2010-02-04 Sebastian P. Luque Version 0.9.7 released. * ChangeLog, README, inst/doc/biblioSPL.bib: Updated bibliography. 2010-02-03 Sebastian P. Luque * R/readTDR.R, data/dives.csv, data/sealLocs.csv, inst/doc/diveMove.Rnw, man/austFilter.Rd, man/distSpeed.Rd, man/diveMove-package.Rd, man/dives.Rd, man/readLocs.Rd, man/readTDR.Rd, man/sealLocs.Rd, tests/calibrations.R, tests/class-tests.R, tests/final-stats.R: New argument '\ldots' to readTDR, passed to read.csv(), for consistency and more flexibility. We changed comma to semi-colon delimiter in data files. This prompted changes in the examples (*.Rd files). Thanks to Kurt Hornik for spotting this in the warning check. 2010-02-02 Sebastian P. Luque * man/dives.Rd, man/sealLocs.Rd: Fixed *.Rd files with markup that is no longer valid. 2009-10-28 Sebastian P. Luque * DESCRIPTION, inst/doc/biblioSPL.bib: Updated DESCRIPTION and *.bib. 2009-10-25 Sebastian P. Luque * .Rbuildignore, inst/doc/biblioSPL.bib, inst/doc/diveMove.Rnw, tests/calibrations.R, tests/final-stats.R: Adding *.bib file because it's needed for R-forge building, but ignore it for building. 2009-10-24 Sebastian P. Luque * inst/doc, inst/doc/diveMove.Rnw, inst/doc/tcltk.png: Saved vignette in UTF-8, as that is what was used. Added tcltk.png, needed for building. 2009-10-21 Sebastian P. Luque Version 0.9.6 released. * DESCRIPTION, R/detDive.R, man/calibrateDepth.Rd: Fixed .cutDive() to behave as intended; wiggles above wiggle.tol should not be allowed to terminate descent phase. Better documentation explaining the basics of dive phase detection. 2009-02-13 Sebastian P. Luque Version 0.9.5 released. * DESCRIPTION, README, man/distSpeed.Rd, man/diveMove-package.Rd, man/dives.Rd, man/sealLocs.Rd: Documentation fixes in preparation for new release. 2008-11-09 Sebastian P. Luque * inst/doc/Makefile: Fixed layout of comments. 2008-11-04 Sebastian P. Luque Version 0.9.4 released. * DESCRIPTION, R/AllGenerics.R, R/AllMethod.R, R/plotTD.R, README, TODO, inst/doc/diveMove.Rnw, man/TDR-accessors.Rd, man/TDR-class.Rd, man/TDRcalibrate-accessors.Rd, man/TDRcalibrate-class.Rd, man/austFilter.Rd, man/bout-methods.Rd, man/bout-misc.Rd, man/bouts2MLE.Rd, man/bouts2NLS.Rd, man/calibrateDepth.Rd, man/calibrateSpeed.Rd, man/detDive-internal.Rd, man/detPhase-internal.Rd, man/distSpeed.Rd, man/diveMove-internal.Rd, man/diveMove-package.Rd, man/diveStats.Rd, man/dives.Rd, man/extractDive-methods.Rd, man/labDive-internal.Rd, man/plotTDR-methods.Rd, man/readTDR.Rd, man/timeBudget-methods.Rd, man/zoc.Rd, tests/class-tests.R: Improved help pages and vignette. 2008-10-23 Sebastian P. Luque Version 0.9.3 released. Minor bugs fixed in inst/doc (we were not building vignette). 2008-10-23 Sebastian P. Luque Version 0.9.2 released. * .Rbuildignore, DESCRIPTION, inst/doc, inst/doc/Makefile, inst/doc/diveMove.Rnw: New Makefile and vignette. This meant also new patterns in .Rbuildignore. * R/diveStats.R: Specified row.names=NULL to avoid warning about duplicated row.names. 2008-06-13 Sebastian P. Luque Version 0.9.1 released. * R/plotTD.R: Use the 'grid' manager rather than 'pack', and rearrange widgets for a better fit. 2008-04-09 Sebastian P. Luque * R/speedStats.R, man/diveStats.Rd: Improved angle description. 2008-03-30 Sebastian P. Luque * R/readLocs.R, man/dives.Rd, man/sealLocs.Rd: Included simple example to show structure. 2008-01-29 Sebastian P. Luque Version 0.9.0 released. * .Rbuildignore: Exclude psvn.el files from build. 2008-01-28 Sebastian P. Luque Version 0.8.9 released. * DESCRIPTION, R/austFilter.R, README: Fixed bug in rmsDistFilter() causing the filter to fail with very small data sets with message warning that window size is larger than available data, because locations at ends were not being counted. 