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oce (version 1.4-0)

Analysis of Oceanographic Data

Description

Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature. This package is discussed extensively in Dan Kelley's book Oceanographic Analysis with R, published in 2018 by 'Springer-Verlag' with ISBN 978-1-4939-8842-6.

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Install

install.packages('oce')

Monthly Downloads

3,613

Version

1.4-0

License

GPL (>= 2)

Maintainer

Last Published

March 28th, 2021

Functions in oce (1.4-0)

Convert from ITS-48 to ITS-90 temperature

ODFNames2oceNames

Translate from ODF Names to Oce Names

GMTOffsetFromTz

Determine time offset from timezone

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

ad2cpHeaderValue

Decode an item from a Nortek AD2CP file header

Convert from IPTS-68 to ITS-90 temperature

abbreviateTimeLabels

Abbreviate a vector of times by removing commonalities

CTD_BCD2014666_008_1_DN.ODF.gz

Sample ctd dataset in odf format

ODFListFromHeader

Create a list of ODF header metadata

Convert from ITS-90 to IPTS-68 temperature

Sample adp (acoustic-doppler profiler) file in RDI format

Sample adp (acoustic-doppler profiler) dataset

adpEnsembleAverage

Ensemble Average an ADP Object in Time

Class to Store adv Data

An amsr dataset for waters near Nova Scotia

Class to Store AMSR-2 Satellite Data

Class to Store Argo Data

Coerce data into a CM object

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

Coerce Data Into a Rsk Object

Coerce Data into a Coastline Object

Convert astronomical angle in degrees to hours, minutes and seconds

Class to Store adp (ADCP) Data

Add a spine to a section object

applyMagneticDeclination

Earth magnetic declination

Sample adv (acoustic-doppler velocimeter) dataset

ARGO float dataset

Trilinear interpolation in a 3D array

Coerce Data Into a Sealevel Object

Coerce Something Into an Oce Object

Apply a function to vector data

Apply a function to matrix data

Coerce Data into met Object

Grid Argo float data

Get names of Acoustic-Doppler Beams

composite,list-method

Composite by Averaging Across Data

Decode BCD to integer

Coerce data into CTD object

Convert Argo Julian Day (juld) to time

Create an ADP Object

Coerce data into a GPS dataset

argoNames2oceNames

Convert Argo Data Name to Oce Name

Coerce data into an ladp object

Coerce Data into an Echosounder Object

Calculate a rounded bound, rounded up to mantissa 1, 2, or 5

Create a Section

A Current Meter (cm) Object

Class to Store Bremen-formatted Data

Convert angles from 0:360 to -180:180

Create tidem object from fitted harmonic data

Coerce Data into a Lobo Object

Coerce Data Into a LISST Object

Create a Windrose Object

Create a composite object by averaging across good data

Create an xbt object

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

Coriolis parameter on rotating earth

cnvName2oceName

Infer variable name, units and scale from a Seabird (.cnv) header line

Smooth and Decimate, or Subsample, an Oce Object

Add Isopycnal Curves to TS Plot

Convert a String to a Unit

Change ADV or ADP coordinate systems

Coerce Data into Topo Object

Convert ADP From Beam to XYZ Coordinates

Bin-average f=f(x,y)

Draw a palette, leaving margins suitable for accompanying plot

Coerce Data Into an Argo Dataset

Bin-map an ADP object

concatenate,adp-method

Concatenate adp objects

Fill a gap in an oce object

beamUnspreadAdp

Adjust ADP Signal for Spherical Spreading

equatorialToLocalHorizontal

Convert equatorial to local horizontal coordinate

Trim Beginning and Ending of a CTD cast

Seawater CTD Profile, Without Trimming of Extraneous Data

Class to Store CTD (or general hydrographic) Data

decodeHeaderNortek

Decode a Nortek Header

concatenate,list-method

Concatenate a list of oce objects

Oce Version of as.POSIXct

Suggest a default flag vector for bad or suspicious data

Bilinear Interpolation Within a Grid

Draw error bars on an existing xy diagram

Find the Ocean Bottom in an Echosounder Object

beamToXyzAdpAD2CP

Convert AD2CP-style adp data From Beam to XYZ Coordinates

Confidence interval in parenthetic notation

Format Geographical Position in Degrees and Minutes

eclipticalToEquatorial

Convert ecliptical to equatorial coordinate

Find indices of times in an ordered vector (defunct)

