Changelog

Source: NEWS.md

oce 1.8.4

• Add bodcNames2oceNames() to rename NERC/BODC variables (issue #2235).
• Add D4902337_219.nc built-in Argo profile data file (issue #2272). (issue #2331).
• Add netcdfTOC() to overview NetCDF files (issue #2232).
• Add oceColorsCubeHelix(), a perceptual colour scheme used in Astronomy
• Add oceRename() to rename variables, flags and units (issue #2238).
• Add read.xbt.edf2() to read a tab-separated file type.
• Add read.xbt.noaa2() to handle UBT format (issue #2289).
• Add Tidal Analysis vignette (issue #2243).
• Change adpRdiFileTrim() to reorder parameters, and to accept indices parameter (issue #2330)
• Change amsr[[ to handle "metadata" parameter (issue #2229).
• Change argo2ctd() (issue #2270).
• Change as.unit() to handle more units (issue #2240).
• Change as.ctd() to handle Argo data better (issue #2270).
• Change binApply1D() to
  • handle the ... argument (issue #2265) and
  • handle time zones better (issue #2266).
• Change concatenate() to handle lists properly (issue #2278).
• Change download.amsr() to handle realtime data files (issue #2231).
• Change imagep() to handle decimate as set in ~/.Rprofile (issue #2263).
• Change lonlat2map() to handle a [coastline-class] object as first parameter (issue #2284).
• Change magneticField() to handle the latest (generation 14) IGRF formulation (issue #2274).
• Change mapScalebar() to
  • handle x="top" (issue #2283) and
  • handle length under 1km (issue #2287).
• Change mapPlot() to handle las as a parameter (issue #1707).
• Change oceRename() to default to a built-in IOOS dictionary (issue #2311).
• Change oce.plot.ts() to
  • handle grid better (issue #2267),
  • handle simplify better (issue #2277) and
  • handle xlab better (issue #2285).
• Change plot.section() to handle eos="gsw" (issue #2256).
• Change pwelch() to fix error if nfft and spec are provided (issue #2299).
• Change read.adp.ad2cp() to
  • handle TOC, datasets and plans better (issue #2303 and related),
  • read temperature correctly (issue #2324),
  • save elements of AST (etc) individually, not within a list (issue #2318) and
  • scale altimeterRawSamples by 1/2^15 (issue #2327).
  • set data@distance only if NC (number of cells) is nonzero (issue #2319).
  • use number of raw altimeter samples from header, if it disagrees with value in record (issue #2326).
• Change read.adp.rdi(..., which="??") to return a data frame that includes ensemble size (issue #2329).
• Change read.amsr() to handle realtime data files (issue #2230).
• Change read.ctd.sbe() to
  • handle files that lack salinity and conductivity (issues #2279 and #2282) and
  • handle time-related header elements better (issues #2280 and #2281).
  • handle “new” format CNV files, at least provisionally (issue #2328).
• Change read.ctd.aml() to handle “type 3” format (issue #2247).
• Change read.coastline() to handle file in “shapefile” format (issue #1850).
• Change read.met() to handle flags better (issue #2298).
• Change read.netcdf() to
  • document flag handling better (issue #2236),
  • handle units better and
  • permit renaming data (issue #2235).
• Change read.rsk() to handle a new file (issue #2291).
• Change sectionSmooth() to disallow method="kriging", because it relied on the automap package, which was removed from CRAN on 2025-06-30 (issue #2332).
• Change subset,amsr-method() to handle "pass" parameter.
• Change subset,ctd-method() to handle items of unexpected length (issue #2250).
• Change tidem() to stop if there are any non-finite time values (issue #2269).
• Change vectorShow() to obey “digits” parameter for list arguments (issue #2313).

oce 1.8.3 (ON CRAN)

• Add swSpiciness0(), swSpiciness1(), and swSpiciness2() (issue #2188).
• Change binMean2D() to use previous (6-month-old) method (issue #2199).
• Change [[ for many seawater properties to handle argo data (issues #2207 and #2208).
• Change concatenate() to handle data slots that are data frames (issue #2213).
• Change ctdDecimate() to add the na.rm argument (issue #2192).
• Change mapDirectionField() to allow wind barbs (issue #2191).
• Change mapContour() to discuss longitude conventions (issue #2218).
• Change mapImage() to handle a user-provided gridding function (issue #2199).
• Change mapImage() to add the gridCoarseness parameter (issue #2199).
• Change oceMagic() to close NetCDF files after checking them (issue #2209).
• Change plot.amsr() to add the zlab parameter (issue #2220).
• Change plot.argo() to handle which="sigma0 profile" (issue #2184).
• Change plot.sealevel() to add the grid parameter (issue #2204).
• Change plot.sealevel() to improve labelling (issue #2203).
• Change plot.section() to handle bottom traces better (issue #2194).
• Change plot.section() to show data as points properly (issue #2195).
• Change plotProfile() to handle xaxs and yaxs when xtype="spiciness0" (issue #2215).
• Change plotTaylor() to handle a few more parameters.
• Change read.adp.rdi() to handle large (> 2.147 GB) files (issue #2196).
• Change read.amsr() to read start/end times plus other metadata (issue #2219).
• Change read.argo() to handle non-UTF characters in metadata (issue #2206).
• Change read.ctd.sbe() to name specc as specificConductance (issue #2211).
• Change read.ctd.ssda() to handle hemisphere tags in location (issue #2227).
• Change read.met() to return data slots that are lists (issue #2213).
• Change resizableLabel() to document partial-match behaviour (issue #2197).
• Change resizableLabel() to handle item=“N”` (issue #2197).
• Change summary() to skip time in the threenum table (issue #2198).
• Change sunAngle() to handle vector arguments better (issue #2178).
• Change sunAngle() to detect non-logical values of useRefraction (issue #2225).
• Change some byte-level work from C to C++ to improve maintainability (issue #2201).

oce 1.8.2 (on CRAN)

