NEWS.md
swSpiciness0(), swSpiciness1(), and swSpiciness2() (issue #2188).binMean2D() to use previous (6-month-old) method (issue #2199).ctdDecimate() to add the na.rm argument (issue #2192).mapDirectionField() to allow wind barbs (issue 2191).mapImage() to add the gridCoarseness parameter (issue #2199).mapImage() to accept a gridder function (issue #2199).plot.argo() to handle which="sigma0 profile" (issue #2184).plot.sealevel() to add the grid parameter (issue #2204).plot.sealevel() to improve labelling (issue #2203).plot.section() to handle bottom traces better (issue #2194).plot.section() to show data as points properly (issue #2195).read.adp.rdi() to handle large (> 2.147 GB) files (issue #2196).resizableLabel() to document partial-match behaviour (issue #2197).resizableLabel() to handle item=“N”` (issue #2197).summary() to skip time in the threenum table (issue #2198).sunAngle() to handle vector arguments better (issue #2178).package?oce documentation (had been missing with a Roxygen2 change).read.ctd.saiv() to read data from SAIV instruments (issue #2141).trimString(), after it had been deprecated for a long time (issue #2123).sp package (issue #2154).amsr dataset and functions to handle new format (issues #2124 to #2133 plus issue #2147).as.ctd() to handle multi-profile Argo better (issue #2173).as.tidem() to handle NOAA constituent names and frequencies (issues #2143, #2144 and #2146).sprintf() calls so all formats match arguments (issue #2172).computableWaterProperties to handle a vector of variable names.plot.adp() to obey xlab if x axis represents time (issue #2162).plot.cm() to obey xlim, ylim, xaxs and yaxs (issue #2121).plotTS() and plotProfile() to accept type="b".plot.windrose() for type="fivenum" (issue #2164).as.ctd() to handle startTime, PRES, PSAL and TEMP better.binCount1D() + 6 related functions by adding include.lowest parameter (issue 2113).imagep() to ensure z (if provided) is a matrix (issue 2091).plot.section() to skip the kriging example (issue 2080).plot.section() to show palette triangles if necessary (issue 2083).plot.section() to show data and bottom correctly (issue 2092).plotTS() to obey the rho1000 parameter again (issue 2085).read.argo() to translate more variable names.read.netcdf() to read more items.read.rsk() to obey the tz parameter (issue 2108).summary.adp() to handle the new format for AD2CP data (issue 2087).advSontekAdrFileTrim() (issue 1994).ctdFindProfilesRBR() (issue 2027).applyMagneticDeclination() to also handle adp and adv (issue 2038).download.topo() to handle new NOAA database (issue 2015).inst/extdata by compressing some files.mapPlot() to remove an infrequent low-level error (issue 2036).mapPlot() to require projection to be a string (issue 2076).numberAsPOSIXct(t, type="gps") to handle week rollover (issue 2077).plot.echosounder() to use oceColorsViridis() by default (issue 2060).plotProfile() to create xlab on vector input (issue 2047).plotTS() to compute isopycnals more accurately (issue 2046).plotTS() to handle lobo objects directly.plot.tidem() to obey ... parameter (issue 2035).read.adp.ad2cp(), and structure of AD2CP objects (issue 2005).read.rsk() to read geographic information (issue 2024).sectionSmooth() to handle method="kriging" againtidem() (and summary method) to handle 6-hourly data (issue 2034).rgeos and raster packages (issue 2028).plotAD2CP(), now superseded by generic plot() method (issue 2005).swThermalConductivity() doc.[[ method handle spiciness.read.adp.ad2cp() extensively, breaking some old behaviours.oceFileTrim(), adpAd2cpFileTrim() and adpRdiFileTrim().renameData(), which had been flagged as defunct in multiple CRAN releases.trimString().gappyIndex().mapImage() to use interp instead of akima, as required by CRAN.read.ctd.sbe() for interpreting Date in headers.as.ctd() for Argo data.read.ctd.ssda().read.argo.copernicus().sectionSort() parameter decreasing (thanks to M. Renner).read.met() tests.read.met() file encoding; remove sample data.https://pubs.usgs.gov/pp/1395/report.pdf, which was reported as unreachable during the attempted CRAN submission of version 1.7.1.class() result with a string, which was reported as an error during the attempted CRAN submission of version 1.7.0.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.)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.r-devel-linux-* machines (but, curiously, no other machines or systems).mapTissot() to trim shapes to earth limits.NEWS.md file so pkgdown::build_news() will notice the subsections.read.ctd.aml().read.met() to handle a new encoding argument.drawPalette() to obey the at and labels arguments.plot.ctd() to recognize which=13 for spice.read.odf() to store ODF header in metadata.makeSection(), after its deprecate/defunct period ended.addColumn(), byteToBinary(), ctdAddColumn(), ctdUpdateHeader(), findInOrdered(), mapZones(), mapMeridians(), oce.as.POSIXlt(), and oce.magic()