Remove spikes from a time series

Format bytes as binary defunct

Bin-count vector data

Bin-average a vector y, based on x values

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

World Coastline

Decimate a CTD profile

Cut a Coastline Object at Specified Longitude

Calculate color map

Class to Store Current Meter Data

handleFlags,oce-method

Handle flags in oce objects

handleFlags,argo-method

Handle Flags in ARGO Objects

ctdFindProfiles

Find Profiles within a Tow-Yow CTD Record

handleFlags,ctd-method

Handle Flags in ctd Objects

initializeFlagScheme,section-method

Establish a data-quality scheme for a section object

handleFlags,section-method

Handle flags in Section Objects

Rotate acoustic-Doppler data to a new coordinate system

Class to Store Lowered-adp Data

concatenate,oce-method

Concatenate oce objects

composite,amsr-method

Create a composite of amsr satellite data

Concatenate oce objects

Convert ADV from Beam to XYZ Coordinates

Convert a time to a Julian day

initializeFlagScheme,ctd-method

Establish a data-quality scheme for a ctd object

initializeFlagScheme

Establish a data-quality scheme for a oce object

Interpret a character string as a time interval

d200321-001.ctd

Sample ctd dataset in .ctd format

Curl of 2D vector field

Locate Points on a Map

initializeFlags,oce-method

Create storage for a flag, and initialize values, for a oce object

Class to Store LISST Data

initializeFlagScheme,oce-method

Establish a data-quality scheme for a oce object

initializeFlags

Create storage for a flag, and initialize values, for a oce object

mapLongitudeLatitudeXY

Convert From Longitude and Latitude to X and Y

Add a Scalebar to a Map

Add a Polygon to a Map

d201211_0011.cnv

Sample ctd dataset in .cnv format

Download and Cache a topo File

Full name of file, including path

echosounder-class

Class to Store Echosounder Data

download.coastline

Download a coastline File

Download and Cache a met File

Echosounder Dataset

Class to Store GPS Data

handleFlagsInternal

Low-level function for handling data-quality flags

Calculate Matrix Gradient

Class to Store G1SST Satellite-model Data

Lunar Angle as Function of Space and Time

Extract The Start of an Oce Object

Grid data using Barnes algorithm

Add Axis Labels to an Existing Map

Convert Longitude and Latitude to X and Y

Trim a landsat Image to a Geographical Region

Add Arrows to a Map

integrateTrapezoid

Trapezoidal Integration

Add a Band to a landsat Object

longitudeTighten

Try to Reduce Section Longitude Range

Format a latitude

handleFlags,vector-method

Signal erroneous application to non-oce objects

Bin-count matrix data

Bin-average f=f(x)