• Add package?oce documentation (had been missing with a Roxygen2 change).
• Add read.ctd.saiv() to read data from SAIV instruments (issue #2141).
• Remove many dontrun examples from the docs (issue #2152).
• Remove trimString(), after it had been deprecated for a long time (issue #2123).
• Remove use of the deprecated sp package (issue #2154).
• Change amsr dataset and functions to handle new format (issues #2124 to #2133 plus issue #2147).
• Change as.ctd() to handle multi-profile Argo better (issue #2173).
• Change as.tidem() to handle NOAA constituent names and frequencies (issues #2143, #2144 and #2146).
• Change C/C++ sprintf() calls so all formats match arguments (issue #2172).
• Change computableWaterProperties to handle a vector of variable names.
• Change plot.adp() to obey xlab if x axis represents time (issue #2162).
• Change plot.cm() to obey xlim, ylim, xaxs and yaxs (issue #2121).
• Change plotTS() and plotProfile() to accept type="b".
• Change plot.windrose() for type="fivenum" (issue #2164).

oce 1.8.1 (on CRAN)

• Change as.ctd() to handle startTime, PRES, PSAL and TEMP better.
• Change binCount1D() + 6 related functions by adding include.lowest parameter (issue #2113).
• Change C++ files to avoid an error relating to include statements (issue #2119).
• Change imagep() to ensure z (if provided) is a matrix (issue #2091).
• Change plot.section() to skip the kriging example (issue #2080).
• Change plot.section() to show palette triangles if necessary (issue #2083).
• Change plot.section() to show data and bottom correctly (issue #2092).
• Change plotTS() to obey the rho1000 parameter again (issue #2085).
• Change read.argo() to translate more variable names.
• Change read.netcdf() to read more items.
• Change read.rsk() to obey the tz parameter (issue #2108).
• Change summary.adp() to handle the new format for AD2CP data (issue #2087).

oce 1.8.0 (on CRAN)

• Add advSontekAdrFileTrim() (issue #1994).
• Add ctdFindProfilesRBR() (issue #2027).
• Change applyMagneticDeclination() to also handle adp and adv (issue #2038).
• Change download.topo() to handle new NOAA database (issue #2015).
• Change inst/extdata by compressing some files.
• Change mapPlot() to remove an infrequent low-level error (issue #2036).
• Change mapPlot() to require projection to be a string (issue #2076).
• Change numberAsPOSIXct(t, type="gps") to handle week rollover (issue #2077).
• Change plot.echosounder() to use oceColorsViridis() by default (issue #2060).
• Change plotProfile() to create xlab on vector input (issue #2047).
• Change plotTS() to compute isopycnals more accurately (issue #2046).
• Change plotTS() to handle lobo objects directly.
• Change plot.tidem() to obey ... parameter (issue #2035).
• Change read.adp.ad2cp(), and structure of AD2CP objects (issue #2005).
• Change read.rsk() to read geographic information (issue #2024).
• Change sectionSmooth() to handle method="kriging" again
• Change tidem() (and summary method) to handle 6-hourly data (issue #2034).
• Remove package dependence on rgeos and raster packages (issue #2028).
• Remove plotAD2CP(), now superseded by generic plot() method (issue #2005).
• Remove plotting tests but retain in developer suite (issue #2073).

oce 1.7.10 (on CRAN)

• Fix a typo in swThermalConductivity() doc.

oce 1.7.9

• Improve the handling of file encodings.
• Make the argo [[ method handle spiciness.
• Improve read.adp.ad2cp() extensively, breaking some old behaviours.
• Add oceFileTrim(), adpAd2cpFileTrim() and adpRdiFileTrim().
• Remove renameData(), which had been flagged as defunct in multiple CRAN releases.
• Deprecate trimString().

oce 1.7.8

• Fix compiler warning of comparing signed and unsigned quantities.

oce 1.7.7

• Add gappyIndex().
• Fix encoding problems that will occur in the upcoming version of R.

oce 1.7.6

• Permit acoustic-Doppler files in excess of 4Gb.

oce 1.7.5

• Remove a stray file.

oce 1.7.4

• Change mapImage() to use interp instead of akima, as required by CRAN.
• Improve read.ctd.sbe() for interpreting Date in headers.
• Improve as.ctd() for Argo data.

oce 1.7.3

• Add read.ctd.ssda().
• Add read.argo.copernicus().
• Add sectionSort() parameter decreasing (thanks to M. Renner).
• Address unused-variable warnings in C++ code.
• Address byte-order mark problem in read.met() tests.
• Change most documentation hyperlinks to plain-text.
• Change read.met() file encoding; remove sample data.
• Speed up some tests.

oce 1.7.2

• Remove a link to https://pubs.usgs.gov/pp/1395/report.pdf, which was reported as unreachable during the attempted CRAN submission of version 1.7.1.

oce 1.7.1

• Fix error in comparing a class() result with a string, which was reported as an error during the attempted CRAN submission of version 1.7.0.

oce 1.7.0

• Fix CRAN-check warning about 2 uninitialized variables on the r-devel-linux-x86_64-debian-gcc test system. (We thank K. Hornik, for an email dated 2022-03-16 notifying us about the problem.)
• Fix CRAN-check error on the r-devel-linux-x86_6-debian-clang, r-devel-linux-x86_6-fedora-clang and r-devel-linux-x86_6-fedora-gcc test systems, relating to a byte-order-mark in a test file, which is evidently treated differently on different systems.
• Remove a kriging example because it causes CRAN-check problems on r-devel-linux-* machines (but, curiously, no other machines or systems).
• Change mapTissot() to trim shapes to earth limits.
• Alter this NEWS.md file so pkgdown::build_news() will notice the subsections.
• Add read.ctd.aml().
• Change read.met() to handle a new encoding argument.
• Fix drawPalette() to obey the at and labels arguments.
• Fix plot.ctd() to recognize which=13 for spice.

oce 1.6.1

• Remove a journal link that has become unavailable.
• Fix “length_1” error (thanks to B. Ripley for the heads-up).

oce 1.6.0

• Fix image-size declarations in 3 man pages (required by CRAN).
• Improve sub-class vignette.

