https://github.com/cran/aqp
Tip revision: 3727c188ec3b3848f8bb92891329087548ee60b0 authored by Dylan Beaudette on 18 January 2011, 00:00:00 UTC
version 0.99-9.51
version 0.99-9.51
Tip revision: 3727c18
NEWS
-------------------------- aqp 0.99-9.4 (2012-01-12) --------------------------
* 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