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oce (version 0.9-17)

Analysis of Oceanographic Data

Description

Supports the analysis of Oceanographic data, including ADCP measurements, CTD measurements, sectional data, sea-level time series, coastline files, etc. Handles dozens of specialized functions for calculating seawater properties such as potential temperature and density, as well as derived properties such as buoyancy frequency and dynamic height. Map projections are calculated using PROJ.4 functions included within the oce.

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Version

Install

install.packages('oce')

Monthly Downloads

2,573

Version

0.9-17

License

GPL (>= 2)

Maintainer

Dan Kelley

Last Published

May 22nd, 2015

Functions in oce (0.9-17)

Convert between temperature scales

Current-meter record

Add a column to an oce object

Gradient of a matrix

Bin-map an ADP object

Coerce data into coastline dataset

Class for drifter data

Plot an image with a color palette

echosounder-class

Class to store echosounder data

Plot arrows on a existing map

Convert a POSIXt time to a Julian day

Look within the first element of a list, replacing other elements from its contents.

Scan a coastline data file

full name of file, including path

Read an ADV data file

Summarize a gps object

Bin-count or bin-average f=f(x) or f=f(x,y), based on x or (x,y) values

coastline-class

Class to store coastline data

Add a column to a CTD file

Summarize a lobo data object

swAbsoluteSalinity

Seawater absolute salinity, in GSW formulation

Class to store LISST data

Class to store logger data

Name an acoustic-doppler beam.

ADP (acoustic-doppler profiler) dataset

base class of oce package

Extract time from an oce object

Sample meteorological object

Earth magnetic declination, inclination, and intensity

Decode BCD to integer

Add a band to a landsat image

Bind CTD profiles together into a cross section

Hydrographic section

Subset an oce object

Coerce ctd data into section dataset

Version of as.raw() that clips data

Plot text on a existing map

Plot a wind rose diagram

Show some values from a vector

Correct for drift in instrument clock

Plot landsat data

Add isopycnal curves to TS plot

Change ADP coordinate system

Draw a polar plot.

Read a LISST data file

Class to store hydrographic data

Convert a numeric time to hour, minute, and second

Find indices of tiems in an ordered vector

World coastline

summary.windrose

Summarize a windrose data object

unabbreviateYear

Determine year from various abbreviations

Plot seawater CTD data

Interpret a character string as a time interval

Plot a model-data comparison diagram.

Pretty lat/lon in deg, min, sec

Find the ocean bottom in an echosounder object

Trim a landsat image to a lat-lon box

Welch periodogram

Plot zones on an existing map [DEPRECATED]

Confidence interval in parenthetic notation

Convert from longitude and latitude to UTM

abbreviateTimeLabels

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

Class to store acoustic Doppler profiler data

Convert angles from 0:360 to -180:180

subset.echosounder

Subset an echosounder object

Coerce data into a lisst object

GMTOffsetFromTz

Determine time offset from timezone

Predict a time series from a tidal model

Coerce data into drifter dataset

Subset a logger object

integrateTrapezoid

Use trapezoidal integration

Trilinear interpolation in a 3D array

Class to store ODF data

Read a CTD data file

ARGO drifter dataset

Access or modify part of an Oce object

Decode integer to corresponding ASCII code

Plot contours on a existing map

Class to store hydrographic section data

Coerce data into echosounder dataset

Subset a topo object

Coerce data into sea-level dataset

beamUnspreadAdp

Adjust ADP signal for spherical spreading

Scan a gps data file

Seawater density

Coerce data into ctd dataset

Subset a lisst object

Determine coordinate system

Plot a time-series, obeying the timezone

Calculate color map

Class to store current meter data

Coerce data into met dataset

Format bytes as binary

Plot an image on a existing map

Curl of 2D vector field

Plot axis labels on an existing map

Extract data from an oce object

ctdFindProfiles

Find profiles within a towyow CTD record

oce.write.table

Write the data portion of object to a file

Trim start/end portions of a CTD cast

Summarize a CTD object

Convert east-north-up to other coordinate

Summarize a tide-model object

equatorialToLocalHorizontal

Convert equatorial to local horizontal coordinate

Coerce data into topo dataset

Detrend a set of observations

Acceleration due to earth gravity

mapLongitudeLatitudeXY

Convert from longitude and latitude to x and y

Summarize a met object

Read a landsat data file

Read a section containing multiple CTD profiles

swConservativeTemperature

Seawater conservative temperature, in GSW formulation

sealevelTuktoyaktuk

Sea-level data set acquired in 1975 at Tuktoyaktuk

Squared buoyancy frequency for seawater

Seawater thermal expansion coefficient

Read an oceanographic data file

Wrapper to give normalized spectrum

Decode a time, similar to as.POSIXct()

Subset a drifter object

read.observatory

Read observatory data file

numberAsPOSIXct

Convert a numeric time to a POSIXct time

Draw a stick-plot diagram

Estimate atmospheric pressure in logger record

subset.sealevel

Subset a sealevel object

Return the header for an Oce data object

Seawater spiciness

Seawater haline contraction coefficient

Draw error bars on an existing xy diagram

Format a latitude-longitude pair

Time interval as colon-separated string

Calculate min, mean, and max values

Grid data using Barnes algorithm

Fill a gap in an oce object

Draw a scalebar on an existing map

plot.echosounder

Plot echosounder data

Fit a tidal model to a timeseries

Class to store acoustic Doppler velocimeter data

julianCenturyAnomaly

Julian-Day number to Julian century

Seawater potential temperature

Plot a CTD profile of various quantities

swAlphaOverBeta

Ratio of seawater thermal expansion coefficient to haline contraction coefficient

applyMagneticDeclination

Earth magnetic declination

Global topographic dataset at half-degree resolution

Coerce data into a GPS dataset

Seawater density anomaly

Format a latitude

swThermalConductivity

Seawater thermal conductivity

sectionAddStation

Add CTD profile to section

Window an oce object by time or distance

mapDirectionField

Plot a direction field on a existing map

Create a windrose object

Great-circle segments between points on earth

Geodesic distance on earth

subtractBottomVelocity

Subtract bottom velocity from ADP velocity

Do ephemeris calculations for tidem

Plot a polygon on a existing map

Make a digital filter

Plot points on a existing map

Plot Tissot indicatrices

Convert from longitude and latitude to x-y coordinates

Smooth a matrix.