oce 1.5.0

• Add [["?"]] facility to all objects.
• Add showNA argument to vectorShow().
• Add adpConvertRawToNumeric().
• Add adpFlagPastBoundary().
• Add ctdRepair().
• Add labelWithUnit().
• Add swSR().
• Add swSstar().
• Change as.ctd() to drop other parameter, deprecated 4y ago.
• Change read.odf() to handle more CODE and UNIT values.
• Change oce.plot.ts() by adding simplify argument.
• Change plot.section(), correcting temperature label to “T” and adding many more plot types.
• Change pwelch(), improving low-frequency results.
• Fix [[ to yield ITS90 temperature for all classes, not just ctd.
• Fix as.ctd() handling of temperature scale of first argument.
• Fix as.section() handling of list of argo objects as first argument.
• Fix colormap() handling of name argument.
• Mark byteToBinary() as defunct (slated for removal in 1.6.0).
• Mark renameData() as defunct (slated for removal in 1.6.0).

oce 1.4.0

• colormap() uses oceColorsViridis as default colour scheme.
• download.topo() uses new NOAA server.
• mapPlot() docs warn about problems with version 0.9-8 of sf package.
• plotProfile() handles units of added columns.
• read.argo() reads more metadata.

oce 1.3.0

• Remove a broken link (OK locally but failing in CRAN tests).
• Fix an error in the example for setFlags.ctd.
• Add addSpine() for defining section spines.
• Add angle2hms().
• Add argoJuldToTime().
• Add data(amsr) and improve subset.amsr().
• Add data(tidalCurrent) dataset of tidal currents from Foreman.
• Add oceAxis().
• Add preferAdjusted() for argo-class data.
• Add read.ctd.odv().
• Add snakeToCamel() to convert variable names in e.g. Argo NetCDF files.
• Add timeToArgoJuld().
• Change drawPalette() default colour palette to oce.colorsViridis().
• Change imagep() default colour palette to oce.colorsViridis().
• Change plot.amsr() default colour palette to oce.colorsViridis().
• Change plot.section() default colour palette to oce.colorsViridis().
• Change plotTS() to trim isopycnals to realistic salinities and temperatures.
• Change read.argo() and data(argo) to use camelCase in all metadata.
• Change user-oriented github website generator to pkgdown.
• Extend [[,argo-method to accept "ID" as an alternative to "id".
• Extend as.cm() to accept adp and adv objects.
• Extend oce.plot.ts(), adding argument logStyle.
• Extend read.adp.rdi() to handle 38kHz RDI adp files.
• Extend read.argo() and data(argo) by adding three more CYCLE variables.
• Extend read.ctd.sbe() to handle 4 new (Beckman) oxygen variables.
• Extend read.ctd.sbe() to handle .btl files.
• Fix plot.coastline error in box drawing.
• Fix plotTS error in auto-scaling if S and T have mixed NA status.
• Fix subset.argo() error in flags, location, and *QC in metadata.
• Remove dependence on rgdal package, using sf for map projections.

oce 1.2.0

• Address argument doc/code warning that blocked CRAN acceptance.
• Accommodate new ocedata (needed to meet new CRAN dependency rule).
• Add oceRenameData() and oceRenamemetadata().
• Deprecate renameData().
• Improve axis control for mapPlot() and plot.coastline.
• Remove addColumn(), ctdAddColumn(), ctdUpdateHeader(), findInOrdered(), mapMeridians(), mapZones(), and oce.as.POSIXlt(), all of which have been marked as “Deprecated” for the past two CRAN releases.
• Extend read.met() to read a new Environment Canada data format.
• Handle some upcoming rgdal/R-devel changes.
• Extend sectionSmooth() to handle grids beyond data range.
• Extend read.adp.rdi() to trim time if it longer than other data.
• Improve geodDist() to handle second location correctly when alongPath=FALSE.
• Improve vignettes.
• Fix itemized-list documentation problem pointed out by Kurt Hornik.

oce 1.1-1

CRAN release: 2019-06-17

• Address “link-time-optimization” issues for CRAN submission.

oce 1.1-0

• fix argument error in a .C() call
• Extend read.odf() to store ODF header as a list in metadata.
• Add presentTime().
• Add vignette on subclassing oce.
• Extend sectionSmooth() to handle output grid better, and offer 2 new methods.
• Extend read.ctd.sbe() to handle more column names.
• Extend mapping code to support i386/windows.
• Extend imagep() to handle combined flipy and ylim arguments better.

oce 1.0-1

CRAN release: 2018-10-04

• Renamed 0.9-24, released with OAR book publication.

oce 0.9-24

• Extend read.odf() to store ODF header in metadata.
• Remove makeSection(), after its deprecate/defunct period ended.
• Make defunct: addColumn(), byteToBinary(), ctdAddColumn(), ctdUpdateHeader(), findInOrdered(), mapZones(), mapMeridians(), oce.as.POSIXlt(), and oce.magic()
• Add as.tidem().
• Extend read.odf() to handle multiple NULL_VALUEs.
• Improve handleFlags().
• Add rotateAboutZ().
• Add concatenate().
• Add read.woa().
• Extend colormap() to include colfunction in return value.

oce 0.9-23

CRAN release: 2018-01-28

• tidem() permits inferred constituents
• tidem() follows T_TIDE phase convention
• adorn argument removed from some plot functions (after being defunct 1+ year)
• deprecate findInOrdered()

oce 0.9-22

CRAN release: 2017-08-28

• plot.section() can use external bathymetry
• lowpass() added
• ctdTrim() can isolate upcasts
• deprecate byteToBinary()
• address a CRAN NOTE about UTF-8 strings in data

oce 0.9-21

CRAN release: 2017-03-30

• adpEnsembleAverage() added
• mapCoordinateSystem() added
• woce-exchange missing-value inference
• woce-exchange autodetection, plus read all data types
• download.amsr() updated for data-server change
• download.met() added
• as.ctd() can specify columns within argo data
• read.adp.rdi() handles more file types and larger RDI files
• read.odf() handles contradictory metadata better
• oce.as.POSIXlt() deprecated
• oceSetData() handles units better
• address R_registerRoutines build-time warning
• fix memory-usage error in coastlineCut()

oce 0.9-20

CRAN release: 2016-11-19

• remove observatory object type (changed format, seldom-used type)
• remove pangaea object type (undocumented format, seldom-used type)
• improvements for BioArgo data
• Spanish translation by Pablo Valdés
• make read.gps() handle more files
• deprecate ctdAddColumn() and ctdUpdateHeader()
• download.topo() added and read.topo() updated to handle new formats
• download.amsr() added
• composite() added
• addColumn() marked as deprecated
• read.cm.s4() reads all data in file
• as.cm() added
• read.odf() handles Aanderaa current meter data
• mapPlot() and mapAxis() get cex.axis parameter
• subset(amsr) added; various other amsr improvements

