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oce (version 0.8-1)

Analysis of Oceanographic data

Description

Supports the analysis of Oceanographic data, including ADP measurements, CTD measurements, sectional data, sea-level time series, coastline files, etc. Provides functions for calculating seawater properties such as potential temperature and density, as well as derived properties such as buoyancy frequency and dynamic height.

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Version

Install

install.packages('oce')

Monthly Downloads

2,416

Version

0.8-1

License

GPL (>= 2)

Maintainer

Dan Kelley

Last Published

October 26th, 2011

Functions in oce (0.8-1)

detrend

Detrend a set of observations
despike

Remove spikes from a time series
ctd

Seawater CTD profile
as.ctd

Coerce data into ctd dataset
coastline-class

Class to store coastline data
geodXy

Convert lat/lon to x/y on earth
accessors

Access or modify part of an Oce object
ctdRaw

Seawater CTD profile, without trimming of extraneous data
addColumn

Add a column to an oce object
cm-class

Class to store current meter data
plot.coastline

Plot a coastline
rangeLimit

Substitute NA for data outside a range
argo

ARGO drifter dataset
drawPalette

Draw a palette on the right-hand side of plot device
adp

ADP (acoustic-doppler profiler) dataset
lobo-class

Class to store LOBO data
adv

ADV (acoustic-doppler velocimeter) dataset
adv-class

Class to store acoustic Doppler velocimeter data
latlonFormat

Format a latitude-longitude pair
as.pt

Create an TDR temperature-depth recorder data file
loggerToc

Decode table-of-contents file from a datalogger
gravity

Acceleration due to earth gravity
coastlineHalifax

Coastline data set, showing Halifax Harbour
plot.lobo

Plot lobo data
plot.ctd

Plot seawater CTD data
head

Returns the first or last parts of an oce object.
bcdToInteger

Decode BCD to integer
beamName

Name an acoustic-doppler beam.
beamToXyzAdv

Convert ADV from beam coordinates to xyz coordinates
airRho

Air density
angleRemap

Convert an angle from the 0:360 range to -180:180
oceApprox

Interpolate with Reiniger-Ross algorithm
ctdAddColumn

Add a column to a CTD file
parseLatLon

Parse a latitude or longitude string
findInOrdered

Find indices of tiems in an ordered vector
drifter-class

Class to store drifter data, e.g. from an ARGOS float
beamToXyz

Convert ADV or ADP data between various coordinate systems
plot.cm

Plot cm (current meter) data
rescale

Rescale values to lie in a given range
fillGap

Fill a gap in an oce object
as.topo

Coerce data into topo dataset
plotProfile

Plot a CTD profile of various quantities
plot.tidem

Plot a tidal fit
ctd-class

Class to store hydrographic data
RRprofile

Seawater profile used by Reiniger and Ross (1968)
as.lisst

Coerce data into a lisst object
ptTrim

Trim start/end portions of a pt cast
beamToXyzAdp

Convert ADP from beam coordinates to xyz coordinates
as.lobo

Coerce data into lobo dataset
lobo

lobo dataset
magneticDeclination

Earth magneticDeclination
as.coastline

Coerce data into coastline dataset
pwelch

Welch periodogram
read.lobo

Read a lobo data file
redfieldNC

Redfield's (1934) NO3 and total CO2 data
decimate

Decimate an oce object
matrixSmooth

Smooth a matrix.
plot.adp

Plot ADP data
enuToOtherAdp

Convert ADP from east-north-up coordinates to other coordinates
beamUnattenuateAdp