Convert a Numeric Time to Hour, Minute, and Second

Locate byte sequences in a raw vector

Base Class for oce Objects

numberAsPOSIXct

Convert a Numeric Time to a POSIXct Time

Oce Variant of plot.ts

matrixShiftLongitude

Rearrange areal matrix so Greenwich is near the centre

initializeFlags,adp-method

Create storage for a flag, and initialize values, for a adp object

initializeFlagSchemeInternal

Establish a data-quality scheme for a oce object

Handle flags in oce objects

Class to Store LOBO Data

coastline-class

Class to Store Coastline Data

oce.write.table

Write the Data Portion of Object to a File

Print a debugging message

oceColorsClosure

Create color functions

oceColorsDensity

Create colors suitable for density fields

Delete Something in an oce data Slot

Find the Name of the Best Coastline Object

oceColorsVorticity

Create colors suitable for vorticity fields

Create colors suitable for CDOM fields

oceColorsChlorophyll

Create colors suitable for chlorophyll fields

Sample LOBO Dataset

A CTD profile in Halifax Harbour

Convolve two time series

Edit an Oce Object

Parse a Latitude or Longitude String

oceDeleteMetadata

Delete Something in an oce metadata Slot

drawDirectionField

Draw a Direction Field

Download and Cache an amsr File

Detrend a set of observations

oceUnits2whpUnits

Translate oce unit to WHP unit

Sample ctd dataset in .cnv format

Wrapper to give normalized spectrum

plot,adv-method

Plot an adv Object

Convert From Geographical to Geodesic Coordinates

Convert ENU to Other Coordinate

Convert ADP ENU to Rotated Coordinate

Perform lowpass digital filtering

Earth magnetic declination, inclination, and intensity

Format a latitude-longitude pair

Add a Longitude and Latitude Grid to an Existing Map

mapDirectionField

Add a Direction Field to an Existing Map

Sample met Object

metNames2oceNames

Convert met Data Name to Oce Name

plot,gps-method

Plot a gps Object

plot,adp-method

Plot an adp Object

plot,ladp-method

Plot an ladp Object

plot,amsr-method

Plot an amsr Object

Interpolate 1D Data with UNESCO or Reiniger-Ross Algorithm

Convert Longitude and Latitude to UTM

plot,landsat-method

Plot a landsat Object

Acceleration due to earth gravity

Inverse Geodesic Calculation

Look Within the First Element of a List for Replacement Values

Draw a Stick Plot

Plot Temperature-Salinity Diagram

Read an ADV data file

Add Lines to a Map

Add an Image to a Map

Add Text to a Map

Add Tissot Indicatrices to a Map

handleFlags,adp-method

Handle Flags in adp Objects

oceColorsFreesurface

Create colors suitable for freesurface fields

Draw an axis, possibly with decade-style logarithmic scaling

read.adv.nortek

Read an ADV data file

Version of as.raw() that clips data

Create colors in a Gebco-like scheme

oceColorsVelocity

Create colors suitable for velocity fields

Plot an Inset Diagram

plot,lisst-method

Plot a lisst Object

Test whether object is an AD2CP type

oceColorsViridis

Create colors similar to the matlab Viridis scheme

Get Something from an oce data Slot

Filter a Time Series

Draw a Polar Plot

julianCenturyAnomaly

Julian-Day number to Julian century

oce.axis.POSIXct

Oce Version of axis.POSIXct

oceRenameMetadata

Rename Something in an oce metadata Slot

read.aquadoppProfiler

Read a Nortek Aquadopp-Profiler File

Welch periodogram

processingLogShow

Show the processing log of an oce object

Substitute NA for data outside a range

Calculate Range, Extended a Little, as is Done for Axes

Set Something in an oce data Slot

plot,argo-method

Plot an argo Object

Read an ITP-type CTD File

Read a WOCE-exchange CTD File

Read an Argo Data File

read.ctd.woce.other

Read a WOCE-exchange EXPOCODE File

Read a CTD file in ODF format

Alter longitudes from -180:180 to 0:360 convention

Read a NOAA ocean index file

Read a GPS File

Add Contours on a Existing map

Format a longitude

mapCoordinateSystem

Draw a coordinate system

plot,bremen-method

Plot a bremen Object

Read a Topo File

Create colors suitable for PAR fields

oceColorsPalette

Create a vector of colors

Create colors similar to the google turbo scheme

Read a NetCDF File

Class to Store Rsk Data

Hydrographic section

Sample Rsk Dataset

Read a World Ocean Atlas NetCDF File

plot,rsk-method

Plot a rsk Object

Read an Oceanographic Data File

Rename items in the data slot of an oce object (deprecated)

Estimate Atmospheric Pressure in Rsk Object

Read a NOAA format for AXBTs

Create a ctd Object from an rsk Object

sectionAddStation

Add a CTD Station to a Section

satellite-class

Class to Store Satellite Data

Extract Something From an ladp Object

plot,satellite-method

Plot a satellite Object

Plot a CTD Profile

Compute Geodesic Distance on Surface of Earth

Create two-color palette

[[,windrose-method

Extract Something From a Windrose Object

[[,landsat-method

Extract Something From a landsat Object

plot,windrose-method

Plot a windrose Object

plot,oce-method

Plot an oce Object

Find the Type of an Oceanographic Data File

plot,xbt-method

Plot an xbt Object

Get Something From an oce metadata Slot

plot,odf-method

Plot an odf Object

Extract Something From an xbt Object

Plot CTD data in a Low-Level Fashion

Smooth a Matrix

Class to Store Meteorological Data

Plot a Model-data Comparison Diagram

Predict a Tidal Signal

Add a Grid to an Existing Oce Plot

oce: A Package for Oceanographic Analysis.