oce 0.9-19

CRAN release: 2016-07-08

• deprecate adorn argument in plot functions
• make read.ctd() obey missingValue (renamed)
• improve map projections
• add renameData()
• improve support for SBE files
• remove is.beam(), is.xyz(), is.enu() and coordinate(), since x[["coordinate"]] now permits these simply
• replace several function-style accessors with [[ style
• fix test-suite error relating to an rgdal change
• add handleFlags() as generic plus specifics for ctd and argo classes
• use S4 documentation, e.g. ?"plot.ctd" instead of ?plot.ctd
• add subset(argo, "adjusted")
• make read.argo() read all documented data and metadata fields
• add trimString()

oce 0.9-18

CRAN release: 2016-02-12

• improve plot.coastline() and mapPlot()
• add support for G1SST satellite
• all objects now have metadata items for units and flags
• ctdTrim() method renamed: old A and B are new A; old C is new B
• support more channels and features of rsk files
• as.adp() added
• convert argo objects to sections
• makeSection() deprecated; use as.section() instead
• read.adp.rdi() handles Teledyne/RDI version 23.19 bottom-track data
• geodXyInverse() added; geod functions now spell out longitude etc
• read.odf() speeded up by a factor of about 30
• add colour palettes from the cmocean Python package by Kristen Thyng
• add as.oce()
• rename drifter class as argo to recognize what it actually handles
• add oceColorsViridis()
• interpBarnes() has new argument pregrid
• binMean2D() has new argument flatten
• data(topoWorld) now has longitude from -179.5 to 180
• ODF2oce() added
• read.odf() handles more data types
• read.adp.rdi() reads more VmDas (navigational) data
• ITS-90 is now the default temperature unit
• ctd objects can have vector longitude and latitude
• logger class renamed to rsk
• bremen class added
• coastlineCut() added
• rgdal package used instead of local PROJ.4 source code
• mapproj-style map projections eliminated

oce 0.9-17

CRAN release: 2015-05-22

• remove an exit() call in a C function

oce 0.9-16

CRAN release: 2015-05-21

• cite PROJ.4 contributors in DESCRIPTION
• address package-build warnings; improve DESCRIPTION (thanks, BR)

oce 0.9-15

• plot.echosounder() gets new argument drawPalette
• data(landsat) taken from ocedata (and shrunk)
• data(nao) and data(soi) moved to ocedata
• mapTissot() added
• read.logger() with ctd-type data infers salinity if necessary
• ctdTrim() can have “method” as a function
• as.topo() can convert “bathy” objects from the marmap package
• "+.section" renamed sectionAddStation()
• oceApprox() renamed oce.approx(), with an alias for compatibility
• oce.grid() added
• "tdr" class renamed "logger"
• swCSTp() added
• swConductivity() now swThermalConductivity(); using Caldwell (1974).
• many sw() functions handle eos=“gsw”
• library(gsw) replaces teos()
• curl() added
• handle new NOAA ascii topography dataset type
• mapGrid() added
• data(soi) moved to ocedata package
• lonlat2map() added
• map2lonlat() made more accurate
• permit proj4 style map projections
• landsat-7 (and possibly 4 and 5) support
• landsat decimation/plotting improvements
• drifterGrid() added
• mapDirectionField() added
• mapArrows() added
• read.index() added
• utm2lonlat() and lonlat2utm() added
• data(met) changed to time of Hurricane Juan

oce 0.9-14

CRAN release: 2014-05-19

• fix compile-time warning
• colormap() added, and functionality added to imagep() and drawPalette()
• imagep() and drawPalette() new arg. axisPalette (suggested C. Richards)
• drawPalette() has new args: plot, pos, levels, and cex.axis
• ctdDecimate() permits user-supplied method function
• data(nao) added; data(soi) updated, and names improved in latter
• landsat support added
• plotProfile() and plotTS() get new argument pt.bg
• plot.section() grids the data if needed
• rename sealevelHalifax dataset as sealevel
• translate some axis names (Spanish, French, German and Mandarin)
• plotProfile() now has ytype="depth"
• mapImage() and friends now demand a map exists first
• runlm() added
• mapScalebar() added
• subset.topo() added
• read.topo() now handles GEBCO NetCDF files
• decimate() now handles topo objects
• reverse oce.colorsGebco colours for water
• drawIsopycnals() and plotTS(): improve isopycnal labels
• ctdDecimate() handles new method unesco
• coastline improvements (now 3 resolutions)
• webtide() improvements
• read.observatory() added
• read.ctd.itp() added
• mapImage() speeded up (60X in 1deg SST example)
• binApply1D() and binApply2D() added
• binCount1D(), binMean1D(), binCount2D(), and binMean2D() added
• numberAsHMS() added
• gps data type added (provisionally)
• various functions: reorder arguments putting longitude before latitude
• magneticField() replaces magneticDeclination()
• ungrid() added
• mapPlot(): improve zone and meridian aesthetics
• detrend() returns list with detrend vector and coefficients
• decodeTime() improvements
• interpBarnes() has new argument trim
• standardDepths() added
• mapLongitudeLatitudeXY() added
• read.ctd.woce() now accepts a format used once by Arctic scientists
• swRrho() added
• plotProfile() now accepts type=“o”
• read.adv.nortek(): read salinity
• ctdDecimate(): fix bug for NULL columns (issue #327)
• plot.section() now chooses best coastline file
• swPressure() added
• ctdFindProfiles() added
• as.ctd(): new arguments filename etc
• remove oceBisect(), which merely reproduces uniroot()
• move large/specialized datasets to library(ocedata)

oce 0.9-13

CRAN release: 2014-01-29

• prepare for an upcoming release of R-devel

oce 0.9-12

CRAN release: 2013-07-05

• move vignette source directory

oce 0.9-11

• numberAsPOSIXct() now handles types “sas” and “spss”
• data(turbulence) added
• plot.echosounder(): use white for below-threshold values
• plot.echosounder(): add arg beam to e.g. display Sv
• read.echosounder(): handle dual-beam and split-beam data
• read.echosounder(): decode bottom-pick
• swSoundAbsorption()
• read.adp() doc improved regarding variable orientation of RDI files

