News
-------------------------- 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) ------------------------
-------------------------- 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) ------------------------
- CIE LAB 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 rbinding
-------------------------- aqp 1.9.13 (2016-10-20) --------------------------
-------------------------- aqp 1.9.10 (2016-07-01) --------------------------
-------------------------- 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:
- 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) --------------------------
-------------------------- 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 [email protected] 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()
- 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