Deprecated and Defunct Elements of the oce package

Oce Variant of contour

Great-circle Segments Between Points on Earth

[[<-,coastline-method

Replace Parts of a Coastline Object

read.adp.nortek

Read a Nortek ADP File

[[<-,ctd-method

Replace Parts of a ctd Object

Class to Store Sealevel Data

[[<-,oce-method

Replace Parts of an Oce Object

[[<-,odf-method

Replace Parts of an ODF Object

Create colors suitable for phase fields

subset,section-method

Subset a Section Object

subset,sealevel-method

Subset a Sealevel Object

Convert each of a vector of strings from SNAKE_CASE to camelCase

oceNames2whpNames

Translate Oce Data Names to WHP Data Names

oceColorsSalinity

Create colors suitable for salinity fields

Standard Oceanographic Depths

processingLogAppend

Append an item to a processing log

Partial matching of strings or numbers

Read a Teledyne/RDI ADP File

processingLogItem

Create an item that can be inserted into a processing log

Plot an Image with a Color Palette

initializeFlagsInternal

Create storage for a flag, and initialize values, for a oce object

initialize,ctd-method

Initialize storage for a ctd object

Read an ADP File

Read an ODV-type CTD File

read.adv.sontek.text

Read an ADV data file

Read an AD2CP File

Read an amsr File

Decode integer to corresponding ASCII code

summary,ctd-method

Summarize a ctd Object

Extract Something from an adv Object

Read a Seabird CTD File

Read a landsat File Directory

Read a Nortek Aquadopp File

Solar Angle as Function of Space and Time

summary,echosounder-method

Summarize an Echosounder Object

summary,rsk-method

Summarize a Rsk Object

Seawater potential density anomaly

summary,satellite-method

Summarize a satellite object

sunDeclinationRightAscension

Sun Declination and Right Ascension

swSoundAbsorption

Seawater sound absorption in dB/m

Seawater freezing temperature

Seawater spiciness

Tidal Current Dataset

Read a LISST File

Read a Section File

Read a Sealevel File

Smooth a Section

Shift Longitude to Range -180 to 180

[[,echosounder-method

Extract Something from an Echosounder Object

Extract Something From a met Object

Set data-quality flags within a oce object

Grid a Section in Pressure Space

Extract Something From a ctd Object

Tidal Constituent Information

read.aquadoppHR

Read Nortek Aquadopp-HR File

Class to Store Topographic Data

topoInterpolate

Interpolate Within a Topo Object

xyzToEnuAdpAD2CP

Convert ADP2CP adp object From XYZ to ENU Coordinates

Convert an ADP from XYZ to ENU Coordinates

Convert UTM to Longitude and Latitude

Calculate lon-lat coordinates of plot-box trace

Adjust the time within Oce object

Read a Rsk file

Read an ODF file

Extract Something From an amsr Object

Rotate velocity components within an oce object

[[,g1sst-method

Extract Something From a G1SST Object

Extract Something From an oce Object

Class to Store landsat Data

Add Points to a Map

Make a digital filter

Sample landsat Dataset

Coordinate Reference System strings for some oceans

Convert X and Y to Longitude and Latitude

Data that define some color palettes

Sealevel data for Halifax Harbour

Class to Store ODF Data

sealevelTuktoyaktuk

Sea-level data set acquired in 1975 at Tuktoyaktuk

showMetadataItem

Show metadata item

standardizeLongitude

Put longitude in the range from -180 to 180

Extract Something from an adp Object

Extract Something From an ODF Object

Convert a POSIXt time to a sidereal time

[[<-,adp-method

Replace Parts of an ADP Object

