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oce

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 install the develop branch instead. This branch may be updated several times per day, as the authors fix bugs or add 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

3,198

Version

0.9-20

License

GPL (>= 2)

Maintainer

Dan Kelley

Last Published

November 19th, 2016

Functions in oce (0.9-20)

airRho

Air density
abbreviateTimeLabels

Abbreviate a vector of times by removing commonalities
addColumn

Add a Column to the Data Slot of an Oce object [deprecated]
applyMagneticDeclination

Earth magnetic declination
amsr-class

Class to Hold amsr Data
angleRemap

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

Class to Hold ADP (ADCP) Data
adp

ADP (acoustic-doppler profiler) dataset
adv-class

Class to Hold adv Data
adv

ADV (acoustic-doppler velocimeter) dataset
as.adp

Create an ADP Object
as.cm

Coerce data into a CM object
argShow

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

ARGO float dataset
as.argo

Coerce Data Into an Argo Dataset
as.coastline

Coerce Data into a Coastline Object
argoGrid

Grid Argo float data
as.ctd

Coerce data into CTD object
approx3d

Trilinear interpolation in a 3D array
argo-class

Class to hold Argo data
as.met

Coerce Data into Met Object
as.rsk

Coerce Data Into a Rsk Object
as.lisst

Coerce Data Into a LISST Object
as.sealevel

Coerce Data Into a Sealevel Object
as.oce

Coerce Something Into an Oce Object
as.section

Create a Section
as.lobo

Coerce Data into a Lobo Object
as.ladp

Coerce data into an ladp object
as.echosounder

Coerce Data into an Echosounder Object
as.gps

Coerce data into a GPS dataset
beamUnspreadAdp

Adjust ADP Signal for Spherical Spreading
bcdToInteger

Decode BCD to integer
as.unit

Convert a String to a Unit
binApply1D

Apply a function to vector data
as.windrose

Create a Windrose Object
beamToXyzAdv

Convert ADV from Beam to XYZ Coordinates
as.topo

Coerce Data into Topo Object
beamName

Get names of Acoustic-Doppler Beams
beamToXyz

Change ADV or ADP coordinate systems
beamToXyzAdp

Convert ADP From Beam to XYZ Coordinates
binMean2D

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

Bin-map an ADP object
bremen-class

Class for data stored in a format used at Bremen
binCount1D

Bin-count vector data
byteToBinary

Format bytes as binary
binApply2D

Apply a function to matrix data
binAverage

Bin-average a vector y, based on x values
bound125

Calculate a rounded bound, rounded up to matissa 1, 2, or 5
binCount2D

Bin-count matrix data
binMean1D

Bin-average f=f(x)
cm

A CM Record
coastlineBest

Find the Name of the Best Coastline Object
composite,amsr-method

Create a composite of amsr satellite data
coastlineCut

Cut a Coastline Object at Specified Longitude
coastline-class

Class to Store Coastline Data
cm-class

Class to Store Current Meter (CM) Data
coastlineWorld

World Coastline
composite,list-method

Create a composite object by averaging across good data stored in a list
ctd-class

Class to Store CTD (or general hydrographic) Data
ctd

A CTD profile in Halifax Harbour
ctdTrim

Trim Beginning and Ending of a CTD cast
ctdUpdateHeader

Update a CTD Header [deprecated]
decodeHeaderNortek

Decode a Nortek Header
decodeTime

Oce Version of as.POSIXct
decodeDataNames

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

Convert ecliptical to equatorial coordinate
enuToOther

Rotate acoustic-Doppler data to a new coordinate system
decodeDataNamesArgo

Convert Data Names From the Argo Convention to the Oce Convention
equatorialToLocalHorizontal