oce 0.9-10

CRAN release: 2013-05-19

• improve line breaks in some help pages (thanks, B. Ripley)

oce 0.9-9

• mapPlot() uses ... graphical parameters (e.g. cex) in labelling axes
• fix recent bug in reading CNV files (issue 318)
• plotTS(...,mar=NULL) now avoids setting par(mar)

oce 0.9-8

CRAN release: 2013-04-25

• fix memory error in teos handler (thanks, B. Ripley)

oce 0.9-7

• make ctdTrim() work in R 3.0
• support for adp vmdas navigation data (coded by Clark Richards)
• approx3d(): added
• drawPalette(): new arg fullpage
• plot.lobo(): add arg which
• read.coastline.openstreetmap() added
• data(levitus) added
• plot.coastline() gets new arguments projection etc to use mapPlot()
• mapContour() permits first argument to be a topo object
• mapPlot() gets new arguments axes, bg, fill, and drawBox

oce 0.9-6

CRAN release: 2012-12-16

• address compilation error on Windows-64 platform
• make some long-running operations more interruptible
• oceApprox(): permit equal x values (issue #279)

oce 0.9-5

CRAN release: 2012-12-15

• halve package check time

oce 0.9-4

• as.section() added
• add data(endeavour)
• add map projections, with provisional functions mapPlot() etc
• plot.ctd(): add argument add
• add crude mapping support
• interpBarnes(): add args xgl and ygl
• read.section(): add directory argument
• sectionSmooth(): add barnes method
• oce.plot.ts() and oce.axis.POSIXct(): add tformat argument
• read.aquadopp() and cousins added (issues #253 and #258)
• read.ctd() guesses waterDepth if not supplied (issue #253)
• plotTS(): extend isopycnal range (issue #252)
• plot.section() contouring improved
• data(oceans) added
• data(papa) added
• fillGap() works on matrices as well as vectors
• read.lobo() is more flexible on column names
• imagep(..., axes=FALSE): no longer plots axis box (issue #249)
• oce.plot.ts(): alter time auto-ranging method
• oceBisect(): increase generality of function whose root is sought
• plotTS(): clean axes after isopycnals drawn
• teos10: update test values (with help from PB)
• read.adp.nortek(): handle missing to argument as documented
• beamUnattenuateAdp() renamed beamUnspreadAdp()
• plotTS() and plotProfile(): permit type=n
• plotProfile() with ytype="z": fix bug in y label
• improve error message if TEOS-10 is missing

oce 0.9-3

CRAN release: 2012-09-04

• example(riley): remove error in R-devel
• plot.ctd() with which=7 improvement
• swSCTp(): accept conductivity in mS/cm and S/m
• as.ctd(): accept TEOS-10 values SA and CT
• make TEOS routines more resistant to unphysical values

oce 0.9-2

CRAN release: 2012-07-29

• remove unwanted files during build process

oce 0.9-1

• pwelch(): fix bug in frequency
• tidem(): add argument regress
• rename oce.plot.sticks() as plotSticks(); delete stickplot()
• use S4 style for all plot() methods
• data(giss) added
• data(topo2) added
• plotPolar() added
• oce.magic() new name for magic(); renamed oceMagic() in 0.9-15
• errorBars() added
• numberAsPOSIXct() add a leap second for July 2012

oce 0.8-10

CRAN release: 2012-06-12

• plot.topo(): automatic cut-point shift
• add support for Nortek aquadopp-profiler instruments
• oce.contour() added
• lisst class added
• plotTaylor() added
• oce.as.raw() added
• binmap() added

oce 0.8-9

CRAN release: 2012-05-25

• make the newly-added TEOS-10 functions compile on Windows

oce 0.8-8

CRAN release: 2012-05-23

• data(cm) added
• plot.coastline(): improve argument geographical
• add prettyPosition()
• add grad()
• add (preliminary) support for TEOS-10, installed separately
• add integrateTrapezoid()
• plotTS(): add argument teos
• add teos() as an interface to the TEOS-10 library
• add moonAngle() plus other astronomy functions, e.g. julianDay()

oce 0.8-7

CRAN release: 2012-04-05

• plotInset(): remove bg and fg arguments
• plotTS(): add bg argument
• rename dt object and functions to tdr
• plotTS(): add argument inset
• read.adp.rdi(): fix a bug in bottom-tracking; add soundSpeed vector
• data(echosounder) created
• formatPosition() created
• plot(echosounder): new arguments atTop and labelsTop
• adp objects now also hold percent good for RDI instruments
• plot.drifter(): improve multi-panel plots
• imagep(): add argument missingColor
• imagep() and drawPalette(): add arguments labels and at

oce 0.8-6

CRAN release: 2012-03-04

• imagep(): permit POSIXt type for zlim.

oce 0.8-5

• reconstruct data(ctd) so plot will focus maps better
• plotInset() added
• grid() works for oce-based time axes
• imagep(..., filledContours): obey ylab argument
• subset(): permit subsetting ADP by pressure
• oce.plot.ts(): obey arguments xaxt and yaxt
• improve support for shapefile coastlines

oce 0.8-4

CRAN release: 2011-12-19

• replace center argument for plotting topography and coastline with clatitude and clongitude
• add echosounder class
• fullFilename(): handle URLs properly
• ADV objects: add access to slow variables (e.g. headingSlow)

oce 0.8-3

CRAN release: 2011-11-18

• add met class
• subset.oce() handles section objects
• draw.section(): permit xtype="latitude" or "longitude"
• imagep() has drawPalette="space" option

oce 0.8-2

CRAN release: 2011-11-03

• fix bug in read.coastline(), reversing lon and lat (issue #162)
• fix bug in S4 adp validity checker
• geodDist(): add argument alongPath
• remove compilation warning about doc for summary.ctd()

oce 0.8-1

CRAN release: 2011-10-26

• switch to S4 classes, and add new accessors and show functions.
• add support for RBR rsk files
• plot.section() now uses col if supplied