2008-01-27 Sebastian P. Luque Version 0.8.8 released. * R/austFilter.R, README, man/austFilter.Rd: The root-mean-square filter in rmsDistFilter() now works as described in Freitas et al. (2008), rather than as in the original McConnell et al. (1992). The latter may not have been the actual implementation, although other studies may have followed it (e.g. Austin et al. 2003). 2008-01-25 Sebastian P. Luque * R/austFilter.R, TODO: Renaming of internal function dist.fun() to travel.fun(), since it returns both distance and speed statistics. 2008-01-11 Sebastian P. Luque Version 0.8.7 released. * README, man/bout-methods.Rd, man/bout-misc.Rd, man/bouts2MLE.Rd: Fixed citations. 2008-01-05 Sebastian P. Luque Version 0.8.6 released. * R/austFilter.R: Fixed bug in grpSpeedFilter() which caused the test to fail if any speed > threshold, rather than if ALL speeds > threshold. Thanks to Bryan Wright (). 2007-11-09 Sebastian P. Luque Version 0.8.5 released. * R/distSpeed.R: Check that input is valid. 2007-11-08 Sebastian P. Luque Version 0.8.4 released. * R/austFilter.R: Added checks for cases where the number of rows equals exactly the test window size. 2007-10-18 Sebastian P. Luque Version 0.8.3 released. * man/austFilter.Rd: Improved explanation of procedure. 2007-07-12 Sebastian P. Luque Version 0.8.2 released. * DESCRIPTION, man/*: Removed "Encoding:" field from Description and "\encoding{latin1}" from *.Rd files, since it is more trouble than any benefit. 2007-07-09 Sebastian P. Luque Version 0.8.1 released. * DESCRIPTION: Use "Encoding: latin1" field. * man/*: Use "\encoding{latin1}" line. 2007-07-07 Sebastian P. Luque Version 0.8.0 released. * DESCRIPTION: Changed 'SaveImage' field to 'LazyLoad' as per deprecated 'SaveImage' in R-devel. 2007-07-02 Sebastian P. Luque * calibrate.R, plotTD.R: Use the '::' operator to be explicit when referring to external packages. 2007-07-01 Sebastian P. Luque * DESCRIPTION: Updated to GPL 3, and added a Suggests: tcltk. 2007-03-20 Sebastian P. Luque * man: Provided better 'Values' section and descriptions. 2007-02-16 Sebastian P. Luque * R/plotTD.R: Better arrangement of tcltk widgets. 2007-02-14 Sebastian P. Luque * R/austFilter.R (rmsFilter): Provided more meaningful error message. 2007-02-13 Sebastian P. Luque * man/plotTDR-methods.Rd: S4 documentation is now being checked in R devel, and a mismatch was found. This was fixed here. 2007-02-11 Sebastian P. Luque * R/plotTD.R: Used unclass() on the first argument in pmax() and pmin() calls, to standardize comparisons on a simple number. Thanks to Brian Ripley. 2007-01-25 Sebastian P. Luque * bouts.R: Renamed revLogit() to unLogit() for appropriateness. 2007-01-24 Sebastian P. Luque * detDive.R: .diveIndices(): Use pmax() and pmin() to avoid returning indices beyond the limits of the input. * AllMethod.R: Use drop=FALSE in extraction methods to keep structure. 2007-01-21 Sebastian P. Luque Moved package to CVS. * bouts.R: plotBouts2.mle(): Removed density plot, we use only curve fit. plotBouts2.mle(): Changed default draw.bec=FALSE. * track.R: Removed track.R, no longer needed. 2007-01-15 Sebastian P. Luque * bouts.R: plotBouts2.cf(): New function for plotting cumulative frequency distribution. 2007-01-12 Sebastian P. Luque * bouts.R: plotBouts.mle(): Show the value of 1-p in the legend. * AllMethod.R: Fixed bug in 'nls' method for plotBouts() which should use eval.parent() to search for data. 2007-01-11 Sebastian P. Luque * bouts.R: boutfreqs(): Fixed bug causing unavailable 'upper' object when method="seq.diff". bouts.mle(): Removed require stats4 call. * zzz.R: require'd stats4. * AllGenerics.R, AllMethod.R: New plotBouts() and bec2() methods. * AllClass.R: Use nls class as S4. * bouts.R: New file. 2007-01-10 Sebastian P. Luque * AllMethod.R: Improved show() method for TDR objects. * plotTD.R: plotTD(): New argument 'cex.pts' passed to points(). plotTD(): Removed the 'lab' par() setting from the initial, as this is better handled with the newly introduced ellipsis arg. plotTD(): Added argument '...' to be passed to par() for more flexibility in how to draw the plot. 2007-01-09 Sebastian P. Luque * AllMethod.R: Display more information for 'TDRcalibrate' show() method. Fixed buglet in 'TDRcalibrate' show() method that causing it to display speed calibration information regardless of what specific class was contained in the tdr slot. * diveStats.R, oneDiveStats.R, speedStats.R: Renamed .getSpeedStats() to speedStats(), as this is not really an accessor. 