Convert equatorial to local horizontal coordinate
errorbars

Draw error bars on an existing xy diagram
grad

Calculate the grad of a matrix by first differences
gravity

Acceleration due to earth gravity
composite

Create a composite object by averaging across good data
coriolis

Coriolis parameter on rotating earth
despike

Remove spikes from a time series
detrend

Detrend a set of observations
download.amsr

Download and Cache an amsr File
download.coastline

Download a coastline File
enuToOtherAdp

Convert ADP ENU to Rotated Coordinate
enuToOtherAdv

Convert ENU to Other Coordinate
geodDist

Compute Geodesic Distance on Surface of Earth
colormap

Calculate colour map
ctdAddColumn

Add a Column to the Data Slot of a CTD Object [deprecated]
colors

Data that define some colour palettes
ctdDecimate

Decimate a CTD profile
dataLabel

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

Add Isopycnal Curves to TS Plot
decimate

Smooth and Decimate, or Subsample, an Oce Object
drawPalette

Draw a palette, leaving margins suitable for accompanying plot
fillGap

Fill a gap in an oce object
ctdFindProfiles

Find Profiles within a Tow-Yow CTD Record
ctdRaw

Seawater CTD Profile, Without Trimming of Extraneous Data
ctimeToSeconds

Interpret a character string as a time interval
integrateTrapezoid

Use trapezoidal integration
curl

Curl of 2D vector field
interpBarnes

Grid data using Barnes algorithm
ladp-class

Class to store lowered-adp data
landsat-class

Class to Hold landsat Data
lisst

LISST Dataset
lobo-class

Class to Store LOBO Data
mapText

Add Text to a Map
mapTissot

Add Tissot Indicatrices to a Map
numberAsPOSIXct

Convert a Numeric Time to a POSIXct Time
oce-deprecated

Deprecated and Defunct Elements of package ‘oce’
echosounder-class

Class to Store Echosounder Data
echosounder

Echosounder Dataset
formatCI

Confidence interval in parenthetic notation
formatPosition

Format Geographical Position in Degrees and Minutes
fullFilename

Full name of file, including path
g1sst-class

Class to Hold G1SST Satellite-model Data
landsatTrim

Trim a landsat Image to a Geographical Region
latFormat

Format a latitude
makeFilter

Make a digital filter
makeSection

Make a Section (DEFUNCT)
geodGc

Great-circle Segments Between Points on Earth
handleFlags,section-method

Handle flags in Section Objects
handleFlags,vector-method

Signal erroneous application to non-oce objects
latlonFormat

Format a latitude-longitude pair
lisst-class

Class to Store LISST Data
lookWithin

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

Earth magnetic declination, inclination, and intensity
mapImage

Add an Image to a Map
mapMeridians

Add Meridians on a Map [deprecated]
mapLines

Add Lines to a Map
findBottom

Find the Ocean Bottom in an Echosounder Object
geodXy

Convert From Geographical to Geodesic Coordinates
geodXyInverse

Inverse Geodesic Calculation
handleFlags,argo-method

Handle Flags in ARGO Objects
handleFlags,ctd-method

Handle Flags in CTD Objects
landsat

Sample landsat Dataset
landsatAdd

Add a Band to a landsat Object
lonlat2map

Convert Longitude and Latitude to X and Y
lonlat2utm

Convert Longitude and Latitude to UTM
map2lonlat

Convert X and Y to Longitude and Latitude
handleFlags

Handle flags in oce objects
head.oce

Extract The Start of an Oce Object
julianCenturyAnomaly

Julian-Day number to Julian century
julianDay

Convert a POSIXt time to a Julian day
mapLocator

Locate Points on a Map
mapLongitudeLatitudeXY

Convert From Longitude and Latitude to X and Y
mapPolygon

Add a Polygon to a Map
mapScalebar

Add a Scalebar to a Map
oce.axis.POSIXct

Oce Version of axis.POSIXct
mapZones

Add Zones to a Map [deprecated]
mapArrows

Add Arrows to a Map
matchBytes

Locate byte sequences in a raw vector
oce.as.POSIXlt

Oce Variant of as.POSIXlt
oce.as.raw

Version of as.raw() that clips data
oce.write.table

Write the Data Portion of Object to a File
oceApprox

Interpolate 1D Data with Unesco or Reiniger-Ross Algorithm
ocePmatch

Partial matching of strings or numbers
oceSetData

Set something in the data slot of an oce object
parseLatLon

Parse a Latitude or Longitude String
plot,landsat-method

Plot a landsat Object
plot,lisst-method

Plot LISST data
plot,adp-method

Plot ADP Data
plot,oce-method

Plot an oce Object
plot,odf-method

Plot an ODF Object
plotSticks

Draw a Stick Plot
plotTaylor

Plot a Model-data Comparison Diagram
read.adp.rdi

Read a Teledyne/RDI ADP File
read.adp.sontek

Read a Sontek ADP File
download.topo

Download and Cache a topo File
drawDirectionField