Seawater CTD profile, without trimming of extraneous data

Coerce data into lobo dataset

Summarize an ADP object

oce.axis.POSIXct

Modified version of axis.POSIXct

Create a palette of colours

showMetadataItem

Show metadata item

Plot drifter data

Class to store gps data

summary.drifter

Summarize a drifter object

Change ADV or ADP coordinate systems

Subset a section object

Tidal constituent information

Coriolis parameter on rotating earth

Seawater viscosity

Unwrap an angle that suffers modulo-360 problems

Plot a gps object

Filter a time-series, possibly recursively

Contour with ability to flip x and y

Print a debugging message

ctdUpdateHeader

Update a CTD header

A CTD profile in Halifax Harbour

Seawater sound speed

Apply a function to binned matrix data

Summarize an odf object

drawDirectionField

Draw a direction field

Read a current-meter data file

Read a meteorological data file

Convert east-north-up to other coordinate

Plot cm (current meter) data

Read an ODF file

Landsat-8 dataset

Plot LISST data

Plot logger data

Subset a ctd object

Convert XYZ to ENU coordinates

Add a grid to an existing plot, with special abilities for those created by oce

Plot seawater data in a low-level fashion

Convert ADV from beam coordinates to xyz coordinates

summary.sealevel

Summarize a sealevel object

summary.coastline

Summarize a coastline data object

Sea-level data set, from Halifax Harbour

Find the name of the best coastline file

Convert from ENU coordinates

Remove spikes from a time series

Plot sealevel data

Plot a tidal fit

swSoundAbsorption

Seawater sound absorption in dB/m

Geographical position in degrees and minutes

Draw palette on RHS of plot device

Class to store LOBO data

Plot topography data

Read a drifter data file

eclipticalToEquatorial

Convert ecliptical to equatorial coordinate

Adjust the time within Oce object

Class to store Landsat data

Calculate running linear models

Decode table-of-contents file from a datalogger

Calculate range, extended a little

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

Plot meridians on an existing map [DEPRECATED]

Create a logger object

Trim start/end portions of a logger cast

Replace the heading for one instrument with the heading for another

A logger dataset, of the temperature-data recorder variety

subset.coastline

Subset a coastline object

Bin-average a vector y, based on x values

Convert from x-y to longitude and latitude

Subset a met object

Substitute NA for data outside a range

Plot a coastline

Salinity from electrical conductivity, temperature and pressure

echosounder dataset

Summarize a LISST object

Plot lines on a existing map

Plot longitude and latitude grid on an existing map

Partial matching of strings or numbers

Interpolate 1D data with Unesco or Reiniger-Ross algorithm

Plot a CTD section

Smooth an oce object

Read a logger file

Smooth a section

Seawater potential density anomaly reference to standardized pressures

Convert from ENU coordinates

Locate byte sequences in a raw vector

Summarize a topography data object

Read a sea-level data file

Read an topography file

velocityStatistics

Report statistics of ADP or ADV velocities.

Seawater temperature from salinity and density

Convert a POSIXt time to a sidereal time

read.echosounder

Read an echosounder data file

Class to store meteorological data

Seawater freezing temperature

Class to store sealevel data

Plot meteorological data

Summarize a cm (current meter) object

Do ephemeris calculations for tidem

Subset an adv object

Read a NOAA ocean index file

Parse a latitude or longitude string

Decode a Nortek header

Electrical conductivity from salinity, temperature and pressure

Plot an inset diagram

Summarize an ADV object

summary.landsat

Summarize a landsat object

Read a lobo data file

summary.section

Summarize a CTD section

Seawater quasi-potential density anomaly

Seawater salinity from temperature and density

Seawater potential density anomaly

Solar angle as function of space and time.

Class to store tidal-constituent models

Seawater specific heat

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

Standard oceanographic depths

Convert XYZ to ENU coordinates

swDynamicHeight

Dynamic height of seawater profile

Seawater lapse rate

Convolve two time series

Convert from UTM to longitude and latitude

Class to store windrose data

Decimate a CTD profile

Smooth and decimate an oce object

Lunar angle as function of space and time.

Find the type of an oceanographic data file

More general form of as.POSIXlt

Write a CTD data object as a .csv file

ADV (acoustic-doppler velocimeter) dataset

Convert lon/lat to x/y on earth

Locate points on a existing map

Edit an oce object

Read an ADP data file

Provide axis names in adjustable sizes

Subset an adp object

Subset a cm object

Ends of oce objects.

Plot an ODF object

Add an item to object processingLog

Format a longitude

Get a tidal prediction from a WebTide database

Rescale values to lie in a given range

Plot temperature-salinity diagram

Summarize a logger object

summary.echosounder

Summarize an echosounder object

topoInterpolate

Interpolate within a topography dataset

Class to store topographic data