as.tidem().read.odf() to handle multiple NULL_VALUEs.handleFlags().rotateAboutZ().concatenate().read.woa().colormap() to include colfunction in return value.plot.section() can use external bathymetrylowpass() addedctdTrim() can isolate upcastsbyteToBinary()
adpEnsembleAverage() addedmapCoordinateSystem() addeddownload.amsr() updated for data-server changedownload.met() addedas.ctd() can specify columns within argo dataread.adp.rdi() handles more file types and larger RDI filesread.odf() handles contradictory metadata betteroce.as.POSIXlt() deprecatedoceSetData() handles units betterR_registerRoutines build-time warningcoastlineCut()
read.gps() handle more filesctdAddColumn() and ctdUpdateHeader()
download.topo() added and read.topo() updated to handle new formatsdownload.amsr() addedcomposite() addedaddColumn() marked as deprecatedread.cm.s4() reads all data in fileas.cm() addedread.odf() handles Aanderaa current meter datamapPlot() and mapAxis() get cex.axis parametersubset(amsr) added; various other amsr improvementsadorn argument in plot functionsread.ctd() obey missingValue (renamed)renameData()
is.beam(), is.xyz(), is.enu() and coordinate(), since x[["coordinate"]] now permits these simply[[ stylergdal changehandleFlags() as generic plus specifics for ctd and argo classes?"plot.ctd" instead of ?plot.ctd
subset(argo, "adjusted")
read.argo() read all documented data and metadata fieldstrimString()
plot.coastline() and mapPlot()
ctdTrim() method renamed: old A and B are new A; old C is new Bas.adp() addedmakeSection() deprecated; use as.section() insteadread.adp.rdi() handles Teledyne/RDI vsn 23.19 bottom-track datageodXyInverse() added; geod functions now spell out longitude etcread.odf() speeded up by a factor of about 30cmocean Python package by Kristen Thyngas.oce()
drifter class as argo to recognize what it actually handlesoceColorsViridis()
interpBarnes() has new argument pregrid
binMean2D() has new argument flatten
data(topoWorld) now has longitude from -179.5 to 180ODF2oce() addedread.odf() handles more data typesread.adp.rdi() reads more VmDas (navigational) databremen class addedcoastlineCut() addedrgdal package used instead of local PROJ.4 source codemapproj-style map projections eliminatedplot.echosounder() gets new argument drawPalette
data(landsat) taken from ocedata (and shrunk)data(nao) and data(soi) moved to ocedatamapTissot() addedread.logger() with ctd-type data infers salinity if necessaryctdTrim() can have “method” as a functionas.topo() can convert “bathy” objects from the marmap package"+.section" renamed sectionAddStation()oceApprox() renamed oce.approx(), with an alias for compatibilityoce.grid() added"tdr" class renamed "logger"
swCSTp() addedswConductivity() now swThermalConductivity(); using Caldwell (1974).sw() functions handle eos=“gsw”library(gsw) replaces teos()
curl() addedmapGrid() addeddata(soi) moved to ocedata packagelonlat2map() addedmap2lonlat() made more accurateproj4 style map projectionsdrifterGrid() addedmapDirectionField() addedmapArrows() addedread.index() addedutm2lonlat() and lonlat2utm() addeddata(met) changed to time of Hurricane Juancolormap() 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.axisctdDecimate() permits user-supplied method functiondata(nao) added; data(soi) updated, and names improved in latterplotProfile() and plotTS() get new argument pt.bg
plot.section() grids the data if neededsealevelHalifax dataset as sealevel
plotProfile() now has ytype="depth"
mapImage() and friends now demand a map exists firstrunlm() addedmapScalebar() addedsubset.topo() addedread.topo() now handles GEBCO netcdf filesdecimate() now handles topo objectsdrawIsopycnals() and plotTS(): improve isopycnal labelsctdDecimate() handles new method unesco
