aqp 1.19 (2020-01-22)

CRAN release
new functions: hzDesgn(), get horizon designations from a SPC
new functions: hzdesgnname()/hzdesgnname()<- and hztexclname()/hztexclname()<- get/set column containing horizon designations and texture classes
better error/logic handling for glom()

aqp 1.18.5 (2020-01-21)

profileApply() enhancement for large SoilProfileCollection objects (https://github.com/ncss-tech/aqp/issues/112)
add profileApply() frameify argument for data.frame output (https://github.com/ncss-tech/aqp/issues/111)
checkHzDepthLogic() replaces test_hz_logic()
thanks to farver >= 2.0.3, rgb2munsell() and colorQuantiles() now uses the CIE2000 distance metric for color comparison

aqp 1.18.4 (2020-01-06)

bug fix (rare) when setting / replacing horizon attributes (https://github.com/ncss-tech/aqp/issues/105)
bug fix in colorQuantiles until farver 2.0.2 is available on CRAN
SoilProfileCollection object gains new slot: @restrictions, fix old objects with rebuildSPC()

aqp 1.18.3 (2019-12-19)

evalMissingData() gets new argument for relative vs. absolute evalulation of missing data
horizonColorIndices(), harden.rubification(), harden.melanization(), thompson.bell.darkness() and associated functions in soilColorIndices.R
fix for https://github.com/ncss-tech/aqp/issues/44
fix for https://github.com/ncss-tech/aqp/issues/66
new example data: rowley2019
dropped some dependencies

aqp 1.17.10 (2019-10-30)

removing imported functions from Hmisc (hdquantile), loading aqp is now much faster
- slab() now uses stats::quantile() as the default slab function
- details at: https://github.com/ncss-tech/aqp/issues/79
- previous behavior of slab() can be activated via argument: slab.fun = aqp:::.slab.fun.numeric.HD

aqp 1.17.08 (2019-10-03)

generalize.hz() gets a argument for passing additional arguments to grep(), e.g. perl=TRUE
addVolumeFraction() can now accept a vector of colors, as many as number of horizons
new sample data: jacobs2000, pending documentation
aggregateColor() faster and more accuracte, using delta-E00 for quantized colors c/o {farver} (see https://github.com/ncss-tech/aqp/issues/98)
new functions contrastChart() and soilPalette()
aqp 1.18 scheduled for next CRAN release

aqp 1.17.06 (2019-07-15)

plotSPC() gains a new argument for relative positioning: relative.pos
relative positioning helper function: fixOverlap(), see manual page for examples
explainPlotSPC(), addDiagnosticBracket(), and addVolumeFraction() updated accordingly

aqp 1.17.05 (2019-05-18)

new functions colorContrast(), contrastClass(), and huePosition()

aqp 1.17.02 (2019-03-15)

fixed nasty bug in [-indexing when SPC contains a single profile (https://github.com/ncss-tech/aqp/issues/85)
new function validSpatialData() to test for place-holder contents of @sp
rebuildSPC() will now correct invalid, place-holder SpatialPoints in @sp

aqp 1.17.01 (2019-02-07)

new version number system
plotSPC() will now attempt to create multi-row legends when using a factor > n.legend levels
plotSPC() will now generate > 10 colors for legends associated with a factor (https://github.com/ncss-tech/aqp/issues/9)
munsell2rgb() will now return CIE LAB coordinates if requested (https://github.com/ncss-tech/aqp/issues/69)

aqp 1.17 (2018-12-28)

CRAN release
aggregateColor() gets a new feature, similar colors can be grouped via cluster::pam()
new functions: previewColors(), colorQuantiles(), plotColorQuantiles()
new function: horizonDepths()<-, edit top/bottom names after SPC init
new function: profile_id()<-, edit profile IDs after init; be careful!
new functions: hzID() and hzID()<-, get/set unique horizon IDs
new functions: hzidname() and hzidname()<-, get/set column containing unique horizon IDs
rbind.SoilProfileCollection() has been deprecated in favor of union(), gains new functionality: https://github.com/ncss-tech/aqp/issues/71
bug fixes in sanity checks within horizonNames()<-
!!! SoilProfileCollection internal structure has changed: https://github.com/ncss-tech/aqp/issues/74
see release notes for more: https://github.com/ncss-tech/aqp/releases/tag/v1.17

aqp 1.16-6 (2018-12-12)

partial bug fix in test_hz_logic() related to missing top AND bottom depths, needs work: https://github.com/ncss-tech/aqp/issues/65

aqp 1.16-5 (2018-11-21)

moved explainPlotSPC from SPC tutorial to aqp::explainPlotSPC()
plotSPC() is a little better at estimating “extra” vetical / horizontal space, still needs work (https://github.com/ncss-tech/aqp/issues/62)

aqp 1.16-2 (2018-05-22)

fixing #53 and #54
bug fix for too many decimal places in legend classes (floating point -> character issue)
plotSPC() gets a new argument, n.legend: approximate number of classes

aqp 1.15.5 (2018-03-14)

enhancement to aggregateColor() for cases when horizon depths are missing or top/bottom logic flipped

aqp 1.15.4 (2018-01-29)

bug fix for addVolumeFraction() when fragment volume > 100%

aqp 1.15.3 (2018-01-24)

added a new argument to addDiagnosticBracket() allowing for specification of column containing diagnostic feature kind
addBracket() now requires a data.frame with plotting details, see manual page

aqp 1.15.2 (2017-11-30)

added shannonEntropy(), confusionIndex(), and brierScore()
bug fix in get.ml.hz() for horizon names that start with number or punctuation
get.ml.hz() now uses internal aqp functions for Shannon entropy and Brier scores

aqp 1.15 (2017-11-11)

push to CRAN, getting ready for aqp 2.0

aqp 1.14 (2017-09-19)

missingDataGrid() relaxing slice() with strict=FALSE

aqp 1.12 (2017-07-05)

