-------------------------- aqp 1.7-7 (2014-11-06) --------------------------
* bug fix c/o José Padarian: SPC objects now understand logical indexing rules
* removed spatial_subset(): this functionality can be accomplished outside of AQP and removes dependency on rgeos package

-------------------------- aqp 1.7-6 (2014-09-26) --------------------------
* bug fix c/o José Padarian: when promoting coordiantes from @site, drop=FALSE is required to prevent a single remaining attribute from being down-graded to a vector-- thanks!
* get.ml.hz() now returns a "pseudo" Brier Score, using the most-likely horizon label as the "correct" value
* new function rgb2munsell()
* new function estimateSoilDepth()
* new function getSoilDepthClass()
* new documentation / tutorials

-------------------------- aqp 1.6-4 (2014-02-14) --------------------------
* When applied to a single categorical variable, the results from slab() now contain an attribute 'original.levels'
  that contains the original factor levels. This is important because when casting from long->wide format, illegal
  column names are scrubbed by make.names(). This process would convert horizon designations like '2Bt' into 'X2Bt'.
  You can recover the original horizon names via attr(x, 'original.levels').

-------------------------- aqp 1.6-3 (2014-02-04) --------------------------
* plotSPC() has a new argument: `label`, used to set site-level attribute containing profile labels

-------------------------- aqp 1.6-2 (2014-01-10) --------------------------
* plotSPC() now registers plotting parameters in the environment aqp.env
* new function addVolumeFraction() for annotating profile plots with volumetric information (e.g. rock fragment volume)

-------------------------- aqp 1.6-1 (2013-12-31) --------------------------
* plotSPC() attempts to guess which column contains horizon designations
* plotSPC() can now color horizons based on continuous soil properties (e.g. clay content)

-------------------------- aqp 1.6 (2013-12-11) --------------------------
* rbind.SoilProfileCollection() now re-orders data according to the new set of profile IDs
  - this fixes several probles associated with assumptions in profile_compare()
* profile_compare() will be re-written soon to work natively with SPC objects

-------------------------- aqp 1.5-6 (2013-11-25) --------------------------
* new function addBracket() for annotating profile sketches with depth-brackets; useful for plotting diagnostic features

-------------------------- aqp 1.5-6 (2013-11-15) --------------------------
* new function missingDataGrid() for graphically describing the presence of missing data in an SPC object

-------------------------- aqp 1.5-2 (2013-04-09) --------------------------
* panel.depth_function() now prints "contributing fraction" values in the same color as corresponding depth-function lines and shaded areas
* panel.depth_function() gains an argument 'cf.col' for manually specifying the CF color
* panel.depth_function() gains an argument 'cf.interval' for manually specifying printed CF depths
* prepanel.depth_function() now extends x-lim by 5% in either direction for cleaner-looking plots
* added some details to slab() documentation
* fixed minor bug in min() and max() methods for SoilProfileCollection objects in the presence of missing data
* min() and max() methods for SoilProfileCollection objects now have a second argument for checking depth based on the presence of data in that column

-------------------------- aqp 1.5-1 (2013-03-07) --------------------------
* removed excessive checking in SoilProfileCollection init code, this may speed things up
  - previously identified horizonation errors may no longer result in ERRORS; be sure to test
* test_hz_logic() now more useful:
  - always checks for NA and overlapping horizons
  - no longer called with initialization of SoilProfileCollection objects
  - note that default behavior has changed since version 1.5
  - moved related documentation to test_hz_logic manual page
* new mini-vignette on dealing with bad data (dealing-with-bad-data.html)
* better documentation for slice()
* new warnings related to missing data in the grouping variable passed to slab()

-------------------------- aqp 1.5 (2013-02-24) --------------------------
* profileApply() can now return arbitrary objects = new subsetting/transformation possibilities
  - see ?profileApply for examples
* panel.depth_function() can now display contributing fraction values with grouped data
  - see multi-variate example in ?slab

-------------------------- aqp 1.4-7 (2013-01-24) --------------------------
* HTML version of all documentation (including images) auto-generated via knitr and available on the r-forge website
* new function: texture.triangle.low.rv.high() plots texture data with low-high range defined by quantiles

-------------------------- aqp 1.4-6 (2013-01-03) --------------------------
* updated documentation and SoilProfileCollection tutorial here:
  - https://r-forge.r-project.org/scm/viewvc.php/*checkout*/docs/aqp/aqp-intro.html?root=aqp
* plans laid for parallel processing in slab() and profileApply() via 'parallel' package
* plotSPC() gets a 'density' argument for shaded coloring of horizons

-------------------------- aqp 1.4-5 (2012-12-29) --------------------------
* slab() re-written from scratch, resulting in reduced memory footprint and quicker running time
  ! older code based on slab() is likely to now broken- sorry, it won't happen again
  - the new code is much slimmer and based on aggregate() rather than ddply
  - function arguments have changed so be sure to check the manual page
  - user-supplied functions are now much simpler to write and rely on vectors rather than data.frames (= faster)
  - the next major release will contain additional examples of how to use the new features

-------------------------- aqp 1.4 (2012-12-18) --------------------------
* new function sim() for simulation based on a template soil profile, proper documentation pending...