webtide() improvementsread.observatory() addedread.ctd.itp() addedmapImage() speeded up (60X in 1deg SST example)binApply1D() and binApply2D() addedbinCount1D(), binMean1D(), binCount2D(), and binMean2D() addednumberAsHMS() addedgps data type added (provisionally)magneticField() replaces magneticDeclination()
ungrid() addedmapPlot(): improve zone and meridian aestheticsdetrend() returns list with detrend vector and coefsdecodeTime() improvementsinterpBarnes() has new argument trim
standardDepths() addedmapLongitudeLatitudeXY() addedread.ctd.woce() now accepts a format used once by Arctic scientistsswRrho() addedplotProfile() now accepts type=“o”read.adv.nortek(): read salinityctdDecimate(): fix bug for NULL columns [issue 327]plot.section() now chooses best coastline fileswPressure() addedctdFindProfiles() addedas.ctd(): new arguments filename etcoceBisect(), which merely reproduces uniroot()
numberAsPOSIXct() now handles types “sas” and “spss”data(turbulence) addedplot.echosounder(): use white for below-threshold valuesplot.echosounder(): add arg beam to e.g. display Svread.echosounder(): handle dual-beam and split-beam dataread.echosounder(): decode bottom-pickswSoundAbsorption()read.adp() doc improved regarding variable orientation of RDI filesmapPlot() uses … graphical parameters (e.g. cex) in labelling axesplotTS(...,mar=NULL) now avoids setting par(mar)
ctdTrim() work in R 3.0approx3d(): addeddrawPalette(): new arg fullpage
plot.lobo(): add arg which
read.coastline.openstreetmap() addeddata(levitus) addedplot.coastline() gets new arguments projection etc to use mapPlot()
mapContour() permits first argument to be a topo objectmapPlot() gets new arguments axes, bg, fill, and drawBox
oceApprox(): permit equal x values [issue 279]as.section() addeddata(endeavour)
mapPlot() etcplot.ctd(): add argument add
interpBarnes(): add args xgl and ygl
read.section(): add directory argumentsectionSmooth(): add barnes methodoce.plot.ts() and oce.axis.POSIXct(): add tformat argumentread.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 improveddata(oceans) addeddata(papa) addedfillGap() works on matrices as well as vectorsread.lobo() is more flexible on column namesimagep(..., axes=FALSE): no longer plots axis box [issue 249]oce.plot.ts(): alter time auto-ranging methodoceBisect(): increase generality of function whose root is soughtplotTS(): clean axes after isopycnals drawnteos10: update test values (with help from PB)read.adp.nortek(): handle missing to argument as documentedbeamUnattenuateAdp() renamed beamUnspreadAdp()
plotTS() and plotProfile(): permit type=n
plotProfile() with ytype="z": fix bug in y labelexample(riley): remove error in R-develplot.ctd() with which=7 improvementswSCTp(): accept conductivity in mS/cm and S/mas.ctd(): accept TEOS-10 values SA and CTpwelch(): fix bug in frequencytidem(): add argument regress
plotSticks(); delete stickplot()
data(giss) addeddata(topo2) addedplotPolar() addedoce.magic() new name for magic(); renamed oceMagic() in 0.9-15errorBars() addednumberAsPOSIXct() add a leap second for July 2012plot.topo(): automatic cut-point shiftoce.contour() addedplotTaylor() addedoce.as.raw() addedbinmap() addeddata(cm) addedplot.coastline(): improve argument geographical
prettyPosition()
grad()
integrateTrapezoid()
plotTS(): add argument teosteos() as an interface to the TEOS-10 librarymoonAngle() plus other astronomy functions, e.g. julianDay()plotInset(): remove bg and fg argumentsplotTS(): add bg argumentdt object and functions to tdr
plotTS(): add argument inset
read.adp.rdi(): fix a bug in bottom-tracking; add soundSpeed vectordata(echosounder) createdformatPosition() createdplot(echosounder): new arguments atTop and labelsToppercent good for RDI instrumentsplot.drifter(): improve multi-panel plotsimagep(): add argument missingColor
imagep() and drawPalette(): add arguments labels and at
imagep(): permit POSIXt type for zlimplotInset() addedgrid() works for oce-based time axesimagep(..., filledContours): obey ylab argumentsubset(): permit subsetting ADP by pressureoce.plot.ts(): obey arguments xaxt and yaxtcenter argument for plotting topography and coastline with clatitude and clongitude
echosounder classfullFilename(): handle URLs properlyheadingSlow)met classsubset.oce() handles section objectsdraw.section(): permit xtype="latitude" or "longitude"
imagep() has drawPalette=“space” optiongeodDist(): add argument alongPath
show functions.rsk filesplot.section() now uses col if suppliedoce.colorsJet()
