSalinity

Seawater absolute salinity, in GSW formulation
sunAngle

Solar Angle as Function of Space and Time
swCSTp

Electrical conductivity ratio from salinity, temperature and pressure
swDepth

Water depth
swSigma4

Seawater potential density anomaly referenced to 4000db pressure
swThermalConductivity

Seawater thermal conductivity
tidemAstron

Astronomical Calculations for Tidem
swTFreeze

Seawater freezing temperature
swSigmaT

Seawater quasi-potential density anomaly
tidemVuf

Nodal Modulation Calculations for Tidem
topo-class

Class to Store Topographic Data
velocityStatistics

Report Statistics of adp or adv Velocities
topoInterpolate

Interpolate Within a Topo Object
webtide

Get a Tidal Prediction from a WebTide Database
windrose-class

Class to Store Windrose Data
woceNames2oceNames

Translate WOCE Data Names to Oce Data Names