oce 0.7-1

CRAN release: 2011-10-07

• improve oce.colorsJet()
• improve plotProfile() vertical range with missing data
• add data(drag)
• plotProfile() and plot.ctd(): add xtype="spice"
• add data(geosecs235)
• plotProfile() and plot.ctd(): add argument keepNA
• as.ctd(): add arguments other and missingValue
• read.lobo(): tolerate more formats, including missing velocities
• add data(schmitt)
• add accessor spice()
• handle O2 and nutrients in CTD data and sections
• swSCTp(): use surface pressure as a default
• plotTS(): add arguments inSitu and `referencePressure.
• plotTS(): handle section objects
• fix bugs reported in issues 150, 151, 153, 155, 156
• imagep(): change default drawContours to FALSE

oce 0.6-1

CRAN release: 2011-09-01

• add adv dataset
• generalize swN2() by adding new arg derivs
• oce.plot.ts() gets new arg axes
• add accessor distance()
• rename to plotTS() and plotScan() to avoid S3 check warnings
• switch makeFilter() argument asKernel default to TRUE

oce 0.5-1

CRAN release: 2011-07-26

• add support for ARGO drifters
• latitude() and longitude(): new argument to repeat byDepth
• addCtdColumn(): replace if column already exists
• add CTD accessors for lat, lon, pressure, salinity, temperature

oce 0.4-1

CRAN release: 2011-07-23

• plot.sealevel(): only show 3 panels, for clarity
• plot.ctd(): add argument type
• imagep(): handle x, y, and z as image() does
• oce.plot.ts(): inferred ylim matches data range within provided xlim
• read.adv.nortek(): handle extra analog data
• add CTD accessors longitude(), latitude(), time(), elevation(), etc

oce 0.3-1

CRAN release: 2011-06-22

• add read.oce.odf()
• add findInOrdered()
• generalize tidem() argument list
• read.adv.nortek(): handle burst-mode data
• add datasets wilson, redfieldNP, redfieldNC, redfieldPlankton, and riley
• change data(ctd) to be derived from data(ctdRaw)
• change to monitor=FALSE for all reading functions
• add accessor functions heading(), latitude(), longitude(), pitch(), pressure(), processingLog(), roll(), salinity(), temperature(), time(), and velocity()
• rename history as processingLog.
• flatten data objects to be 1 level thick (for future matlab exports)
• add threenum() added, and use it in all summaries (for speed)

oce 0.2-3

• head.adp() added
• tail.adp() added
• extract() added

oce 0.2-2

CRAN release: 2011-05-09

• velocityStatistics() added
• new names: oceApprox() integerToAscii() rangeLimit() ctdRaw
• topoInterpolate() added
• numberAsPOSIXct(): add type argos
• rename beamAttenuateAdp() as beamUnattenuateAdp()

oce 0.2-1

CRAN release: 2011-04-28

• camel-case function and argument names (and the NEWS file)

oce 0.1-83

• add binAverage()
• fillGap(): add rule argument, analogous to same for approx()
• add rescale()
• read.pt(): fix timing error; use as.pt() to create return value
• add as.pt()
• read.adp.rdi() uses checksums
• number.as.POSIXct(type="gps"): account for leap seconds

oce 0.1-82

CRAN release: 2011-03-21

• remove warning that occurs for R 2.13.0 (alpha)
• number.as.POSIXct(): accept GPS times
• rename e.g. adv.2enu() as to.enu.adv()
• speed up conversion of ADP and ADV to enu by more than a factor of 10
• change RDI coordinate handling
• rename match.bytes() as matchBytes()
• add drawPalette()
• remove matlab2POSIXt(), now a sub-case of number.as.POSIXct()
• number.as.POSIXct(): added
• oceBiset(): added
• despike(): add argument action
• detrend(): added
• read.adp.sontek(): handle PCADP type
• read.adp.sontek.serial(): added
• read.section(): handle WOCE quality flags for salinity
• retime(): added
• read.adv.sontek.serial(): correct error in class of a and c
• despike(): use string value for argument method
• logger.toc(): fix bug in discovering files ranging over days
• as.ctd(): make temperature and salinity into vectors, if not already
• plot.TS(): add argument use.smoothScatter
• oce.debug(): flush the console after printing a message
• sw.theta(): rename the method possibilities, to lower case
• in some sw functions, rename pref as reference.pressure
• read.ctd(): fix bug in getting start.time for some time formats
• pwelch() added
• plot.sealevel(): make y axis obey range in data subset, if xlim is given
• adp.2enu() added
• coastline.world: improve resolution by a factor of 4 or so
• read.ctd.woce(): infer water depth as max(pressure) if not in header
• section.smooth(): handle misordered stations; handle missing values better
• plot.section(): allow strings for which; improve contouring
• plot.ctd() and plot.profile(): add use.smoothScatter argument
• coriolis(): improve omega value

oce 0.1-81

CRAN release: 2010-10-18

• add despike()
• add range.limit()
• add unabbreviate.time()
• add support for bottom-tracking RDI ADCPs
• add support for interocean s4 current meters
• add unwrap.angle()
• read.adv.nortek(): detect the velocity range
• add processing.log.add(), an alternative to processing.log.append()
• plot.ctd(): add more plot types; which=9 for salinity, not density
• as.ctd(): improve flexibility
• predict.tidem(): add newdata argument
• adv.2enu() added
• adp.xyz2enu(): make it correct for heading.bias
• make.filter(): can now produce tskernel type
• improve (but temporarily limit) fill.gap
• plot.adp(): add use.layout argument
• window.oce() added
• make objects remember full filename, not just local filename (issue #8)
• plot.tidem(): remove argument plot.type, using which instead
• read.pt(): add arguments from, by, and to
• fix issue 57; read.adp.rdi() read the heading incorrectly
• add “rr” method to ctdDecimate()
• oceApprox() added
• topoWorld dataset added
• plot.ctd(): by default, make coastlines extend to box boundaries
• reformulate sun.angle in R
• fix google-code issue 56; plot.topo() should accept land.z=NULL]
• fix google-code issue 55; plot.topo() could go past poles]
• fix google-code issue 54; plot.topo() was resetting par() on exit]
• fix google-code issue 53; interp.barnes() gives poor error message for mismatched x and y
• fix google-code issue 52; plot.section() draws incorrect bottom shape

oce 0.1-80

CRAN release: 2009-11-05

• add sun.angle; not tested yet; needs R reformulation
• fix google-code issue 51; summary.section() does not report water depth
• fix google-code issue 50; non-bug relating to sun elevation
• fix google-code issue 49; demo(TS) broken

oce 0.1-79

CRAN release: 2009-10-26

• fix google-code issue 48; oce.plot.sticks() ignored page ratio
• fix google-code issue 47; cannot read new MEDS sea level format

oce 0.1-78

CRAN release: 2009-10-02

• add data(RRprofile)
• to plot.TS(), add arguments lwd.rho and lty.rho.