Draw a Direction Field
findInOrdered

Find indices of times in an ordered vector
firstFinite

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

Determine time offset from timezone
gps-class

Class to Store GPS Data
imagep

Plot an Image with a Color Palette
integerToAscii

Decode integer to corresponding ASCII code
lobo

LOBO Dataset
mapAxis

Add Axis Labels to an Existing Map
mapContour

Add Contours on a Existing map
matrixShiftLongitude

Rearrange areal matrix so Greenwich is near the centre
met-class

Class to Store Meteorological Data
matrixSmooth

Smooth a Matrix
oceConvolve

Convolve two time series
met

Sample Met Object
oceCRS

Coordinate Reference System strings for some oceans
oceGetMetadata

Get metadata element from an oce object
prettyPosition

Pretty lat/lon in deg, min, sec
processingLog<-

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

Welch periodogram
processingLogShow

Show the processing log of an oce object
read.bremen

Read a Bremen File
read.argo

Read an Argo Data File
read.coastline.openstreetmap

Read a Coastline File in Openstreetmap Format
read.coastline.shapefile

Read a Coastline File in Shapefile Format
read.rsk

Read a Rsk file
read.odf

Read an ODF file
rskPatm

Estimate Atmospheric Pressure in Rsk Object
rskToc

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

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

[[,lisst-method

Extract Something From a LISST Object
[[,tidem-method

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

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

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

Replace Parts of a CM Object
[[<-,coastline-method

Replace Parts of a Coastline Object
read.aquadoppHR

Read Nortek Aquadopp-HR File
read.aquadoppProfiler

Read a Nortek Aquadopp-Profiler File
read.echosounder

Read an Echosounder File
read.ctd.odf

Read a CTD file in ODF format
read.ctd.sbe

Read a Seabird CTD File
read.g1sst

Read a G1SST file
read.sealevel

Read a Sealevel File
section-class

Class to Store Hydrographic Section Data
read.section

Read a Section File
section

Hydrographic section
mapPoints

Add Points to a Map
oceDebug

Print a debugging message
oceDeleteData

Delete data from an oce object
ODF2oce

Create ODF object from the output of ODF::read_ODF()
oceGetData

Get data from an oce object
oceFilter

Filter a time-series
plot,ctd-method

Plot CTD Data
ODFNames2oceNames

Translate from ODF Names to Oce Names
plot,echosounder-method

Plot Echosounder Data
plot,rsk-method

Plot Rsk Data
plot,satellite-method

Plot a satellite object
processingLogAppend

Append an item to a processing log
processingLogItem

Create an item that can be inserted into a processing log
rangeLimit

Substitute NA for data outside a range
rangeExtended

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

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

Read an ADV data file
read.cm

Read a CM file
read.coastline

Read a Coastline File
read.landsat

Read a landsat File Directory
[[<-,tidem-method

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

Replace Parts of a Topo Object
subset,lobo-method

Subset a LOBO Object
summary,bremen-method

Summarize a Bremen Object
subset,echosounder-method

Subset an Echosounder Object
summary,cm-method

Summarize a CM Object
summary,coastline-method

Summarize a Coastline Object
summary,ctd-method

Summarize a CTD Object
summary,topo-method

Summarize A Topo Object
lonFormat

Format a longitude
mapDirectionField

Add a Direction Field to an Existing Map
mapGrid

Add a Longitude and Latitude Grid to a Map
moonAngle

Lunar Angle as Function of Space and Time
numberAsHMS

Convert a Numeric Time to Hour, Minute, and Second
oce.contour

Oce Variant of contour
oce.colorsTwo

Create a Palette of Colours
oceSetMetadata

Set something in the metadata slot of an oce object
oceSmooth

Smooth an Oce Object
plot,argo-method

Plot Argo Data
[[,argo-method

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

Extract Something From a Bremen Object
[[,sealevel-method

Extract Something From a Sealevel Object
[[,section-method

Extract Something From a Section Object
subset,met-method

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

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

Replace Parts of a LISST Object
subset,oce-method

Subset an oce Object
subset,sealevel-method

Subset a Sealevel Object
summary,windrose-method

Summarize a windrose object
swBeta

Seawater haline contraction coefficient
swConservativeTemperature

