-------------------------- aqp 0.99-8.47 (2011-11-20) --------------------------
* started VERY basic AQP Introduction vignette... still experimental
* adding coercion methods for common objects and sp-class objects
* matrix-style subsetting almost works:
  - s[i, j] ---> i is the profile index, and j is the horizon/slice index
* added a 'slice' method for SoilProfileCollection objects
  - returns selected variables along depth slice(s) (i.e. no aggregation)
* added NAMESPACE file for R >= 2.14 compatibility
* stabilized S4 class, working on S4-izing all related functions
* preliminary documentation on the new S4 classes/methods
* logistic power peak (LPP) can now be used to generate synthetic depth functions
* added contributing fraction annotation in panel.depth_function()

-------------------------- aqp 0.99-8.4 (2011-10-04) --------------------------
* minor bug fixes and enhancements in PedonPC function
* S4 interface to soil.slot.multiple()

-------------------------- aqp 0.99-8.2 (2011-09-21) --------------------------
* added S4 class/methods for `SoilProfileCollection`
  - this supercedes the (now removed) S3 `SoilProfileList` classes
  - basic accessors/settors are in place, subject to change
* profile_plot() now uses the `SoilProfileCollection` class
! initSoilProfileList() is no longer supported; see depths() for similar functionality
! expect some tumultous times ahead in the API... should be ironed out by 1.0 release

-------------------------- aqp 0.99-8 (2011-09-14) --------------------------
* soil.slot() will now accept boundaries defining a 'slab' over which aggregates are computed
* soil.slot.multiple() now cleanly wraps soil.slot(), accepting all arguments
  - these two changes make it possible to ask: 
    "what is the wt. mean value of some property within this slab, and among these groups?"
  - soil.slot.multiple() now uses a formula interface: NOTE that this will break existing scripts (sorry)
    
-------------------------- aqp 0.99-7 (2011-09-01) --------------------------
* new functions for getting data out of PedonPC (MS Access) databases [windows only for now]
  - get_site_data_from_pedon_db() : site and pedon aggregate data
  - get_hz_data_from_pedon_db() : horizon level data
  - get_colors_from_pedon_db() : formats and mixes multiple colors / horizon
  + implemented in mix_and_clean_colors()

* test_hz_logic() : basic function for testing horizon logic, returns TRUE/FALSE by ID
* parallel operations now NON-functional, while we wait for plyr to support doSMP...
* new ID plotting style for profile_plot() : handy when plotting large collections and/or long IDs

-------------------------- aqp 0.99-4 (2011-08-15) --------------------------
* code and documentation clean-up
* Soil Sata Access (SDA) query functions have been added
  - mapunit_geom_by_ll_bbox() : get map unit geometry by bounding box
  - MUKEYS_by_ll_bbox() : get map unit keys by bounding box
  - SDA_query() : retrieve soil tabular data via query written in SQL
* additional customizations added to profile_plot
* two new sample data sets + examples

-------------------------- aqp 0.99-1 (2011-01-26) --------------------------
* soil.slot() and profile_compare() now have support for parallel computation thanks to bug-fixes in plyr 1.4
  - plyr >= 1.4, foreach, and doMC packages are required
  - specific examples are not yet documented, but should be soon
  - this feature is still experimental! testing is advised
* profile_compare() now calculates slice-wise dissimilarity matrices in 1/3 the time (thanks llply!)

-------------------------- aqp 0.98-4 (2010-12-15) --------------------------
* fixed minor bug in soil.slot() when computing probabilities from profiles that had
  missing horizons and that had only a single class within the variable to be aggregated

-------------------------- aqp 0.98-1 (2010-11-23) --------------------------
* added basic demo: demo(aqp)
* soil.slot() now computes aggregate probabilities over user-defined segments
* re-write of weighted profile aggregation functions
  - aqp package now requires Hmisc package
  - using Hmisc::wtd.{mean,var,quantile} to compute values
	+ better adjustment of weights when computing weighted SD
	+ fixes long-standing bugs with wt. mean/SD when NA present in x_i and not in wt_i
	+ weighted quantiles now computed
* addition of new (experimental) S4 classes and methods
  - these are now in the aqp_S4 branch
* added n.depth.ticks option to profile_plot()
* profile_compare() algorithm stabilized, new default settings
* removed code in profile_compare() that is now obsolete
  - note that this will cause changes to numerical classification of soil profiles

-------------------------- aqp 0.97-1 (2010-10-06) --------------------------
* verified that weighted standard deviations are correct when seg_size > 1
* removed notices about possible problems with sd calculations

-------------------------- aqp 0.97 (2010-09-22) --------------------------
* soil.slot() streamlined and functionality restored to pre-0.95 condition

-------------------------- aqp 0.96-1 (2010-09-21) --------------------------
* fixed weighted mean / SD calculation when using 1 unit segments in soil.slot()
  - wt. mean / SD still disabled for user-defined segment sizes

-------------------------- aqp 0.96 (2010-09-20) --------------------------
* temporarily disabled parallel computation, will be re-added in next release
* bug fixes in panel.depth_function where 'groups' was not defined
* bug fixes and major re-factoring of soil.slot() when called with user-defined 
  segment size, or segmenting vector:
  - SD values are probably too low due to an inflated 'n' in the calculation
  - calculation of weighted mean and sd is currently disabled

-------------------------- aqp 0.95 (2010-09-15) --------------------------
* added VERY experimental support for parallel processing based on the latest versions
  of plyr, doMC, and foreach packages
* updated vignette with technical details on aggregation and dissimilarity computation
* new options to profile_plot()

-------------------------- aqp 0.94 (2010-08-11) --------------------------
* fixed bug in soil.slot() when aggregating a categorical variable,
  with a user-supplied segmenting vector
* soil.slot() now requires that categorical variables be encoded as factors

-------------------------- aqp 0.93 (2010-08-07) --------------------------
* bug fixes, new documentation + examples
* AQP now requires R >= 2.9.0

-------------------------- aqp 0.92 (2010-08-03) --------------------------
* including a new column in the results from soil.slot(), 
  denoting number of profiles used in slice-wise aggregation
* added note to soil.slot() manual page highlighting possible problems with SD calculation

-------------------------- aqp 0.90 (2010-07-13) --------------------------
* better error checking on profile aggregation and classification functions
* most functions now require that horizon depths are integers

-------------------------- aqp 0.89 (2010-07-10) --------------------------
* added plot_distance_graph() function for visualizing between-profile dissimilarity
* updated documentation: extended manual is now accessible as a vignette
* major improvements in profile_compare() when add_soil_flag=TRUE and replace_na=TRUE
| appears to create much more realistic groupings when there are both shallow and
| deep soils in the collection
+---> new functionality requires further testing
* plotting under dendrograms generated by ape::plot.phylo() may need some manual adjustments


-------------------------- aqp 0.88 (2010-07-06) --------------------------
* new version of plyr (1.0) should speed up most functions in aqp pacakge 
* added support for user-defined aggregate functions in soil.slot and soil.slot.multiple
* planning addition of PCA by depth slice
* planning addition of equal-area spline fitting