An Overview of the aqp Package

Soil morphology, observed properties, and geomorphic context represent a complex package of interrelated information that can be difficult to analyze and communicate as a whole. Graphical methods such as soil profile sketches and cross-sections represent a few of the possible methods commonly used to report on these kind of data. The Algorithms for Quantitative Pedology (AQP) project encompasses several related R packages tailored to this style of work. A specialized data structure (SoilProfileCollection) maintains linkages between soil horizons, diagnostic features, above-ground data, and geomorphic context. SoilProfileCollection objects can be filtered, subset, resampled (over new depth intervals), and re-ordered; all while preserving links to above and below-ground, linked data. Functions are provided for the conversion of soil colors to and from Munsell notation and several other color space coordinates. Graphical methods for the SoilProfileCollection provide a simple but flexible framework for the design and layout of soil profile sketches, aligned to x and or y axes defined by linked data.

Function Index by Topic

SoilProfileCollection Objects

Creation

  • depths(): init an SPC from data.frame
  • site(): set or add site-level attributes of an SPC
  • quickSPC(): quickly build an SPC from simple text templates
  • random_profile(): generate random SPC from suite of depth functions

Metadata

  • hzdesgnname(): get/set column containing horizon designations
  • hzDesgn(): get vector of horizon designations
  • hztexclname(): get/set column containing horizon texture class
  • metadata(): get/set SPC metadata (list)
  • hzID(): get vector of horizon IDs
  • hzidname(): get/set column containing horizon IDs
  • horizonDepths() get/set columns containing horizon top and bottom depths

Properties

  • length(): number of profiles in a SPC
  • nrow(): number of horizons in a SPC
  • names(): list of horizon and site names
  • siteNames(): site-level column names
  • horizonNames(): horizon-level column names

Subset

  • glom(): extract horizons based on overlap criteria defined by point or interval
  • trunc(): truncate SPC to given depth interval
  • subset(): subset profiles based on logical expressions
  • subsetHz(): subset horizons based on logical expressions
  • [: data.frame-like subsetting of profiles (i-index) and/or horizons (j-index)
  • [[: access site or horizon-level columns by name
  • k-index expressions: .FIRST, .LAST, .HZID, .NHZ

Depth

  • min(): minimum bottom depth within a SPC
  • max(): maximum bottom depth within a SPC
  • depthOf(): generalized “depth to” based on REGEX matching
  • minDepthOf(): special case of depthOf()
  • maxDepthOf(): special case of depthOf()
  • getSoilDepthClass(): estimate soil depth based on REGEX matching applied to horizon designation and associated depth class
  • aggregateSoilDepth(): statistical estimation of soil depth (REGEX matching of horizon designation) within groups of profiles

Utility

  • combine(), c(): combine multiple SPCs into a single SPC
  • duplicate(): duplicate profiles within a SPC
  • perturb(): randomly adjust horizon thickness or depths to simulate from a template SPC
  • warpHorizons(): expand / contract horizon thickness
  • harmonize(): create new profiles within a SPC based sets of related horizon-level data
  • hzAbove(), hzBelow(): locate horizons above or below some criteria
  • unique(): determine uniqueness among profiles of an SPC via MD5 hash
  • split(): split SPC into list of SPCs based on grouping factor
  • site(): get site data as data.frame
  • horizons(): get horizon data as data.frame
  • replaceHorizons(): replace horizon data
  • diagnostic_hz(): get/set diagnostic features
  • restrictions(): get/set restrictions
  • denormalize(): convert site-level data into horizon-level data via replication
  • compositeSPC(): downgrade an SPC to list of site and horizon-level data

Iteration

  • profileApply(): apply a function to each profile within an SPC (slow but simple interface)
  • summarizeSPC(): perform group-wise summaries over profiles within an SPC
  • transform(): modify a SPC using expressions that operation on site or horizon-level data

Change of Support

  • dice(): convert SPC to 1 depth-unit intervals by replication
  • slab(): apply an aggregate function over groups within a “dice()-ed” SPC
  • spc2mpspline(): interface to equal-area spline fitting from mpspline2 package
  • segment(): generate segment labels for depth-weighted aggregation
  • L1_profiles(): create representative profiles via multivariate median (L1 estimator)
  • slicedHSD(): apply Tukey’s HSD over groups within a “dice()-ed” SPC

Horizon Depth Logic

  • accumulateDepths(): fix horizon depths when old-style O horizon notation has been used
  • fillHzGaps(): fill topological gaps in horizon depth
  • repairMissingHzDepths(): attempt fixing missing or duplicated horizon bottom depths
  • flagOverlappingHz(): flag horizons with perfect overlap
  • checkHzDepthLogic(): apply battery of horizon depth topological tests
  • splitLogicErrors(): split an SPC according to variety of possibly horizon depth errors
  • HzDepthLogicSubset(): remove profiles from an SPC if any depth logic errors are present