oce 0.1-77

CRAN release: 2009-09-13

• refactor adp code with respect to transformation matrices
• add matrix.smooth()
• improve labels for oce.axis.POSIXct()
• set default for debug argument to getOption("oceDebug") in all functions
• plot.profile(): add argument ytype; change type to xtype
• add swZ()
• add oce.smooth()
• add read.adv(), etc., supporting Nortek and Sontek devices
• add read.adp(), etc., supporting Nortek, RDI and Sontek devices
• add oce.plot.ts()
• add imagep()
• add bcd2integer()
• add matlab2POSIXt()
• to most plot functions, add mgp and mar arguments
• plot.pt(): add plim and Tlim arguments.
• gravity(): give default for latitude argument.
• plot.sealevel(): remove argument focus.time and add argument which.
• rename tdr functions as pt, to reflect common phrasing.
• add geod.xy().
• add argument mgp to all plotting functions.
• use abbreviations for axis names if space is tight.
• add argument adorn to all plot() functions.
• add oce.colorsTwo(), oce.colorsJet(), and oce.colorsPalette().
• add byte2binary()
• add “lty.grid” to all CTD plotting functions
• add “+.section”, a more convenient way to build sections from stations
• rework summary() for all existing objects
• as.sealevel(): rename sampling.interval as deltat

oce 0.1-76

CRAN release: 2009-03-02

• sw.N2(): make it tolerate NAs; adjust df to make result smoother
• add makeFilter()
• add decimate(), which may eventually replace ctd.decimate()
• read.tdr(): handle 5-column data files; add tz argument
• plot.profile(): add types sigma+dpdt and sigma+time
• ctdTrim(): add pmin parameter
• plot.ctd(): add Slim, Tlim, plim, lonlim, latlim args; add maps
• add coastline.sle dataset
• plot.TS(): fix isopycnal labels for fresh water; add args Slim, Tlim
• read.ctd(): make it understand another SBE format
• add parseLatlon()
• oce.edit(): add argument action
• add oce.write.table()
• add fillGap()

oce 0.1-75

CRAN release: 2009-01-06

• add addColumn()
• add undriftTime()
• add tdrPatm()
• make readTdr() gather serial no. info; show this on plot.pt()
• switch to recommended version-number format
• remove section.subset(), replaced by subset()
• improve log items in functions that read and assemble oce objects
• add subset.oce()
• add header()
• add argument which to read.rbrdtr()
• make read.rbrdtr() understand headers better
• add arguments xtype and ytype to plot.section()
• improve accuracy of bottom drawn by plot.section()
• add section.smooth()
• fix bug making section.smooth() fail if <4 good data at a level
• fix bug making summary.ctd() fail for results of section.smooth()
• fix bug making sw.dynamic.height() choke on empty stations
• fix bug making plot.section() die if x is unordered
• rename rbrpt functions to tdr functions, improving generality

oce 0.1.74

CRAN release: 2008-11-18

• add argument “src” to as.ctd()
• plot.section() RHS axis needs tics
• trim axis whitespace in plot.profile() and plot.TS()
• make read.oce() understand WOCE section type
• speed up swSpice()
• add read.pt(), summary.pt(), plot.pt(), and ptTrim()
• make plot.TS() isopycnal label size be same on top and right sides
• add lwd argument to plot.profile()
• give plot.section() ability to control contour levels and labels
• give plot.section() tics for station-location

oce 0.1.73

CRAN release: 2008-09-14

• plot.topo() narrows autoscale to xlim-ylim region, if provided
• add plot.ctd() arg textpanel, and put the profiles in the same row
• fix bug in plot.profile() to let it take Slim,…, as args
• fix bug in plot.profile() font size
• fix bug in plot.profile(type="S_T") positioning
• fix bug in section plot (bottom was missing)
• fix bug in size of salinity axis label for plot.ctd()
• use pch=21 for TS plots (so data density is more visible)

oce 0.1.72

CRAN release: 2008-06-09

• add interp.barnes()

oce 0.1.71

CRAN release: 2008-04-14

• fix bug in makeSection() (ignored the list, if a list provided)
• add oce.edit(), later renamed oceEdit()
• add topoMaritimes dataset
• add read.topo(), plot.topo(), and summary.topo()
• add gebcoColors() … renamed oce.colorsGebco() in version 0.1.77
• make plot.section() check that pressures coincide

oce 0.1.70

CRAN release: 2008-04-01

• plot.TS(): make isopycnal list work better for nearly-fresh water
• trimCtd(): improve equilibration-phase deletion
• read.ctd(): handle cases without cruise information or scan column
• permit setting xlab and ylab in plot.TS()
• make processing log timestamps be in GMT
• add as.windrose() and plot.windrose()
• add sealevel.tuk sea-level dataset
• add tidem(), predict.tide(), summary.tide(), plot.tide(), data(tidedata)
• establish a uniform form for objects created by “read” and “as”
• let swRho() and similar functions take a ctd object as a single argument
• add swDynamicHeight()
• make section.grid() and ctd.decimate() extrapolate to surface
• add summary.oce()
• make all objects inherit from a new class “oce”
• fix google-code issue 12: read.sealevel() had a hard-wired filename