2007-01-08 Sebastian P. Luque * AllMethod.R: createTDR(): Provided useful default to 'concurrentData', and added a test for missing 'dtime', producing it if it is. * distSpeed.R: Removed 'id' argument. Removed arguments 'speed' and 'subset', as they are no longer necessary. * austFilter.R: Functions adapted to new structure in distSpeed(), making it more efficient. * distSpeed.R: We now handle two matrices of the same shape and size, with argument 'id' for dividing up the matrices into groups, and a 'subset' argument to subset them. 2007-01-07 Sebastian P. Luque * distSpeed.R: New arguments 'id' and 'subset' so that track() is no longer necessary; we return a matrix with an 'id' column. * readLocs.R: New argument ... passed to read.csv(). Added a check for missing location ID and individual ID columns. * calibrate.R, detDive.R, detPhase.R: Made .detPhase() and .detDive() private, as these are too specialized for end users. 2007-01-06 Sebastian P. Luque * AllMethod.R, calibrate.R, detDive.R, detPhase.R, plotTD.R, stampDive.R: Documented private objects .speedNames, .speedCol(), .diveIndices(), and .night(). Also made .labDive(), .labDivePhase(), and .rleActivity() private. * zoc.R: Fixed bug caused by relying on the plotTDR method, rather than on the function plotTD() as it should be. * plotTD.R: .night(): Changed %F format string for POSIXct to %Y-%m-%d as the former fails in Windows platforms. 2007-01-04 Sebastian P. Luque * readTDR.R, AllClass.R, AllMethod.R, detDive.R, diveStats.R, oneDiveStats.R: Make calls to private objects more precise using ':::' operator. * AllGenerics.R, AllMethod.R, plotTD.R, zoc.R: Removed 'plot' method and replaced it with 'plotTDR', using the new function 'plotTD' for doing most of the work. * AllMethod.R, detPhase.R, stampDive.R: Renamed function 'getAct' to 'rleActivity'. * AllMethod.R, detPhase.R, stampDive.R: Renamed references to components 'trip.act', 'trip.beg', and 'trip.end' to 'activity', 'begin', and 'end', respectively, in returned objects and methods using these. 2007-01-03 Sebastian P. Luque * AllMethod.R: Moved generics to AllGenerics.R * AllGenerics.R: New file. 2006-12-28 Sebastian P. Luque * AllMethod.R: 'TDR' method for "[" now uses drop=FALSE (bug fix). 'TDRcalibrate' method for plot() now tests whether we have no dives. * detDive.R: labDivePhases(): Test if we have at least one dive, otherwise return 1-level factor. plotDive(): No longer color lines traces to stay close to standard guidelines. 2006-12-27 Sebastian P. Luque * calibrate.R: rqPlot(): New argument col.line for coloring the regression line. calibrateSpeed(): Fixed bug where only the first component from the list returned by contourLines() was being used. This caused problems when a chosen contour level produced several contour lines. rqPlot(): abline() call is now called right after contour() to increase visibility. * AllClass.R, AllMethod.R, calibrate.R, detDive.R: Renamed argument 'divethres' to 'dive.thr' and slot 'dive.threshold' to 'dive.thr' for consistency. * AllMethod.R, calibrate.R, detPhase.R, AllClass.R: Renamed arguments 'seaerr' and 'landerr' to 'wet.thr' and 'dry.thr', respectively. Renamed slots 'land.threshold' and 'sea.threshold' to 'dry.thr' and 'wet.thr', respectively. 2006-12-26 Sebastian P. Luque * plotDive.R: plotDive(): New argument 'depth.lim' to set the depth limits. .night(): New function to do night time calculations separately and more efficiently. * calibrate.R, detDive.R: .cutDive() and calibrateDepth(): New argument 'wiggle.tol' to control the proportion of maximum depth above which wiggles should be ignored during descent, or below which they should be considered as belonging to bottom phase. 