Unattenuate ADP beam signal strength
oce.as.POSIXlt

More general form of as.POSIXlt
munk

Munk's (1966) temperature profile
lonFormat

Format a longitude
oceSpectrum

Wrapper to give normalized spectrum
as.sealevel

Coerce data into sea-level dataset
matchBytes

Find spots in a raw vector that match a given byte sequence.
drag

Wind drag coefficient
oce.plot.ts

Plot a time-series, obeying the timezone
coastlineSLE

Coastline of St Lawrence Estuary
coastlineWorld

World coastline
magic

Find the type of an oceanographic data file
geosecs235

GEOSECS station 235 data
airHalifax

Time-series of wind and temperature at Halifax, Canada.
secondsToCtime

Convert a time interval to a colon-separated string
is.beam

Determine coordinate system for acoustic-doppler device
schmitt

Schmitt's (1981) NACW temperature-salinity data
makeSection

Bind CTD profiles together into a cross section
header

Return the header for an Oce data object
drawIsopycnals

Draw isopycnal curves on an existing temperature-salinity plot
ctdTrim

Trim start/end portions of a CTD cast
ptPatm

Estimate atmospheric pressure in pt record
as.drifter

Coerce data into drifter dataset
oceBisect

Find the root of a function by bisection
formatCI

Format a confidence interval in parenthetic notation
extract

Extract data from an oce object
coastlineMaritimes

Coastline data set, showing Maritime provinces of Canada
ctimeToSeconds

Interpret a character string as a time interval
adp-class

Class to store acoustic Doppler profiler data
applyMagneticDeclination

Earth magnetic declination
coriolis

Coriolis parameter on rotating earth
oceEdit

Edit an oce object
oce-class

base class of oce package
pt-class

Class to store pressure-temperature recorder data
oce.axis.POSIXct

Modified version of axis.POSIXct
oceDebug

Print a debugging message
plot.topo

Plot topography data
read.drifter

Read a drifter data file
summary.coastline

Summarize a coastline data object
plot.drifter

Plot drifter data
oce.write.table

Write the data portion of object to a file
makeFilter

Make a digital filter
sealevelTuktoyaktuk

Sea-level data set acquited in 1975 at Tuktoyaktuk
summary.windrose

Summarize a windrose data object
plot.sealevel

Plot sealevel data
swConductivity

Seawater conductivity
tidedata

Tidal constituent information
summary.pt

Summarize a pt object
topoInterpolate

Interpolate within a topography dataset
as.echosounder

Coerce data into echosounder dataset
plotScan

Plot seawater data in a low-level fashion
predict.tidem

Predict a time series from a tidal model
processingLog

Add an item to object processingLog
sectionSmooth

Smooth a section (preliminary version that may change)
GMTOffsetFromTz

Determine time offset from timezone
summary.cm

Summarize a cm (current meter) object
swTFreeze

Seawater freezing temperature
summary.section

Summarize a CTD section
soi

Southern Oscillation Index
velocityStatistics

Report statistics of ADP or ADV velocities.
write.ctd

Write a CTD data object as a .csv file
read.adp

Read an ADP data file
window.oce

Window an oce object by time or distance
topo-class

Class to store topographic data
vectorShow

Show some values from a vector
ctdDecimate

Decimate a CTD profile
swSpecificHeat

Seawater specific heat
swRho

Seawater density
oce.as.raw

A version of as.raw() that clips data to prevent warnings
section-class

Class to store hydrographic section data
summary.adv

Summarize an ADV object
xyzToEnuAdv

Convert ADP or ADV from xyz coordinates to enu coordinates
enuToOtherAdv

Convert ADV from east-north-up coordinates to other coordinates
swSpice

Seawater spiciness
sealevel-class

Class to store sealevel data
oceColors

Create a palette of colours
numberAsPOSIXct

Convert a numeric time to a POSIXct time
geodDist

Geodesic distance on earth
julianDay

Convert a POSIXt time to a Julian day
swSCTp

Seawater salinity from conductivity ratio, temperature and pressure
threenum

Calculate min, mean, and max values
plotInset

Plot an inset diagram
swDepth

Water depth
plot.section

Plot a CTD section
summary.sealevel

Summarize a sealevel object
swSigmaT

Seawater quasi-potential density anomaly
plotTS

Plot temperature-salinity diagram for seawater (CTD) data
tidem-class

Class to store tidal-constituent models
read.ctd

Read a CTD data file
oce.plot.sticks

Draw a stick-plot diagram
unwrapAngle

Unwrap an angle that suffers modulo-360 problems
read.pt

Read an TDR temperature-depth recorder data file
swSigmaTheta

Seawater potential density anomaly
tidemAstron

Do ephemeris calculations for tidem
swTheta

Seawater potential temperature
swTSrho

Seawater temperature from salinity and density
lisst

LISST dataset
read.coastline

Scan a coastline data file
retime

Adjust the time within Oce object
sealevelHalifax

Sea-level data set, from Halifax Harbour
read.section

Read a section containing multiple CTD profiles
tidem

Fit a tidal model to a timeseries
sectionGrid

Grid a section
summary.topo

Summarize a topography data object
useHeading

Replace the heading for one instrument with the heading for another
resizableLabel