oce 0.1.69

CRAN release: 2007-12-14

• modify documentation slightly
• start a migration to more uniform object structures
• rename as.CTD() to as.ctd(), to make it consistent with similar functions
• add read.section()
• add sectionGrid(), which only grids in p at the moment
• add a03 dataset (renamed section in 0.9-13)
• fix SF bug 1833719: warnings from read.ctd()
• fix google-code issue 8: read.coastline() not producing data
• improve ability of trimCtd() to ignore spurious initial data
• add “connectPoints” option to plot.TS()
• add “station” item to “ctd” object
• change as.CTD() to produce sigma.theta instead of sigma

oce 0.1.68

• add coastline.world; increase resolution of coastline.maritimes
• plot.TS() no longer rotates the RH margin isopycnal labels

oce 0.1.67

CRAN release: 2007-10-21

• allow swRho() and similar take matrices as arguments for S, T, etc

oce 0.1.66

• fix bug in plot.TS() that prevented it from showing some isopycnals

oce 0.1.65

• switch to UNESCO formulation for sw potential temperature by default
• prevent warnings with C90 compiler on some machines

oce 0.1.64

CRAN release: 2007-07-17

• add read.oce(), a generic function for reading several oceanographic files
• make read.ctd() understand WOCE-exchange files
• make read.sealevel() understand comma-separated data from MEDS
• make plot.sealevel() skip spectral graphs if timeseries has NA values
• improve aesthetics of plot.ctd()
• extend plot.sealevel() by adding focus.time argument
• add ctdDecimate()
• add oce.as.POSIXlt()
• add latlonFormat(), latFormat(), and lonFormat()
• add as.coastline()
• add make.section()
• add summary.section()
• add plot.section()
• add data(section)

oce 0.1.63

CRAN release: 2007-06-02

• add swSoundSpeed()

oce 0.1.62

CRAN release: 2007-05-29

• add historyAppend() (later named processingLogAppend()) and related code
• improve ctdTrim()

oce 0.1.61

• add rudimentary read/summary/plot functions for lobo datasets

oce 0.1.60

• add vignette; address some build-stage warning messages

oce 0.1.59

CRAN release: 2007-05-20

• set up data files to permit latin1 encoding of some content

oce 0.1.58

• rename all seawater-related functions to e.g. swTheta(), to allow for atmospheric analogs

oce 0.1.57

• make as.CTD() accept length(p)=1 e.g. for surface plots

oce 0.1.56

• make read.coastline() handle S files

oce 0.1.55

• keep swTheta() from complaining if length(p) equals 1

oce 0.1.54

• add swAlpha() and swBeta()

oce 0.1.53

• add swAlphaOverBeta()

oce 0.1.52

• document the use of df in swN2(), plot.ctd(), etc.

oce 0.1.51

• permit swRho() (and similar) to take NAs in args (bug B32)

oce 0.1.50

• permit swRho() and descendants to take scalar pressure.

oce 0.1.49

• add as.CTD()

oce 0.1.48

• add "UNESCO1983" formulation to swTheta() as an alternative

oce 0.1.47

• speed up swTheta() by moving vector work from R to C

oce 0.1.46

• make geodDist() accept a vector for location 1 and a scalar for location 2

oce 0.1.45

• make read.coastline() understand matlab and Splus formats

oce 0.1.44

• make plot.coastline() scale lat and lon correctly

oce 0.1.43

• add read.coastline(), summary.coastline(), and plot.coastline()

oce 0.1.42

• add as.sealevel()

oce 0.1.41

• add read.sealevel(), summary.sealevel(), and plot.sealevel()

oce 0.1.40

• add name option to plot.ctd.scan()

oce 0.1.39

• add lapse.rate()

oce 0.1.38

• fix B27 (header not updated for columns added during read.ctd)

oce 0.1.37

• rename as ctdTrim()
• rename to ctdWrite()

oce 0.1.36

• add write.ctd()
• add ctdAddColumn()
• add ctdUpdateHeader()

oce 0.1.35

• add plot.ctd.scan()

oce 0.1.34

• make read.ctd() calculate S if missing but C, T, and p are given
• add swSCTp()

oce 0.1.33

• add swConductivity()

oce 0.1.32

• rename oceRho() to swRho()

oce 0.1.31

• use namespace

oce 0.1.30

• add oce.viscosity()

oce 0.1.29

• fix B23 (not done yet)
• fix B22 (not done within oce; done at system level)

oce 0.1.28

• add pressure method to trimCtd()

oce 0.1.27

• vectorize swRho() since it was too slow on large datasets

oce 0.1.26

• make demo(oce.ctd) print data

oce 0.1.25

• fix some documentation errors that the 2.0.0 CHECK noticed

oce 0.1.24

• profiles have correct y-axis
• OSX port, but must first do e.g. export PKG_LIBS="-L/sw/lib"

oce 0.1.23

• OSX port (you must first do export PKG_LIBS="-L/sw/lib")

oce 0.1.22

• add trim.ctd()

oce 0.1.21

• permit lat/lon with the “N”-type indicator at start

oce 0.1.20

• fix bug B16 (label the isopycnals on TS diagram)

oce 0.1.19

• make read.ctd() handle more file types

oce 0.1.18

• add oceCoriolis(), oceDepth(), oceGravity(), oceTFreeze()

oce 0.1.17

• add oceSpecificHeat() and oce.N2(); fix bug B18

oce 0.1.16

• get data(ctd) working

oce 0.1.15

• add oceSTRho()

oce 0.1.14

• fix bug B15 (maybe)

oce 0.1.13

• add oceTSRho

oce 0.1.12

• fix bugs B10, B11, and B13

oce 0.1.11

• fix bugs B6, B7, and B12

oce 0.1.10

• add geodDist().
• add plot.ctd(), which is rudimentary for now.
• fix bug B8.

oce 0.1.9

• add spice() function

oce 0.1.8

• permit all eos functions to handle missing values
• fix bug B4

oce 0.1.7

• add summary.ctd() method.
• make read.ctd() return an object of type ctd.
• get tests/ working.

oce 0.1.6

• create tests/oce.test1.R

oce 0.1.5

• add oceSigma(), oceSigmaT(), and oceSigmaTheta()

oce 0.1.4

• permit various EOS functions to handle lists
• fix bug B3

oce 0.1.3

• add ocerho()

oce 0.1.2

• fix file-path bug
• fix bug B2

oce 0.1.1

• add theta()
• fix bug B1

oce 0.1.0

• add read.ctd()