Data QC

  • evalMissingData(): report metrics of missing data by profile within SPC
  • missingDataGrid(): visual indication of missing data
  • profileInformationIndex(): experimental indices of “information content” by profile

Object Coercion

  • as(SPC, 'list'): convert SPC to list
  • as(SPC, 'data.frame'): convert site and horizon data to data.frame
  • as(SPC, 'sf'): convert site and spatial data to sf object

Spatial Data

  • prj(): get/set coordinate reference system (CRS) metadata
  • initSpatial(): set (site-level) column names containing coordinates
  • getSpatial(): get spatial data (site + coordinates) from an SPC

Internal Consistency

  • checkSPC(): check SPC for internal consistency
  • rebuildSPC(): re-make an SPC from a previous version of aqp (rarely required)

Soil Profile Sketches

Soil Color / Color Science

Color Conversion

  • col2Munsell(): convert various color notations to Munsell notation
  • munsell2rgb(): convert Munsell notation to sRGB or CIELAB color coordinates
  • parseMunsell(): parse and optionally convert a munsell color
  • spec2Munsell(): estimate the closest Munsell color given reflectance spectra in the visible range
  • getClosestMunsellChip(): estimate a reasonably close Munsell color given non-standard notation
  • estimateSoilColor(): estimate moist soil color from dry soil color (and vice versa)

Comparison

  • colorContrast(): pair-wise color contrast and CIE2000 (dE00) based on colors in Munsell notation
  • colorContrastPlot(): visual explanation of soil color contrast and dE00
  • contrastChart(): Munsell color book style explanation of soil color contrast and dE00
  • soilColorSignature(): derive soil color signatures for profiles within an SPC

Aggregation

  • colorChart(): Munsell color book representation of color frequency
  • aggregateColor(): estimate color proportions within an SPC according within groups of horizons
  • colorQuantiles(): marginal and L1 quantiles of color in CIELAB coordinates

Utility

  • huePosition(): generate an ordered factor of the standard Munsell hues
  • huePositionCircle(): graphical representation of the standard Munsell hues, with optional simulation of common color vision deficiency
  • simulateColor(): simulate a range of Munsell colors given measures of central tendency and spread
  • previewColors(): graphical preview of colors as a grid or via nMDS
  • soilPalette(): generate swatch-like arrangements of colors and labels
  • equivalentMunsellChips(): for a specified Munsell color, identify other Munsell colors with a very lower CIE2000 color contrast difference

Simulation of Mixtures

  • mixMunsell(): simulate an subtractive mixture of pigments specified in Munsell notation
  • plotColorMixture(): simulate a subtractive mixture of pigments, display reflectance spectra

Numerical Classification of Soil Profiles

Pedology

Soil Texture

  • textureTriangleSummary(): graphical summary of sand, silt, clay fractions on a soil texture triangle
  • bootstrapSoilTexture(): simulation of realistic compositions (sand, silt, clay) from a small set of example data
  • SoilTextureLevels(): ordered factor of soil texture classes
  • texcl_to_ssc(): convert soil texture classes to sand, silt, clay centroids
  • ssc_to_texcl(): convert sand, silt, clay values to soil texture class
  • texture_to_taxpartsize(): convert soil texture to Soil Taxonomy particle size class

Coarse Fragments

  • fragmentSieve(): classify coarse fragments by fragment diameter
  • texmod_to_fragvoltot(): estimate ranges in coarse fragment volume based on a soil texture modifier
  • texture_to_texmod()
  • fragvol_to_texmod()
  • fragmentClasses(): coarse fragment diameter thresholds used by USDA-NRCS

Soil Taxonomy

  • getArgillicBounds(): estimate the upper and lower boundaries of an argillic horizon
  • getCambicBounds(): estimate the upper and lower boundaries of a cambic horizon
  • getSurfaceHorizonDepth()
  • getMineralSoilSurfaceDepth()
  • getPlowLayerDepth()
  • hasDarkColors()
  • estimatePSCS()

Generalized Horizon Labels (GHL)

  • generalize.hz(): apply REGEX rules to group horizon designations into a reduced set of “generalized horizon labels”
  • evalGenHZ(): evaluate internal consistency of assigned GHL
  • genhzTableToAdjMat(): convert a cross-tabulation of GHL vs. original horizon designations to adjacency matrix
  • get.ml.hz(): extract most likely horizon boundary depths from probability depth functions
  • guessGenHzLevels(): estimate the correct ordering of GHL given horizon depths
  • GHL(): get/set GHL metadata for a SoilProfileCollection

Misc.

Accuracy and Uncertainty

  • shannonEntropy(): Shannon entropy
  • brierScore(): Brier’s score
  • tauW(): weighted tau statistic

Overlapping Annotation

  • findOverlap(): identify overlap within a vector of positions based on a given threshold
  • overlapMetrics(): metrics of overlap within a vector or positions based on a given threshold
  • fixOverlap(): attempt the minimum of adjustments to vector of positions such that a given distance threshold is enforced

Example Data