plotProfile() vertical range with missing datadata(drag)
plotProfile()' andplot.ctd(): addxtype=“spice”`data(geosecs235)
plotProfile() and plot.ctd(): add argument keepNA
as.ctd(): add arguments other and missingValue
read.lobo(): tolerate more formats, including missing velocitiesdata(schmitt)
spice()
swSCTp(): use surface pressure as a defaultplotTS(): add arguments inSitu and `referencePressure.plotTS(): handle section objectsimagep(): change default drawContours to FALSEadv datasetswN2() by adding new arg derivs
oce.plot.ts() gets new arg axes
distance()
plotTS() and plotScan() to avoid S3 check warningsmakeFilter() argument asKernel default to TRUElatitude() and longitude(): new argument to repeat byDepth
addCtdColumn(): replace if column already existsplot.sealevel(): only show 3 panels, for clarityplot.ctd(): add argument type
imagep(): handle x, y, and z as image() doesoce.plot.ts(): inferred ylim matches data range within provided xlimread.adv.nortek(): handle extra analog datalongitude(), latitude(), time(), elevation(), etcread.oce.odf()
tidem() argument listread.adv.nortek(): handle burst-mode datadata(ctd) to be derived from data(ctdRaw)
heading(), latitude(), longitude(), pitch(), pressure(), processingLog(), roll(), salinity(), temperature(), time(), and velocity()
threenum() added, and use it in all summaries (for speed)velocityStatistics() addedoceApprox() integerToAscii() rangeLimit() ctdRaw
topoInterpolate() addednumberAsPOSIXct(): add type argos
beamAttenuateAdp() as beamUnattenuateAdp()
binAverage()
fillGap(): add rule argument, analogous to same for approx()
rescale()
read.pt(): fix timing error; use as.pt() to create return valueas.pt()
read.adp.rdi() uses checksumsnumber.as.POSIXct(type="gps"): account for leap secondsnumber.as.POSIXct(): accept GPS timesadv.2enu() as to.enu.adv()
match.bytes() as `matchBytes()drawPalette()
matlab2POSIXt(), now a sub-case of number.as.POSIXct()
number.as.POSIXct(): addedoceBiset(): addeddespike(): add argument action
detrend(): addedread.adp.sontek(): handle PCADP typeread.adp.sontek.serial(): addedread.section(): handle WOCE quality flags for salinityretime(): addedread.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 daysas.ctd(): make temperature and salinity into vectors, if not alreadyplot.TS(): add argument use.smoothScatter
oce.debug(): flush the console after printing a messagesw.theta(): rename the method possibilities, to lower casepref as reference.pressure
read.ctd(): fix bug in getting start.time for some time formatspwelch() addedplot.sealevel(): make y axis obey range in data subset, if xlim is givenadp.2enu() addedcoastline.world: improve resolution by a factor of 4 or soread.ctd.woce(): infer water depth as max(pressure) if not in headersection.smooth(): handle misordered stations; handle missing values betterplot.section(): allow strings for which; improve contouringplot.ctd() and plot.profile(): add use.smoothScatter argumentcoriolis(): improve omega valuedespike()
range.limit()
unabbreviate.time()
s4 current metersunwrap.angle()
read.adv.nortek(): detect the velocity rangeplot.ctd(): add more plot types; which=9 for salinity, not densityas.ctd(): improve flexibiltypredict.tidem(): add newdata argumentadv.2enu() addedadp.xyz2enu(): make it correct for heading.biasmake.filter(): can now produce tskernel typeplot.adp(): add use.layout argumentwindow.oce() addedplot.tidem(): remove argument plot.type, using which insteadread.pt(): add arguments from, by, and toread.adp.rdi() read the heading incorrectlyctdDecimate()
oceApprox() addedplot.ctd(): by default, make coastlines extend to box boundariesplot.topo() should accept land.z=NULL]plot.topo() could go past poles]plot.topo() was resetting par() on exit]interp.barnes() gives poor error msg for mismatched x and yplot.section() draws incorrect bottom shapesummary.section() does not report water depthdemo(TS) brokenoce.plot.sticks() ignored page ratiomatrix.smooth()
oce.axis.POSIXct()
debug argument to getOption(“oceDebug”) in all functionsplot.profile(): add argument ytype; change type to xtype
oce.smooth()
read.adv(), etc., supporting Nortek and Sontek devicesread.adp(), etc., supporting Nortek, RDI and Sontek devicesoce.plot.ts()
imagep()
bcd2integer()
matlab2POSIXt()
