aqp 2.0

This is an abbreviated version of the "What is new in aqp 2.0?" vignette. Many thanks to @brownag, @smroecker, @pierreroudier, @jskovlin, @jjmaynard, and all of the other contributors to this version of aqp.

This is a major update to aqp that may create some issues for code depending on specific inputs/outputs in aqp < 1.42, particularly those relying on slice(), slab(), and profile_compare(). slice() and profile_compare() are now deprecated, but will continue to work for the rest of calendar year 2023. There are no plans to maintain these functions beyond aqp 2.0. The new version of slab() is a drop-in replacement for the previous version of the function.

New Vignettes:

• Numerical Classification of Soil Profiles
• Overlapping Annotation

Notable changes include:

• deprecation of slice() in favor of the new, faster, more robust implementation in dice()
• complete overhaul of slab(), with new arguments, faster back-end, and weighted aggregation implemented (finally)
• deprecation of profile_compare() in favor of the NCSP()--a complete overhaul based on Maynard et al., 2020
  • site level attributes now handled by compareSites()
  • variable weights now possible via argument
• perturb() and estimatePSCS() are now vectorized, and optimized for larger collections
• mixMunsell() now uses mixingMethod = 'exact' by default for the simulation of subtractive mixtures
• gower package moved to SUGGESTS
• plotColorMixture() now using grid graphics functions to determine color swatch geometry and setting overlap detection threshold
• removal of PMS2Munsell() and support data
• deprecation of coordinates()<- and proj4string()<- in favor of initSpatial()<-
• removal of rruff.sample example XRD patterns
• get.ml.hz() no longer uses the name argument

Major changes to plotSPC():

• The maximum depth range of the figure is now based on max.depth or max(x). This means that sketches generated with aqp 2.x will generally have less white space at the bottom of the figure. Make more room for additional annotation or visual effect by setting the desired depth range with the max.depth argument.
• now uses electroStatics_1D() for fixing horizon depth label overlap, solutions are deterministic and almost always better
• better depth axis interval heuristics (if not specified), varying based on figure depth range
• depth axis adjustments via new argument depth.axis, logical or list
• deprecation of arguments:
  • plot.depth.axis: set via depth.axis = TRUE, depth.axis = FALSE, or customize depth.axis = list(...)
  • cex.depth.axis: set via depth.axis = list(cex = 1)
  • axis.line.offset: set via depth.axis = list(line = -2)

New features:

• example data, wilson2022
• fast prototyping of SPCs via quickSPC() and list / character templates
• re-use arguments to plotSPC() via options(.aqp.plotSPC.args = list(...))
• coarse fragment classification via fragmentSieve() and fragmentClasses()
• S4 as.data.frame(<SPC>) as shorthand for as(<SPC>, 'data.frame')
• plotSPC() now marks truncated profiles with a ragged bottom
• fixOverlap() now has two label-placement solvers, based on 1) electrostatics and 2) simulated annealing
• new depth axis styles in plotSPC()

Incremental changes, should have no effect on previous code:

• bug fix in plotSPC() when fixLabelCollisions = TRUE, adjustments suggested to fixOverlap() are now scaled correctly
• explainPlotSPC() reports label adjustment index when label collision repair is enabled
• aesthetic cleanup in explainPlotSPC()
• soilColorSignature() gains arguments and perceptual color distances (dE00) via farver package
• as(<SPC>, "data.frame"): Replace plyr::join() with merge()
• correctAWC(): NA handling - return NA when frags are NA
• mutate_profile(): Faster (data.table-based) evaluation of profile-level expressions (#255)
• profileApply: Add support for custom lapply()-like function (APPLY.FUN) for processing chunks (#256)
• Add .interpretHorizonColor() outputs to last_spc_plot in aqp.env for use in custom legend() (#254)
• Add simplify argument to SoilTextureLevels() and ssc_to_texcl() to optionally convert to an ordered factor with maximum of 12 levels (rather than 21). This smaller list of classes excludes sand grain size variants such as fine sand, loamy coarse sand, and very fine sandy loam.