Provide axis names in adjustable sizes
read.cm

Read a current-meter data file
riley

Riley's (1946) observation and theory of phytoplankton concentration
sectionSort

Sort a section
plot.windrose

Plot a wind rose diagram
topoMaritimes

Topographic dataset, showing Maritime region of Canada
read.sealevel

Read a sea-level data file
summary.lisst

Summarize a LISST object
topoWorld

Global topographic dataset at half-degree resolution
read.topo

Read an topography file
showMetadataItem

Show metadata item
swDynamicHeight

Dynamic height of seawater profile
eclipticalToEquatorial

Convert from ecliptical to equatorial coordinates
summary.lobo

Summarize a lobo data object
swSoundSpeed

Seawater sound speed
equatorialToLocalHorizontal

Convert from equatorial coordinates to local horizontal coordinates
met

Sample meteorological object
interpBarnes

Grid data using Barnes algorithm
redfieldNP

Redfield's (1934) NO3 and PO4 data
section

Seawater CTD section
swN2

Squared buoyancy frequency for seawater
swLapseRate

Seawater lapse rate
swSTrho

Seawater salinity from temperature and density
oceFilter

Filter a time-series, possibly recursively
oceConvolve

Convolve two time series
windrose-class

Class to store windrose data
cm

Current-meter record
abbreviateTimeLabels

Abbreviate a list of times by removing commonalities (e.g. year)
as.windrose

Create a windrose object
plot.tdr

Plot tdr (temperature-depth recorder) data
read.adv

Read an ADV data file
summary.met

Summarize a met object
findBottom

Find the ocean bottom in an echosounder object
read.oce

Read an oceanographic data file
plot.pt

Plot pt (pressure-temperature) recorder data
imagep

Plot an image with a colour palette
subset.oce

Subset an oce object
binmapAdp

Bin-map an ADP object
swAlpha

Seawater thermal expansion coefficient
byteToBinary

Format bytes as binary
plot.adv

Plot ADV data
ctdUpdateHeader

Update a CTD header
lisst-class

Class to store LISST data
summary.ctd

Summarize a CTD object
sunAngle

Solar angle as function of space and time.
swSigma

Seawater density anomaly
moonAngle

Lunar angle as function of space and time.
as.met

Coerce data into met dataset
formatPosition

Format geographical positions to degrees, minutes, and hemispheres
echosounder-class

Class to store echosounder data
time.oce

Extract time from an oce object
xyzToEnuAdp

Convert ADP or ADV from xyz coordinates to enu coordinates
fullFilename

full name of file, including path
stickplot

Draw a stick-plot diagram
swViscosity

Seawater viscosity
echosounder

echosounder dataset
swConservativeTemperature

Seawater conservative temperature, as defined in TEOS-10.
integrateTrapezoid

Use trapezoidal integration
latFormat

Format a latitude
grad

Gradient of a matrix
plot.lisst

Plot LISST data
swAlphaOverBeta

Ratio of seawater thermal expansion coefficient to haline contraction coefficient
plot.echosounder

Plot echosounder data
toEnuAdv

Convert ADV to enu coordinates, from any other coordinates
toEnuAdp

Convert ADP to enu coordinates, from any other coordinates
tdr

tdr (temperature-data recorder) dataset
plot.met

Plot meteorological data
redfieldPlankton

Redfield's (1934) Table II
unabbreviateYear

Determine year from various abbreviations
oceContour

Contour with ability to flip x and y
undriftTime

Correct for drift in instrument clock
binAverage

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

Convert a Julian-Day number to a time in julian centuries since noon on January 1, 1900.
oceSmooth

Smooth an oce object
wind

Wind dataset
swBeta

Seawater haline contraction coefficient
tdr-class

Class to store temperature-depth recorder data
read.tdr

Read an TDR temperature-depth recorder data file
plotTaylor

Plot a model-data comparison diagram.
read.echosounder

Read an echosounder data file
swAbsoluteSalinity

Seawater absolute salinity, as defined in TEOS-10.
ptr

ptr (pressure-temperature) dataset
read.met

Read a meteorological data file
as.tdr

Create a TDR object
teos

Interface to TEOS-10 library
prettyPosition

Round a geographical positions in degrees, minutes, and seconds
tdrTrim

Trim start/end portions of a tdr cast
summary.adp

Summarize an ADP object
summary.echosounder

Summarize an echosounder object
summary.drifter

Summarize a drifter object
tidemVuf

Do ephemeris calculations for tidem
integerToAscii

Decode integer to corresponding ASCII code
summary.tidem

Summarize a tide-model object
tdrPatm

Estimate atmospheric pressure in tdr record
wilson

Wilson's (1963) table of seafloor spreading
met-class

Class to store meteorological data
webtide

Get a tidal prediction from a WebTide database
siderealTime

Convert a POSIXt time to a sidereal time
subtractBottomVelocity

Subtract bottom velocity from ADP velocity
summary.tdr

Summarize a tdr object
teosSetLibrary

Set location of TEOS-10 library
a03

WOCE section a03
drawDirectionField

Draw a direction field
drifter

ARGO drifter dataset
read.lisst

Read a LISST data file