mgp and mar argumentsplot.pt(): add plim and Tlim arguments.gravity(): give default for latitude argument.plot.sealevel(): remove argument focus.time and add argument which.geod.xy().mgp to all plotting functions.adorn to all plot() functions.oce.colorsTwo(), oce.colorsJet(), and oce.colorsPalette().byte2binary()
summary() for all existing objectsas.sealevel(): rename sampling.interval as deltat
sw.N2(): make it tolerate NAs; adjust df to make result smoothermakeFilter()
decimate(), which may eventually replace ctd.decimate()read.tdr(): handle 5-column data files; add tz argumentplot.profile(): add types sigma+dpdt and sigma+timectdTrim(): add pmin parameterplot.ctd(): add Slim, Tlim, plim, lonlim, latlim args; add mapsplot.TS(): fix isopycnal labels for fresh water; add args Slim, Tlimread.ctd(): make it understand another SBE formatparseLatlon()
oce.edit(): add argument action
oce.write.table()fillGap()
addColumn()
undriftTime()tdrPatm()
readTdr() gather serial no. info; show this on plot.pt()
section.subset(), replaced by subset()
subset.oce()header()
which to read.rbrdtr()
read.rbrdtr() understand headers betterxtype' andytypetoplot.section()`plot.section()
section.smooth()
section.smooth() fail if <4 good data at a levelsummary.ctd() fail for results of section.smooth()sw.dynamic.height() choke on empty stationsplot.section() die if x is unorderedplot.section() RHS axis needs ticsread.oce() understand WOCE section typeswSpice()
read.pt(), summary.pt(), plot.pt(), and ptTrim()
plot.TS() isopycnal label size be same on top and right sidesplot.profile()
plot.section() ability to control contour levels and labelsplot.section() tics for station-locationplot.topo() narrows autoscale to xlim-ylim region, if providedplot.ctd() arg textpanel, and put the profiles in the same rowplot.profile() to let it take Slim,…, as argsplot.profile() font sizeplot.profile(type="S_T") positioningmakeSection() (ignored the list, if a list provided)oce.edit(), later renamed oceEdit()
read.topo(), plot.topo(), and summary.topo()
gebcoColors() … renamed oce.colorsGebco() in version 0.1.77plot.section() check that pressures coincideplot.TS(): make isopycnal list work better for nearly-fresh watertrimCtd(): improve equilibration-phase deletionread.ctd(): handle cases without cruise information or scan columnplot.TS()
as.windrose() and plot.windrose()
sealevel.tuk sea-level datasettidem(), predict.tide(), summary.tide(), plot.tide(), data(tidedata)`swRho() and similar functions take a ctd object as a single argumentswDynamicHeight()
section.grid() andctd.decimate()` extrapolate to surfacesummary.oce()
read.sealevel() had a hard-wired filenameas.CTD() to as.ctd(), to make it consistent with similar functionsread.section()
sectionGrid(), which only grids in p at the momentsection in 0.9-13)as.CTD() to produce sigma.theta instead of sigmaplot.TS() no longer rotates the RH margin isopycnal labelsswRho() and similar take matrices as arguments for S, T, etcread.oce(), a generic function for reading several oceanographic filesread.ctd() understand WOCE-exchange filesread.sealevel() understand comma-separated data from MEDSplot.sealevel() skip spectral graphs if timeseries has NA valuesplot.ctd()
plot.sealevel() by adding focus.time argumentctdDecimate()
oce.as.POSIXlt()
latlonFormat(), latFormat(), and lonFormat()
as.coastline()
make.section()
summary.section()
plot.section()
data(section)
swSoundSpeed()
historyAppend() (later named processingLogAppend()) and related codectdTrim()
swTheta(), to allow for atmospheric analogsread.coastline() handle S filesswTheta() from complaining if length(p) equals 1df in swN2(), plot.ctd(), etc.swRho() (and similar) to take NAs in args (bug B32)swRho() and descendants to take scalar pressure."UNESCO1983" formulation to swTheta() as an alternativeswTheta() by moving vector work from R to CgeodDist() accept a vector for location 1 and a scalar for location 2read.coastline() understand matlab and Splus formatsplot.coastline() scale lat and lon correctlyas.sealevel()
read.sealevel(), summary.sealevel(), and plot.sealevel()
ctdTrim()
ctdWrite()
write.ctd()
ctdAddColumn()
ctdUpdateHeader()
read.ctd() calculate S if missing but C, T, and p are givenswSCTp()
oceRho() to swRho()
swRho() since it was too slow on large datasetsexport PKG_LIBS="-L/sw/lib"
read.ctd() handle more file typesgeodDist().plot.ctd(), which is rudimentary for now.summary.ctd() method.read.ctd() return an object of type ctd.read.ctd()