* Changes/New Features					     -*-outline-*-
======================

See ChangeLog for more details.

** Changes in version 1.2.5:

   o New methods for models consisting of three Poisson processes for
     detection of dive bouts.  For now, only log-frequency NLS procedure is
     supported.  Corresponding maximum likelihood approach or better might
     be available later.

   o readTDR() and readLocs() now accept reading from text-mode
     connections, as allowed in read.csv().

   o New ellipsis argument for boutfreqs() and boutinit() for more
     flexibility in plots.

   o NAMESPACE now uses an empty exportClassPattern() to over-ride
     exportPattern(), and keep using the explicit exportClasses().

** Changes in version 1.2.4:

   o Updated reference for "filter" method in zero offset correction.

** Changes in version 1.2.3:

   o If smooth.par is NULL, then then the smoothing parameter is determined
     by Generalized Cross-validation (GCV) when fitting spline dive model
     for determining dive phases.  This approach is only useful when
     studying individual dives, hence it is not the default in
     calibrateDepth() for TDR objects, which may contain multiple dives.

** Changes in version 1.2.2:

   o New argument plot.points in plotTDR() methods allows plotting points
     when plotting basic TDR objects.

** Changes in version 1.2.1:

   o Implemented new plotTDR() generic, providing more consistent interface
     for all classes.

   o diveStats() provides more dive summary statistics, including
     derivative summaries.  

   o When interp.wet=TRUE and there are no missing depth observations,
     calibrateDepth() no longer performs interpolation.

** Changes in version 1.2:

   o Improved procedure for defining dive phases. The method uses smoothing
     splines and their derivatives to find the end of descent and the
     beginning of ascent, which form the basis for the identification of
     the rest of the phases.  This prompted the creation of a new S4 class
     to hold the details of the dive modelling process.  New plotting and
     accessor methods are also provided to examine the process.  Additional
     methods are being developed to take full advantage of the information
     available in objects of this class.

   o Removed /data objects 'divesTDRcalibrate' and 'divesSummary' because
     it is better to generate and inspect them in examples in help files.

   o New slot 'call' for 'TDRcalibrate' class recording the matching call
     to the corresponding generator calibrateDepth().

** Changes in version 1.1:

   o New method for zero-offset correction based on sequential running
     quantile smoothing/filtering.  Thanks to Roland Fried for suggesting
     this approach.  Although still under development, it already produces
     reliable results.  This has made it necessary to change how
     calibrateDepth() is used, so that the old 'offset' argument is now
     passed as part of the ellipsis ('...') argument, and a new argument
     'zoc.method' is required to choose among the three available methods.
     Function zoc() has been relegated to an internal function (.zoc()) to
     avoid duplication of arguments.

   o New argument 'interp.wet' (logical) in calibrateDepth() that controls
     whether a spline interpolation method should be used to impute missing
     data during periods coded as wet.  This is useful to rectify problems
     with some instruments or on-board software that produce incomplete
     dive traces, where observations near or at the surface are often
     missing.

   o Removed unnecessary default in .detDive().

   o Removed unused arguments 'interval' and ellipsis from .labDive() and
     .detDive(), respectively.

   o Replaced ellipsis argument with 'interval' in .detPhase().

   o The package now depends on caTools (for new ZOC method) and
     RColorBrewer (for better coloring of points in plot methods).

** Changes in version 1.0:

   o Fixed bug in "[" method for TDR objects with empty 'concurrentData'
     'data.frame'.

   o Minor documentation fixes.

** Changes in version 0.9.9:

   o readLocs() now accepts a string for a path or an existing
     `data.frame' to read data from.

** Changes in version 0.9.8:

   o New function .POSIXct() is used for assignments to S4 time slots,
     in preparation for 2.12.0.

** Changes in version 0.9.7:

   o New argument '...' to readTDR for more flexibility in formats of input
     files.  This is passed to read.csv().

   o Comma-delimited files (*.csv) under data/ are now delimited by
     semi-colon so they load as proper 'data.frame' objects with data().

** Changes in version 0.9.6:

   o Fixed .cutDive() to behave as intended: wiggles above wiggle.tol
     should not be allowed to terminate descent phase.

   o Better documentation explaining the basics of dive phase detection.

** Changes in version 0.9.5:

   o Documentation fixes in preparation for new release.  New parser has
     more strict rules for syntax.

