What is new in aqp 2.x?

This is a major update to {aqp} that may create some issues for code depending on specific inputs/outputs as of {aqp} <= 1.42, particularly those relying on slice(), slab(), and profile_compare(). As of {aqp} 2.0, slice() and profile_compare() are 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.

See the manual pages for dice(), NCSP(), and slab(). Note that these new / updated functions perform stricter tests for horizon depth logic errors. Messages and warnings are issued when invalid depth logic is reported by checkHzDepthLogic(). New functions accumulateDepths(), repairMissingHzDepths(), and fillHzGaps() can usually salvage problematic profiles.

The replace_na and add_soil_flag arguments to profile_compare() are not present in NCSP(); missing data are always replaced by maximum dissimilarity (1 when Gower’s distance metric is used) and the soil/non-soil matrix is always used to compare profiles of different depth.

Notable Changes

  • Deprecation of slice() in favor of the new, faster, more robust implementation via dice(). Be sure to update existing code to use dice() from now on. Some argument names have changed.
  • Complete overhaul of slab() (thanks to @brownag), with new arguments, faster back-end, and weighted aggregation implemented (finally).
  • Deprecation of profile_compare() in favor of the new NCSP() function–a complete overhaul based on Maynard et al., 2020. Note that:
    • site level attributes are now handled by compareSites()
    • variable weights are specified by argument
  • The functions perturb() and estimatePSCS() are now vectorized, and optimized for larger SoilProfileCollection objects.
  • mixMunsell() now uses mixingMethod = 'exact' by default for the simulation of subtractive color mixtures
  • gower package moved to SUGGESTS
  • plotColorMixture() now using grid graphics functions to determine color swatch geometry and setting overlap detection threshold
  • Deprecation of rgb2munsell() in favor of the more general col2Munsell()
  • 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 using the electroStatics_1D() method for fixing horizon depth label overlap, solutions are deterministic and almost always better. Adjust label overlap adjustment strategy with fixOverlapArgs = list(...).
  • 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

  • New example data, wilson2022.
  • Fast prototyping of SoilProfileCollection objects via quickSPC() and list / character templates.
  • Re-use arguments to plotSPC() via setting options(.aqp.plotSPC.args = list(...)). Set to options(.aqp.plotSPC.args = NULL) to disable.
  • 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:
    • electrostatic simulation (method = "E")
    • simulated annealing (method = "S")
  • New depth axis styles in plotSPC().
  • New function flagOverlappingHz() for identifying horizons with perfect overlap
  • New function warpHorizons() for warping horizon thickness (inflate/deflate)
  • simulateColor() adds multivariate simulation in CIELAB colorspace

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.
  • profileApply: Add support for custom lapply()-like function (APPLY.FUN) for processing chunks.
  • Add .interpretHorizonColor() outputs to last_spc_plot in aqp.env for use in custom legend().
  • 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.
  • Major updates to profileInformationIndex() methods and performance boost.
  • Enhancements to evalMissingData().