2006-07-17  Sebastian Luque  <spluque@gmail.com>

	* 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  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* 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  <spluque@gmail.com>

	* velCalib.R:
	Added argument postscript to choose whether to output to eps.

2006-04-17  Sebastian Luque  <spluque@gmail.com>

	* calibrate.R:
	Added argument coefs to allow using known coefficients for calibration.

2006-04-16  Sebastian Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* track.R: Corrected id default value.

	* distSpeed.R: Better names in value.

	* track.R: Renamed function.

2006-03-28  Sebastian Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* diveStats.R:
	Fixed bug whereby postdive.dur was only being calculated for TDR class.

2006-03-24  Sebastian Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* velCalib.R: Changed argument name rate to rdepth in rqPlot.

2006-03-17  Sebastian Luque  <spluque@gmail.com>

	* detDive.R:
	labDivePhase and .cutDive now detect phases based on changes in depth.

2006-03-16  Sebastian Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* detDive.R:
	labDive now returns a 2-col matrix with dive and postdive labels.

2006-03-12  Sebastian Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* 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 Luque  <spluque@gmail.com>

	* austfilter.R:
	  Replaced sapply by lapply in first stage filter.

2005-06-16  Sebastian Luque  <spluque@gmail.com>

	* velcalib.R:
	  Removed require()'s, since the package depends take care of that.