plot,echosounder-method

Plot an echosounder Object

plot,sealevel-method

Plot a sealevel Object

plot,ctd-method

Plot a ctd Object

Create colors in a red-yellow-blue color scheme

plot,section-method

Plot a section Object

[[<-,amsr-method

Replace Parts of an amsr Object

Extract Something From a Rsk Object

[[<-,landsat-method

Replace Parts of a landsat Object

[[<-,lisst-method

Replace Parts of a LISST Object

[[<-,argo-method

Replace Parts of an Argo Object

[[<-,echosounder-method

Replace Parts of an Echosounder Object

[[<-,topo-method

Replace Parts of a Topo Object

Extract Something From a GPS Object

[[<-,g1sst-method

Replace Parts of a G1SST Object

plot,tidem-method

Plot a tidem Object

plot,topo-method

Plot a topo Object

[[<-,bremen-method

Replace Parts of a Bremen Object

Replace Parts of a CM Object

subset,coastline-method

Subset a Coastline Object

[[<-,adv-method

Replace Parts of an ADV Object

oceColorsOxygen

Create colors suitable for oxygen fields

subset,ctd-method

Subset a ctd Object

Create colors similar to the Matlab Jet scheme

oceColorsTemperature

Create colors suitable for temperature fields

oceColorsTurbidity

Create colors suitable for turbidity fields

Wrapper to sf::sf_project()

subset,rsk-method

Subset a Rsk Object

subset,odf-method

Subset an ODF object

summary,adv-method

Summarize an ADV object

[[<-,windrose-method

Replace Parts of a Windrose Object

Pretty lat/lon in deg, min, sec

Plot a cm Object

Smooth an Oce Object

Set Something in an oce metadata Slot

Rename Something in an oce data Slot

summary,amsr-method

Summarize an amsr Object

processingLog<-

Add an item to a processing log (in place)

Read a Bremen File

[[<-,lobo-method

Replace Parts of a LOBO Object

plot,coastline-method

Plot a coastline Object

plot,lobo-method

Plot a lobo object

subtractBottomVelocity

Subtract Bottom Velocity from ADP

subset,argo-method

Subset an Argo Object

[[<-,met-method

Replace Parts of a met Object

subset,cm-method

Subset a CM Object

read.coastline.shapefile

Read a Coastline File in Shapefile Format

Read a General CTD File

summary,section-method

Summarize a Section Object

summary,tidem-method

Summarize a Tidem Object

summary,sealevel-method

Summarize a Sealevel Object

summary,adp-method

Summarize an ADP Object

[[<-,xbt-method

Replace Parts of an xbt Object

plot,met-method

Plot a met Object

Get the present time, in a stated timezone

Set Preference for Adjusted Values

Read a LOBO File

summary,cm-method

Summarize a CM Object

swAbsoluteSalinity

Seawater absolute salinity, in GSW formulation

subset,adp-method

Subset an ADP Object

summary,coastline-method

Summarize a Coastline Object

Seawater thermal expansion coefficient

Read a met File

Decode table-of-contents File from a Rsk File

Calculate running linear models

Time interval as colon-separated string

summary,oce-method

Summarize an oce Object

summary,topo-method

Summarize A Topo Object

Seawater lapse rate

Squared buoyancy frequency for seawater

Seawater potential density anomaly referenced to 4000db pressure

Seawater quasi-potential density anomaly

Seawater temperature from salinity and density

swThermalConductivity

Seawater thermal conductivity

Practical salinity from electrical conductivity, temperature and pressure

Seawater potential density anomaly referenced to 2000db pressure

test_met_csv1.csv

Sample met dataset (CSV format prior to October 2019)

test_met_csv2.csv

Sample met dataset (CSV format as of October 2019)