** Changes in version 0.9.4:

   o More helpful help pages, particularly in readTDR(), to indicate that
     problems in input text files are better dealt with outside GNU R.

   o Vignette now includes introduction to the bout detection functions.

** Changes in version 0.9.3:

   o Fixed bug that avoided vignette to be built.

** Changes in version 0.9.2:

   o New vignette now builds up on R News article.

   o Fixed bug in diveStats() so that a warning regarding duplicate
     row.names is no longer given.

** Changes in version 0.9.1:

   o Use the 'grid' manager rather than 'pack', and rearrange widgets for a
     better fit in plotTD().

** Changes in version 0.9.0:

   o Minor package-building improvements.

** Changes in version 0.8.9:

   o 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.

** Changes in version 0.8.8:

   o 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).

** Changes in version 0.8.7:

   o Fixed citations in *.Rd files and CITATION.

** Changes in version 0.8.6:

   o Fixed bug in grpSpeedFilter() whereby the test to fail if any speed >
     threshold, rather than if ALL speeds > threshold.

** Changes in version 0.8.5:

   o Improved validity check for input in distFilter().

** Changes in version 0.8.4:

   o Fixed bug in rmsDistfilter() to intercept an error due to the number
     of rows being exactly equal to the test window size.  The dimensions
     of internal objects are now handled properly.

** Changes in version 0.8.3:

   o Better explanation of location filtering procedures in man pages.

** Changes in version 0.8.0:

   o New methods for identification and analysis of bouts of behaviour
     (mostly diving, but apply to others too).

** Changes in version 0.7-8:

   o Better arrangement of widgets in plotTD() and its methods.

** Changes in version 0.7-7:

   o S4 documentation bug fix.

** Changes in version 0.7-6:

   o Fixes bug in plotTD() to work with stricter object class management in
     R devel.

** Changes in version 0.7-5:

	* Full examples for movement functions.

** Changes in version 0.7-4:

   o distSpeed() no longer uses 'id' argument.

   o Complete examples for location filtering functions.

   o createTDR() now provides useful default for 'concurrentData', and test
     for missing 'dtime'.  Completed example accordingly.

   o Improved show() method for 'TDRcalibrate' objects.

   o plotTD(), and hence the plotTDR() methods now accept an ellipsis
     argument to pass to par() for more flexibility drawing the plot.  They
     also now accept a new argument 'cex.pts' to set the relative size of
     points.

** Changes in version 0.7-3:

   o detPhase() and detDive() are now private functions (renamed with a
     preceding dot), and should only be used through calibrateDepth().

   o Rearranged documentation, reflecting the higher importance of
     calibrateDepth() and calibrateSpeed() functions.

   o distSpeed() no longer uses 'speed' and 'subset' arguments, and always
     returns a matrix.  All location filtering functions are now adapted to
     this change.

** Changes in version 0.7-2:

   o More examples for important functions.

** Changes in version 0.7-1:

   o 'TDRcalibrate' method for plot() now plots correctly if no dives were
     identified.  New argument 'interact' to allow for static plots,
     without 'tcltk' interaction.

   o plot method replaced by 'plotTDR', to avoid unusual introduction of
     arguments in methods and simplify code.  This method is now based on
     the new function plotTD(), which replaces plotDive(). This system now
     makes the relationships between functions much more clear.

   o Function getAct() renamed to rleActivity() to make it clearer that it
     calculates statistics from running series of readings with the same
     activity.

** Changes in version 0.7-0:

   o Arguments 'seaerr', 'landerr', and 'divethres' were renamed to
     'wet.thr', 'dry.thr', and 'dive.thr'.  Likewise, slots
     'land.threshold', 'sea.threshold', and 'dive.threshold' in class
     TDRcalibrate were renamed to 'dry.thr', 'wet.thr', and 'dive.thr',
     respectively, for consistency/appropriateness.

   o The argument 'contours' to rqPlot() should now be a list with 2
     components.

** Changes in version 0.6-9:

   o New arguments for calibrateDepth(), offering improved control over
     detection of descent, bottom, and ascent phases.  We now use rates of
     vertical movement for detection, with a further argument for defining
     what determines a bottom wiggle.

   o New arguments for plotDive() to decide whether to plot legend and to
     set limits for depth plot.

   o Documentation for formal classes and methods was split to make them
     easier to read.

   o attendance() has been renamed to timeBudget().