-------------------------- aqp 1.3-3 (2012-12-06) --------------------------
* new function subsetProfiles() for simpler subsetting of SoilProfileCollection objects via site or horizon-level attributes
* get.ml.hz() now returns a 'confidence' for each horizon (as a percent)
* added experimental 'filter' argument to profile_compare()-- see manual page for usage
* added new argument to plot.SoilProfileCollection()-- alt.label: used to add secondary labeling via data in @site
* plot.SoilProfileCollection() will now do a better job of selecting the location for profile IDs based on label length, font size, and figure size

-------------------------- aqp 1.3-2 (2012-11-01) --------------------------
* minor tweaks to plot.SoilProfileCollection() for improved output with small/large size collections
* new function get.ml.hz() attempts to determine the most likely horizonation after slabbing
* fixed bug in profileApply() where further arguments to FUN weren't passed on to FUN
* missing data report from profile_compare() now only includes horizons with some data (e.g. Cr and R horizons are skipped)

-------------------------- aqp 1.3-1 (2012-10-17) --------------------------
* speed-bump in profileApply()
  - splitProfiles() function is no longer defined/used/needed
* bug fix in SoilProfileCollection subsetting via []
  - SoilProfiles with a single horizon confused subsetting in the presence of spatial data

-------------------------- aqp 1.3 (2012-10-07) --------------------------
* added rbind.SoilProfileCollection() for concatenating SPC objects
  - this function performs basic sanity checks, but cannot combine unlike objects

-------------------------- aqp 1.2-10 (2012-09-05) --------------------------
* fixed minor bug in prepanel.depth_function() where an error would occur when input data was all NA

-------------------------- aqp 1.2-9 (2012-08-31) --------------------------
* new 'unique' method for SoilProfileCollection objects, returns indices of unique profiles
* fixed bug in NAMESPACE that caused an error when 'sp' library wasn't loaded
* added another sanity check to 'site<-' for cases where duplicates occur in the source data set
* added some new documentation to package help page see 'help(aqp)' for details

-------------------------- aqp 1.2-8 (2012-08-28) --------------------------
* the names() method for SoilProfileCollection objects now returns a named list of horizon and site column names
* improved examples: see ?sp4 and ?ca630
* fixed minor bug related to subsetting a SoilProfileCollection object, followed by coercion to SpatialPointsDataFrame

-------------------------- aqp 1.2-7 (2012-08-23) --------------------------
* plot() method for SoilProfileCollection object no longer sets page margins, this will cause some figures to change
* added demo 'slope_effect_hz_thickness'

-------------------------- aqp 1.2-6 (2012-06-26) --------------------------
* fixed minor bug in panel.depth_function(): grouping + paneling ignored full suite of colors
* fixed minor bug in NAMESPACE
* minor bug fix in unroll(), was not previously respecting the max depth argument
* minor speed-bump and simplification of profile_compare()
* documentation updates
* added helper message related to profile_compare() stopping when any profile contains insufficient data
* profile_compare() now issues a notice when _some_ data are missing, leading to biased results
* slice() now computes the fraction of variables within a slice that are missing data
! bug introduced into slab() when use.wts=TRUE [should have a fix soon]

-------------------------- aqp 1.1 (2012-04-18) --------------------------
* merged documentation for soil.slot() and slab()
  - slab() should be used in all places where soil.slot() was used
  - soil.slot() will dissapear from the package NAMESPACE eventually, so don't use it directly!
* minor bug fix in panel.depth_function()
* cleanup of documentation and examples
* added horizon boundary distinctness code conversions and plotting functionality
  - see ?sp1 and ?random_profile for new examples

-------------------------- aqp 1.0-2 (2012-03-29) --------------------------
* More NAMESPACE cleaning

-------------------------- aqp 1.0-1 (2012-03-28) --------------------------
* Cleaned NAMESPACE and DESCRIPTION
* removed un-necessary dependencies
* join added to the plyr imports
* added scales to the Imports as well, and removed rescaler() in the code, repaced by scales::rescale
* hack in munsell2rgb to avoid the 'no visible binding for global variable 'munsell' at package R CMD check and make the whole thing more robust (using load and system.file rather than data(...)
* Dylan is now the only maintainer, as per Uwe request
* when using plyr **ply function, switched from using the .(foo) interface to "foo" - seems more foolproof

-------------------------- aqp 1.0 (2012-03-26) --------------------------
* 1.0 release, still missing condensed vignettes- should be ready soon
* see http://casoilresource.lawr.ucdavis.edu/drupal/taxonomy/term/56 for samples
* A small bug in profile_compare() was fixed, where slices were evaluated as 'soil' based on the bottom depth of the profile, and NOT on the presence of actual data. See ?profile_compare for details. This change will have a minor affect on profile comparisons in cases where Cr or R horizons (usually missing most characterization data) have been extended down to some arbitrary depth (usually 150 or 200 cm) AND a maximum depth of evaluation (max_d) was set beyond the actual depth of most profiles in the collection.

