-------------------------- 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