Seawater conservative temperature, in GSW formulation
swSigma0

Seawater potential density anomaly referenced to surface pressure
swSigma1

Seawater potential density anomaly referenced to 1000db pressure
T90fromT68

Convert from IPTS-68 to ITS-90 temperature
swSoundAbsorption

Seawater sound absorption in dB/m
swSigmaTheta

Seawater potential density anomaly
tail.oce

Extract the End of an Oce Object
topoInterpolate

Interpolate Within a Topo Object
plot,lobo-method

Plot LOBO data
plot,bremen-method

Plot a Bremen Object
plot,met-method

Plot Met Data
plot,tidem-method

Plot a Tidem Prediction
plotPolar

Draw a Polar Plot
plotScan

Plot CTD data in a Low-Level Fashion
plot,topo-method

Plot a Topo Object
read.aquadopp

Read a Nortek Aquadopp File
read.amsr

Read an amsr File
read.ctd.itp

Read an ITP-type CTD File
oceMagic

Find the Type of an Oceanographic Data File
plot,adv-method

Plot ADV data
plot,amsr-method

Plot an amsr Object
plot,gps-method

Plot a GPS Object
plot,ladp-method

Plot an ladp object
plotTS

Plot Temperature-Salinity Diagram
plot,section-method

Plot a Section
plot,sealevel-method

Plot Sealevel Data
predict.tidem

Predict a Time Series from a Tidem Tidal Model
read.adp

Read an ADP File
read.adp.nortek

Read a Nortek ADP File
read.adv.sontek.serial

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

Read an ADV data file
read.lobo

Read a LOBO File
read.met

Read a Met File
rsk-class

Class to Store Rsk Data
retime

Adjust the time within Oce object
satellite-class

Class to hold satellite data
runlm

Calculate running linear models
siderealTime

Convert a POSIXt time to a sidereal time
subset,section-method

Subset a Section Object
summary,met-method

Summarize a Met Object
summary,oce-method

Summarize an oce Object
summary,odf-method

Summarize an ODF Object
summary,rsk-method

Summarize a Rsk Object
tidem

Fit a Tidem (Tidal Model) to a Timeseries
swTSrho

Seawater temperature from salinity and density
swTheta

Seawater potential temperature
tidemAstron

Astronomical Calculations for Tidem
read.lisst

Read a LISST File
read.topo

Read a Topo File
sealevelTuktoyaktuk

Sea-level data set acquired in 1975 at Tuktoyaktuk
renameData

Rename items in the data slot of an oce object
secondsToCtime

Time interval as colon-separated string
sectionAddStation

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

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

Extract Something From a Met Object
sectionGrid

Grid a Section
oce.colorsGebco

Gebco Colors
[[<-,ctd-method

Replace Parts of a CTD Object
oce.grid

Add a Grid to an Existing Oce Plot
oce.plot.ts

Oce Variant of plot.ts
oceDeleteMetadata

Delete metadata from an oce object
oceEdit

Edit an Oce Object
oceSpectrum

Wrapper to give normalized spectrum
plot,coastline-method

Plot a Coastline
plot,cm-method

Plot CM data
odf-class

Class to Store ODF data
plotInset

Plot an Inset Diagram
read.adp.sontek.serial

Read a serial Sontek ADP file
plot,windrose-method

Plot Windrose data
read.adv

Read an ADV data file
read.ctd.woce

Read a WOCE-type CTD file with First Word "CTD"
read.ctd.woce.other

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

Read a NetCDF File
rescale

Rescale values to lie in a given range
read.oce

Read an Oceanographic Data File
resizableLabel

Provide axis names in adjustable sizes
rsk

Sample Rsk Dataset
rsk2ctd

Create a ctd Object from an rsk Object
sectionSmooth

Smooth a Section
sectionSort

Sort a Section
[[,ctd-method

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

Extract Parts of an Echosounder Object
[[,g1sst-method

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

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

Extract Something From a GPS Object
[[<-,echosounder-method

Replace Parts of an Echosounder Object
[[<-,sealevel-method

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

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

Replace Parts of a Section Object
subset,coastline-method

Subset a Coastline Object
subset,ctd-method

Subset a CTD Object
summary,amsr-method

Summarize an AMSR Object
summary,tidem-method

Summarize a Tidem Object
summary,section-method

Summarize a Section Object
summary,argo-method

Summarize an Argo Object
swPressure

Water pressure
swN2

Squared buoyancy frequency for seawater
swSCTp

Salinity from electrical conductivity, temperature and pressure
swSigma

Seawater density anomaly
swSoundSpeed

Seawater sound speed
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
standardDepths