2006-12-24 Sebastian P. Luque * plotDive.R: New argument 'key'. * detDive.R, calibrate.R: .cutDive() and calibrate(): New arguments 'descent.crit.q' and 'ascent.crit.q' to control which quantiles should define the critical rate of descent/ascent below/above which descent and ascent should end/begin, respectively. 2006-12-21 Sebastian P. Luque * AllMethod.R: Renamed attendance() to timeBudget() for appropriateness. 2006-12-20 Sebastian P. Luque * AllMethod.R: getCCData(): We ensure that value is a data.frame. getCCData(): We use a more standard name for the method and provided mechanism to extract any number of named components. * calibrate.R: rqPlot(): We plot the regression line with a more appropriate range using all the countours found for the contour.levels argument provided. calibrateSpeed(): Now uses time differences between all sampling intervals. * diveStats.R: Reflect renaming of diveStats() to oneDiveStats(). * oneDiveStats.R: Renamed to oneDiveStats(). 2006-12-19 Sebastian P. Luque * plotDive.R: drop argument is now used properly: phaseCol[, drop=TRUE]. * AllMethod.R: plot method for TDRcalibrate objects now provides only levels used for plot legend (corrects bug causing all levels to be shown when subsetting only some of them). Test for "[" method for TDR objects should use || in if() statement. 2006-12-04 Sebastian P. Luque * calibrate.R: calibrateSpeed(): New argument 'postscript'. New approach based on bivariate kernel density estimates for doing the calibration. rqPlot(): Moved here for convenience, since we no longer need the other functions in speedCalib.R. * speedCalib.R: rqPlot(): New approach to calibrate on entire file. 2006-12-03 Sebastian P. Luque * calibrate.R: calibrateSpeed(): We no longer need test for calType argument at the end. We always replace speed and coefficients based on value returned by doSpeedCalib(). * calibrate.R, speedCalib.R: doSpeedCalib(): We provide an argument to set tau in quantile regression, for more flexibility. This can be passed through ... in calibrateSpeed(). * speedCalib.R: doSpeedCalib(): We always return a list; with coefficients and corrected speeds if asked for, or with (0, 1) and input speed if argument calType is "none". .descAsc(): We use the sequential differences during each phase. New local function to perform the calculations for each phase for debugging purposes. .doSpeedCalib(): Provide more meaningful legend. 2006-11-21 Sebastian P. Luque * AllMethod.R: Corrected replacement methods to take only the right signature. Removed unnecessary if test for as.data.frame method. 2006-11-20 Sebastian P. Luque * AllMethod.R: New subset method for TDR objects. plot(): TDRcalibrate method adjusted to new plotDive() arguments. getccData(): Subsetting is now done using [, y], rather than [[y]] for more flexibility. * plotDive.R: Better default for xlab format string. New arguments concurVars, concurVarTitles, sunrise.time, and sunset.time for better control of extra variables to plot. Removed legend for sunrise/sunset times, as this is better left to the user to handle. 2006-11-18 Sebastian P. Luque * AllMethod.R: Removed time replacement method. as.data.frame(): return also the entire concurrent data data frame. extractDive(): Now handles new representation of TDR objects properly. Adjusted show method according to new representation of TDR objects. Modified getSpeed() accessor as above. New replacement methods for time, depth, and speed. Hidden function .speedCol() for calculating the column number of speed vector in concurrentData slot of TDR objects. * AllClass.R: Added new slot concurrentData to TDR objects to handle additional data that may need to be included for plotting/analyses for later development. * calibrate.R: calibrateSpeed(): Make use of new replacement method for speed. * readTDR.R: readTDR(): We don't rely on the input file's name to decide the class of the value returned. New arguments to map the input to the corresponding class. 