Class to Store Hydrographic Section Data

Convert an ADP Object to ENU Coordinates

Class to Store Tidal Models

Capitalize first letter of each of a vector of words

Fit a Tidal Model to a Timeseries

Seawater potential density anomaly referenced to 3000db pressure

setFlags,adp-method

Set data-quality flags within a adp object

summary,odf-method

Summarize an ODF Object

Convert an ADV Object to ENU Coordinates

Extract Something From a CM Object

Rotate acoustic-Doppler data to the enu coordinate system

Decode units, from strings

summary,windrose-method

Summarize a windrose object

unabbreviateYear

Determine year from various abbreviations

Get a Tidal Prediction from a WebTide Database

Correct for drift in instrument clock

summary,xbt-method

Summarize an xbt Object

[[,coastline-method

Extract Something From a Coastline Object

unitFromStringRsk

Infer Rsk units from a vector of strings

Convert Acoustic-Doppler Data From xyz to enu Coordinates

Convert ADP From XYZ to ENU Coordinates

swDynamicHeight

Dynamic height of seawater profile

Seawater potential density anomaly referenced to 1000db pressure

Seawater potential density anomaly referenced to surface pressure

Seawater potential temperature

Seawater viscosity

[[,lisst-method

Extract Something From a LISST Object

Global Topographic Dataset at Half-degree Resolution

woceNames2oceNames

Translate WOCE Data Names to Oce Data Names

woceUnit2oceUnit

Translate WOCE units to oce units

Extract Something From a LOBO Object

read.adp.sontek

Read a Sontek ADP File

[[,section-method

Extract Something From a Section Object

[[,sealevel-method

Extract Something From a Sealevel Object

read.adp.sontek.serial

Read a serial Sontek ADP file

Sample xbt dataset

[[<-,ladp-method

title Replace Parts of a ladp Object

[[<-,gps-method

Replace Parts of a GPS Object

[[<-,rsk-method

Replace Parts of a Rsk Object

[[<-,sealevel-method

Replace Parts of a Sealevel Object

read.adv.sontek.adr

Read an ADV data file

read.adv.sontek.serial

Read an ADV data file

Read a Coastline File

subset,echosounder-method

Subset an Echosounder Object

Remove leading and trailing whitespace from strings

read.coastline.openstreetmap

Read a Coastline File in Openstreetmap Format

Read an xbt file

read.echosounder

Read an Echosounder File

Read a G1SST file

unduplicateNames

Rename duplicated character strings

Read a Sippican '.edf' format xbt file

subset,lobo-method

Subset a LOBO Object

Rescale values to lie in a given range

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

subset,met-method

Subset a met Object

setFlags,ctd-method

Set data-quality flags within a ctd object

Extract Something From an Argo Object

Provide axis names in adjustable sizes

Write a CTD Data Object as a CSV File

setFlags,oce-method

Set data-quality flags within a oce object

[[,bremen-method

Extract Something From a Bremen Object

Extract Something From a Topo Object

[[,tidem-method

Extract Something From a Tidem Object

[[<-,section-method

Replace Parts of a Section Object

subset,oce-method

Subset an oce Object

Class to Store XBT Data

[[<-,tidem-method

Replace Parts of a Tidem Object

subset,adv-method

Subset an ADV Object

subset,amsr-method

Subset an amsr Object

subset,topo-method

Subset a Topo Object

subset,xbt-method

Subset an xbt Object

summary,argo-method

Summarize an Argo Object

summary,bremen-method

Summarize a Bremen Object

summary,lobo-method

Summarize a LOBO Object

summary,met-method

Summarize a met Object

Seawater density

Seawater salinity from temperature and density

summary,ladp-method

Summarize an ladp object

summary,gps-method

Summarize a GPS Object

Seawater density anomaly

Vertical coordinate

swAlphaOverBeta

Ratio of seawater thermal expansion coefficient to haline contraction coefficient

summary,lisst-method

Summarize a LISST Object

Seawater haline contraction coefficient

summary,landsat-method

Summarize a landsat Object

Extract the End of an Oce Object

Seawater sound speed

Astronomical Calculations for Tidem

Electrical conductivity ratio from salinity, temperature and pressure

swConservativeTemperature

Seawater conservative temperature, in GSW formulation

tidemConstituentNameFix

Change tidal constituent name from T-TIDE to Foreman convention

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),

Calculate min, mean, and max values

test_met_xml2.xml

Sample met dataset (XML format as of October 2019)

Unwrap an angle that suffers modulo-360 problems

Nodal Modulation Calculations for Tidem

Convert time to Argo Julian Day (juld)

Window an Oce Object by Time or Distance

Class to Store Windrose Data

Show some values from a vector

Replace the Heading for One Instrument With That of Another

velocityStatistics

Report Statistics of adp or adv Velocities