CIELAB colors are now in the munsell look-up table

aqp 1.12 (2017-07-05)

plotSPC() now able to deal with missing horizon data (thanks Stephen R.)
this is likely the last release before aqp 2.0

aqp 1.11 (2017-06-13)

rgb2munsell() now uses CIELAB colorspace for lookup, results are more accurate as compared to using sRGB colorspace

aqp 1.10-4 (2017-05-02)

texture.triangle.low.rv.high() renamed to textureTriangleSummary(). The old name still works, but a message is issued
new argument to textureTriangleSummary() texture.names: for toggling texture class names
minor bug fix in textureTriangleSummary(…, sim=TRUE), previous simulated compositional data was not correct because the stats::var() was being used vs. compositions::var.acomp(). the variance / covariance values were 2-5x too small.
new function tauW(), addd by D.G. Rossiter: see manual page for references

aqp 1.10 (2017-01-05)

fixed major bug (https://github.com/ncss-tech/aqp/issues/23) related to editing horizon-level attributes after rbind-ing

aqp 1.9.13 (2016-10-20)

new dataset soil_minerals with some common soil mineral colors source: http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054286
added clarification to Munsell color conversion: changed “RGB” to “sRGB”.

aqp 1.9.10 (2016-07-01)

new function for estimating the closest Munsell chip: getClosestMunsellChip()
new example data set (sp6) based on http://www.sciencedirect.com/science/article/pii/S0016706111001972

aqp 1.9.8 (2016-03-07)

munsell2rgb() can now accommodate neutral hues (N), and values of “2.5”, see manual page for details

aqp 1.9.7 (2016-02-25)

new function: soilColorSignature(), see manual page
new function: parseMunsell() for converting strings of ‘10YR 2/2’ into R colors or RGB triplets
- this is a convenience function that calls munsell2rgb on parsed strings of full Munsell notation

aqp 1.9.6 (2016-02-23)

minor changes to profile_compare(), getting ready for a complete overhaul to this function
new function: evalMissingData(), see manual page

aqp 1.9.5 (2015-12-28)

documentation for new transition probability functions, see ?hzTransitionProbabilities for details

aqp 1.9.4 (2015-12-22)

better checking for other places where the bug fixed in rbind.SoilProfileCollection (aqp 1.9.3) could occur
new functions: genhzTableToAdjMat, hzTransitionProbabilities

aqp 1.9.3 (2015-12-18)

fixed a nasty bug in rbind.SoilProfileCollection() related to object re-ordering
- in aqp < 1.9.3: there was a chance than profile_id(x) and site(x)[[idname(x)]]) would not match
- bugs like this will no longer be a possibility after aqp 2.0, new SPC object structure planned

aqp 1.9.1 (2015-11-18)

groupedProfilePlot() gains some new arguments and better documentation (see manual page)
plot.SoilProfileCollection gains argument: default.color (see manual page)

aqp 1.9 (2015-08-26)

added neutral colors to munsell2rgb()
new function guessGenHzLevels()
new function aggregateColor() and associated helper function sharpshootR::aggregateColorPlot()
more code clean-up and fixes in examples to make R CMD check --as-cran happy
fixed some ancient examples in the profileApply() manual page

aqp 1.8-5 (2015-04-17)

bug fixes and documentation updates
digest::digest is now imported by default
better documentation for unique-method of SoilProfileCollection objects

aqp 1.8-3 (2015-03-02)

updated documentation
plotSPC gets a new argument: x.idx.offset: allows for plotting of multiple SPC objects within the same figure, see examples
plotSCP gets a new argument: plot.depth.axis: enable / disable depth axis, useful for multi-collection plots
new function: profileGroupLabels: simple annotation for groups of profiles within a profile sketch, see manual page for examples
new function: plotMultipleSPC: plot several SPC objects on the same axis, see manual page for examples

aqp 1.7-11 (2015-01-30)

fixed bugs in addBrackets(), panel.depth_function(), and plotSPC()
new arguments to addBrackets() allow for annotation of brackets

aqp 1.7-10 (2015-01-15)

names() method for SoilProfileCollection objects returns a concatenated vector of horizon + site names
siteNames() and horizonNames() can now be used to extract from SoilProfileCollection
siteNames<- and horizonNames<- can now be used to change names; experimental!
note: internal structure of SoilProfileCollection objects will be changing soon!!!

aqp 1.7-8 (2014-12-08)

texture.triangle.low.rv.high(): new arguments, likely breaking previous usage when method=‘closest’, see manual page for details

aqp 1.7-7 (2014-11-06)

bug fix c/o Jos? 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 Jos? 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 plotSPC
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