2006-11-15 Sebastian P. Luque * plotDive.R: More arguments for flexibility in axis label formatting and labelling. 2006-11-03 Sebastian P. Luque * AllMethod.R: For as.data.frame method, return the file and dtime slots as attributes. 2006-10-05 Sebastian P. Luque * plotDive.R: Moved 'if' statement checking for number of levels of labels, so legend drawing is conditional on it, but not the labelling of points. * detDive.R (labDive): Use arg 'along' in seq() call within rle. This bug was causing an error when only one section was present. * detPhase.R (getAct): Modified seq() call within rle so it uses its 'along' arg. This bug was causing errors when only one phase was present. 2006-10-04 Sebastian P. Luque * plotDive.R: Added a par("usr") call when plotting velocity to watch out for change in y coordinates. 2006-10-03 Sebastian P. Luque * AllMethod.R: Fixed bug in 'show' TDR method causing inconsistencies in the units shown for the "Total Duration (d)". New plot method for TDRcalibrate objects, with control over which dives to plot, and whether to plot surface readings. * plotDive.R: Fixed bug due to out of range xright and xleft arguments to rect(). Drop unused levels from phaseCol argument, for creating meaningful legend. Do not include a legend for the point labels if there are more than 10 of them. * detDive.R (.diveIndices): New internal function to extract indices of dives and their surface beginning/ending. 2006-10-02 Sebastian P. Luque * plotDive.R: More control is now possible for zooming. Better arrangement of tk widgets. 2006-10-01 Sebastian P. Luque * speedCalib.R: Renamed arguments, objects and calls to methods related to speed. * readTDR.R (readTDR): Renamed argument to specify speed column and call to create new class object, to reflect changes in slot name. * plotDive.R: Renamed argument velocity to speed. * getSpeedStats.R: Renamed objects related to speed. * getDive.R: Renamed argument vel to speed, and renamed calls to methods and functions related to speed. * diveStats.R: Renamed calls to methods to reflect the new names of methods and functions related to speed. * distSpeed.R: Renamed argument vel to speed. * calibrate.R: Renamed function calibrateDepth to calibrateSpeed and reflected changes in methods names related to speed. * austFilter.R: Renamed argument velthres to speedthres. * AllMethod.R: Renamed methods related to velocity to speed to reflect changes in class slot. * AllClass.R: Renamed class TDRvel to the more appropriate TDRspeed. 2006-09-30 Sebastian P. Luque * plotDive.R: Do not call X11, hard-wiring the device, rather than using the current one. 2006-09-29 Sebastian P. Luque * austFilter.R: austFilter now passes a data frame to the other filtering functions to conserve POSIXct class properties across the procedure. * distSpeed.R: Made the last difftime object into a numeric object, so it is understood by 'abs'. 2006-09-28 Sebastian P. Luque * AllClass.R, AllMethod.R, austFilter.R, calibrate.R * detDive.R, detPhase.R, distSpeed.R, diveStats.R * getDive.R, getVelStats.R, plotDive.R, readLocs.R * readTDR.R, stampDive.R, track.R, velCalib.R, zoc.R: All objects now handle date and time using the standard POSIXct class. 2006-08-01 Sebastian P. Luque * plotDive.R: Removed silly first line of legend and x grid. 2006-07-18 Sebastian P. Luque NAMESPACE is now successfully implemented. * AllMethod.R: New accessor getFileName(). * zzz.R: New file. * stampDive.R, diveStats.R, calibrate.R, detDive.R, AllMethod.R: Standardized accessor method names. 2006-07-17 Sebastian P. Luque * plotDive.R: Removed require() call to chron, since whole package depends on it. Better par() values for multiplot case. * velCalib.R: Added a fourth plot to doVelCalib() to show the density distributions of both variables, and the combined vector. 