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

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

	* plotDive.R: new argument 'colsec' to color dive sections

	* diveStats.R: Returns a data frame now

	* 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

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.