-------------------------- aqp 0.99-9.8 (2012-03-02) --------------------------
* profile_compare() will now use site-level attributes if input is a SoilProfileCollection
  - horizon / site level data currently weighted equally
  - NOTE: this feature is new, test-first!
* minor bug fixes in profile_compare() to remove spurious warnings
* better error check in slice()
* removed old code and documentation: format_slices() and plot_slices()

-------------------------- aqp 0.99-9.6 (2012-02-21) --------------------------
* spurious warnings from profile_compare() caused by daisy() now suppressed
  - warnings were generated when calling daisy() on a matrix of all NA
    which typically occured when using too-large a lower depth for evaluation of D
* preliminary support for diagnostic horizons via diagnostic_hz()
* new examples
* error and warnings messages cleaned-up

-------------------------- aqp 0.99-9.52 (2012-01-31) --------------------------
* converting all messages passed to the user from cat() to message() and warning()
* profile_compare() and slab() now default to _no_ progress bars, see 'progress' argument to adjust
* profileApply() now provides access to all aspects of the SoilProfileCollection object
  - that means that:
    profileApply(SPC, function(x) ... ) 
    operates on x, which is a soilProfileCollection containing only profile_i
  !!! note that this may break functionality based on aqp 0.99-9.3

-------------------------- aqp 0.99-9.4 (2012-01-09) --------------------------
* `site(SCP) <- d` now tries to merge data from SPC@site with 'd' via left join
  - this means that all new SPC objects will have a single column of @site data, containin profile IDs
* plot-SoilProfileCollection now tries to guess the best orientation of IDs
  - override with id.style='top' or id.style='side'
* slice-SoilProfileCollection now accepts '.' to define all columns should be returned at requested slices
  - slice(SPC, 1:50 ~ . )   # this means all vars. ID, top, bottom are automatically removed

-------------------------- aqp 0.99-9.1 (2011-12-27) --------------------------
* pedonPC, NASIS, and SDA functions moved *out* of aqp, and *into* new package: soilDB
  - removed assocated, suggested packages from aqp
  - soilDB will be on CRAN shortly
* new argument to plot(SoilProfileCollection, ..., divide.hz=TRUE|FALSE) tha can optionally suppress 
  plotting of dividing lines between horizons (suggested by Ludwig Hilger)
* new function profileApply() for applying functions by profile

-------------------------- aqp 0.99-9 (2011-12-22) --------------------------
* almost ready for AQP 1.0, vignettes are the last missing piece :)
* slice(SPC, ...) is now 10-100x faster, scales linearly
* slice(SPC, ...) can simultaniously slice categorical and continuous variables
* converted ID column in sample data to character class
* fixed a bug in slice() where NA would be returned when IDs were factors
* added test to depths()<- such that factor IDs are converted into character IDs and a warning is issued
* added join conditions for most functions using plyr::join(), resulting in less chatter on the console 

-------------------------- aqp 0.99-8.58 (2011-12-21) --------------------------
* WARNING: soil.slot.multiple() renamed to slab()
* fixed minor bug in slice(), when numerical IDs are used: ddply() and cast() implicitly re-order data...
* added `strict` argument to many functions, to gracefully account for bad horizon data
  - enforce quality control with strict=TRUE
* munsell2rgb() is now 100x faster thanks to plyr::join()
  - note that factors cannot be used in the conversion, see: https://github.com/hadley/plyr/issues/43
    + there is a check and conversion within the function that should prevent segfaults
* documentation updates, demo(aqp) updates, more examples
* bug fix in slice(), now works with numeric OR categorical vars, but NOT both...
* matrix-style subsetting functional:
  - s[i, j] ---> i is the profile index, and j is the horizon/slice index
  - s[i, ] returns a SoilProfileCollection
  - s[, j] returns a SpatialPointsDataFrame when a single slice is used
* spatial_subset() can be used to extract members of a SoilProfileCollection with a geometry (uses rgeos)
* smarter $<- methods so that site/horizon data slots are auto-selected

-------------------------- aqp 0.99-8.50 (2011-11-29) --------------------------
* added "site(SoilProfileCollection) <-" method for data.frame
* 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