2006-07-13 Sebastian P. Luque * plotDive.R: Provided better labelling of axes. * detDive.R: Eliminated unnecessary call to gsub() in labDive. * detPhase.R: Eliminated unnecessary call to gsub for creating returned objects. * readTDR.R: Eliminated rather useless message() call. 2006-05-04 Sebastian P. Luque * AllMethod.R: The data frame returned by 'attendance' now has separate element to identify the phase number (phaseno), and activity performed at each of them (activity), rather than the single trip identifier, with zeroes for land phases. This facilitates further manipulations. 2006-04-19 Sebastian P. Luque * velCalib.R: Made plot regions square in rqPlot, to make it conform to equal scale comparisons. Included respect=TRUE for creating plots. 2006-04-18 Sebastian P. Luque * velCalib.R: Added argument postscript to choose whether to output to eps. 2006-04-17 Sebastian P. Luque * calibrate.R: Added argument coefs to allow using known coefficients for calibration. 2006-04-16 Sebastian P. Luque * plotDive.R: renamed argument colsec to phaseCol. * readTDR.R: More appropriate default velCol argument to readTDR. * velCalib.R: bandwidths for the calibration plots are now chosen optimally through bw.nrd. Added a box() around image plot. Got rid of contour plot which were not very useful; replaced them with image plots. Postscript output has been made horizontal. * calibrate.R: Added ellipsis argument to calibrateVel to pass to doVelCalib. * AllMethod.R: Removed white space at beginning and of 'show' method. Renamed velCCoefs to velCoef. 2006-04-15 Sebastian P. Luque * calibrate.R: New argument 'offset' to be passed to calibrateDepth. * zoc.R: Removed initial message and 'readline' call, as it fits better in the documentation. * zoc.R: Added argument 'offset' to allow providing of known offset to use for entire record. * AllMethod.R: Modified messages in show method for TDRcalibrate to more accurate ones. 2006-04-14 Sebastian P. Luque * readTDR.R: New function .createChron and new arguments to readTDR to provide flexibility in input file structure. * AllMethod.R: Renamed buildTDR to createTDR. Modified messages in show method for TDRcalibrate to more accurate ones. 2006-03-31 Sebastian P. Luque * track.R: Corrected id default value. * distSpeed.R: Better names in value. * track.R: Renamed function. 2006-03-28 Sebastian P. Luque * diveStats.R: Returns a data frame now. * diveStats.R: Changed units output from postdive.dur to s. * getDive.R: Changed output units for duration (time) variables so they're in s. * AllMethod.R: new method for dPhaseLab to extract the factor for given dives. * plotDive.R: new argument 'colsec' to color dive sections. 2006-03-26 Sebastian P. Luque * getVelStats.R: Test for missing or NULL coefVcal arg now uses || rather than |. * calibrate.R: Include calibrated velocity in value only if asked. Fixed bug where velocity wasn't being returned in calibrateVel. 2006-03-25 Sebastian P. Luque * diveStats.R: Fixed bug whereby postdive.dur was only being calculated for TDR class. 2006-03-24 Sebastian P. Luque * diveStats.R: Grave bug fixed where results were not being assigned for class TDR. * AllMethod.R: as.data.frame method was not giving proper column names. * austFilter.R: More helpful messages. 2006-03-23 Sebastian P. Luque * austFilter.R: Broke up austFilter into more discrete functions, which improved efficiency considerably. * distSpeed.R: Reversed the order of lat and lon in args, as lon lat, order makes more sense. 