Standard Oceanographic Depths
window.oce

Window an Oce Object by Time or Distance
titleCase

Capitalize first letter of each of a vector of words
tidemVuf

Nodal Modulation Calculations for Tidem
[[,amsr-method

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

Extract Parts of an ADV Object
[[,ladp-method

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

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

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

Replace Parts of a Bremen Object
summary,adp-method

Summarize an ADP Object
subset,amsr-method

Subset an amsr Object
subset,adv-method

Subset an ADV Object
read.ctd

Read a General CTD File
read.gps

Read a GPS File
read.index

Read a NOAA ocean index file
sealevel-class

Class to Store Sealevel Data
sealevel

Sealevel data for Halifax Harbour
shiftLongitude

Shift Longitude to Range -180 to 180
showMetadataItem

Show metadata item
[[,cm-method

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

Extract Something From a Coastline Object
windrose-class

Class to Store Windrose Data
[[,odf-method

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

Replace Parts of a Met Object
[[<-,oce-method

Replace Parts of an Oce Object
[[<-,odf-method

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

Replace Parts of a Rsk Object
subset,odf-method

Subset an ODF object
subset,rsk-method

Subset a Rsk Object
summary,lisst-method

Summarize a LISST Object
subtractBottomVelocity

Subtract Bottom Velocity from ADP
subset,topo-method

Subset a Topo Object
summary,lobo-method

Summarize a LOBO Object
toEnu

Rotate acoustic-Doppler data to the enu coordinate system
toEnuAdp

Convert an ADP Object to ENU Coordinates
undriftTime

Correct for drift in instrument clock
unduplicateNames

Rename duplicated items (used in reading CTD files)
woceNames2oceNames

Translate WOCE Data Names to Oce Data Names
write.ctd

Write a CTD Data Object as a CSV File
unwrapAngle

Unwrap an angle that suffers modulo-360 problems
unitFromStringRsk

Infer Rsk units from a vector of strings
topoWorld

Global Topographic Dataset at Half-degree Resolution
xyzToEnuAdv

Convert an ADP from XYZ to ENU Coordinates
summary,adv-method

Summarize an ADV object
summary,echosounder-method

Summarize an Echosounder Object
summary,gps-method

Summarize a GPS Object
summary,satellite-method

Summarize a satellite object
summary,sealevel-method

Summarize a Sealevel Object
swCSTp

Electrical conductivity ratio from salinity, temperature and pressure
swSigma3

Seawater potential density anomaly referenced to 3000db pressure
swSigma2

Seawater potential density anomaly referenced to 2000db pressure
swDepth

Water depth
swTFreeze

Seawater freezing temperature
swDynamicHeight

Dynamic height of seawater profile
swLapseRate

Seawater lapse rate
swSigma4

Seawater potential density anomaly referenced to 4000db pressure
swSigmaT

Seawater quasi-potential density anomaly
swSpice

Seawater spiciness
swSTrho

Seawater salinity from temperature and density
trimString

Remove leading and trailing whitespace from strings
tidem-class

Class to Store Tidal Models
threenum

Calculate min, mean, and max values
unabbreviateYear

Determine year from various abbreviations
T68fromT90

Convert from ITS-90 to IPTS-68 temperature
T90fromT48

Convert from ITS-48 to ITS-90 temperature
swThermalConductivity

Seawater thermal conductivity
toEnuAdv

Convert an ADV Object to ENU Coordinates
topo-class

Class to Store Topographic Data
vectorShow

Show some values from a vector
velocityStatistics

Report Statistics of adp or adv Velocities
xyzToEnu

Convert acoustic-Doppler data from xyz coordinates to enu coordinates
useHeading

Replace the Heading for One Instrument With That of Another
utm2lonlat

Convert UTM to Longitude and Latitude
xyzToEnuAdp

Convert ADP From XYZ to ENU Coordinates
[[,rsk-method

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

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

Replace Parts of an AMSR Object
[[<-,g1sst-method

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

Replace Parts of a GPS Object
subset,argo-method

Subset an Argo Object
subset,adp-method

Subset an ADP Object
subset,cm-method

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

Replace Parts of a Windrose Object
summary,ladp-method

Summarize an ladp object
summary,landsat-method

Summarize a landsat Object
sunAngle

Solar Angle as Function of Space and Time
swAbsoluteSalinity

Seawater absolute salinity, in GSW formulation
swAlpha

Seawater thermal expansion coefficient
swAlphaOverBeta

Ratio of seawater thermal expansion coefficient to haline contraction coefficient
ungrid

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

Density ratio
unitFromString

Decode units, from strings
swRho

Seawater density
webtide

Get a Tidal Prediction from a WebTide Database
wind

Wind dataset