2006-03-22 Sebastian P. Luque * diveStats.R: Value is now a data frame; makes life easier afterwards. * stampDive.R, getDive.R, diveStats.R, calibrate.R, detDive.R: Replaced calls to generic time to tdrTime. * AllMethod.R: changed name of time generic to tdrTime to avoid conflict with base. * stampDive.R, diveStats.R, calibrate.R: Renamed argument obj to x. * AllMethod.R: Standardized arg names in all methods. * AllMethod.R: Changed argument name from 'x' to 'obj' when method is not an accessor; for convenience. * stampDive.R: Added a class test for the 1st arg. * AllMethod.R: Added attendance method to obtain an attendance table. * stampDive.R: New file. 2006-03-21 Sebastian P. Luque * AllMethod.R: grossAct method was not extracting properly due to use of "[" rather than "[[". * velCalib.R: Fixed axlims object in rqPlot that was only taking x to define the range. * readTDR.R: Included a tolower() for making it easier to recognize the TDR model in readTDR(). * calibrate.R: Fixed bug in calibrateDepth which was testing for wrong class for its argument. 2006-03-20 Sebastian P. Luque * calibrate.R: Took into account change in name for doVelCalib. Included test for validity of obj argument. * AllMethod.R: Moved calibrateDepth, calibrateVel, and diveStats to separate files, as I can't get them to work like methods. Fixed signatures for TDRcalibrate method extractDive. Added diveStats method for TDRcalibrate. * getDive.R: Moved diveStats to AllMethod.R and getDive now works with a matrix with ncol >= 3. 2006-03-18 Sebastian P. Luque * velCalib.R: Changed argument name rate to rdepth in rqPlot. 2006-03-17 Sebastian P. Luque * detDive.R: labDivePhase and .cutDive now detect phases based on changes in depth. 2006-03-16 Sebastian P. Luque * zoc.R: No longer use 'invalid' so as to avoid requiring gtools. * plotDive.R: Removed require(gplot), as package no longer needed. * detDive.R: Moved .cutDive and labDivePhase here, makes more sense. 2006-03-15 Sebastian P. Luque * detPhase.R: Renamed output names in both getAct and detPhase. Changed detPhase ... arg to be at the end. getAct now takes a factor, rather than a numeric vector as its second argument. Modified code in detPhase accordingly. 2006-03-14 Sebastian P. Luque * plotDive.R: Eliminated dependency on gplots -- now uses simpler legend() from graphics base package. * AllClass.R: Improved validity tests for TDR and TDRvel class. * getVelStats.R: Single function .getVelStats now returns a 3-col matrix with total distance travelled, mean velocity, and angle if appropriate. * velCalib.R: Settled on using one data point for speed calibration per dive. * getDive.R: diveStats now calls .getVelStats for velocity statistics, if needed. 2006-03-13 Sebastian P. Luque * detDive.R: labDive now returns a 2-col matrix with dive and postdive labels. 2006-03-12 Sebastian P. Luque * detDive.R: detDive now returns a data frame with dive ids and dive activity factor. * detPhase.R: detPhases now uses a factor to label rows, rather than numeric vector. 2006-03-11 Sebastian P. Luque * zoc.R: Arguments are now separate for time and depth. * readTDR.R: Moved .getInterval here, makes more sense. * detDive.R: Much improved labelling of dives. 2006-03-10 Sebastian P. Luque * detDive.R: More efficient handling of args in detDive. * detPhase.R: More versatile handling of args, passing '...' to getAct, in case it needs more args in the future. 2005-12-16 Sebastian P. Luque * getDive.R: Added rownames for output matrix because it's used by other functions. Split velStats and it calls a new function breakDive() now. Per dive statistics are now done with a call to by() preceded by building a data frame. * detDive.R: We now do numbering of dives in separate function labdive(). 2005-12-15 Sebastian P. Luque * readLocs.R: Replaced assignment after testing for NULL argument, to a call to `missing'. * getVelStats.R: Split large function into two: getVelStats and velStats. 2005-12-14 Sebastian P. Luque * getDive.R: Removed unused argument from argument list: `divethres', and renamed `diveinds' to `dives'. * detDive.R: Replaced argument name: `phases' instead of previous `byphase'. 2005-07-12 Sebastian P. Luque * austfilter.R: Replaced sapply by lapply in first stage filter. 2005-06-16 Sebastian P. Luque * velcalib.R: Removed require()'s, since the package depends take care of that.