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.
depths(): init an SPC from data.framesite(): set or add site-level attributes of an
SPCquickSPC(): quickly build an SPC from simple text
templatesrandom_profile(): generate random SPC from suite of
depth functionshzdesgnname(): get/set column containing horizon
designationshzDesgn(): get vector of horizon designationshztexclname(): get/set column containing horizon
texture classmetadata(): get/set SPC metadata (list)hzID(): get vector of horizon IDshzidname(): get/set column containing horizon IDshorizonDepths() get/set columns containing horizon top
and bottom depthslength(): number of profiles in a SPCnrow(): number of horizons in a SPCnames(): list of horizon and site namessiteNames(): site-level column nameshorizonNames(): horizon-level column namesglom(): extract horizons based on overlap criteria
defined by point or intervaltrunc(): truncate SPC to given depth intervalsubset(): subset profiles based on logical
expressionssubsetHz(): 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 namek-index expressions: .FIRST,
.LAST, .HZID, .NHZmin(): minimum bottom depth within a SPCmax(): maximum bottom depth within a SPCdepthOf(): generalized “depth to” based on REGEX
matchingminDepthOf(): special case of
depthOf()maxDepthOf(): special case of
depthOf()getSoilDepthClass(): estimate soil depth based on REGEX
matching applied to horizon designation and associated depth classaggregateSoilDepth(): statistical estimation of soil
depth (REGEX matching of horizon designation) within groups of
profilescombine(), c(): combine multiple SPCs into
a single SPCduplicate(): duplicate profiles within a SPCperturb(): randomly adjust horizon thickness or depths
to simulate from a template SPCwarpHorizons(): expand / contract horizon
thicknessharmonize(): create new profiles within a SPC based
sets of related horizon-level datahzAbove(), hzBelow(): locate horizons
above or below some criteriaunique(): determine uniqueness among profiles of an SPC
via MD5 hashsplit(): split SPC into list of SPCs based on grouping
factorsite(): get site data as data.framehorizons(): get horizon data as
data.framereplaceHorizons(): replace horizon datadiagnostic_hz(): get/set diagnostic featuresrestrictions(): get/set restrictionsdenormalize(): convert site-level data into
horizon-level data via replicationcompositeSPC(): downgrade an SPC to list of site and
horizon-level dataprofileApply(): apply a function to each profile within
an SPC (slow but simple interface)summarizeSPC(): perform group-wise summaries over
profiles within an SPCtransform(): modify a SPC using expressions that
operation on site or horizon-level datadice(): convert SPC to 1 depth-unit intervals by
replicationslab(): apply an aggregate function over groups within
a “dice()-ed” SPCspc2mpspline(): interface to equal-area spline fitting
from mpspline2 packagesegment(): generate segment labels for depth-weighted
aggregationL1_profiles(): create representative profiles via
multivariate median (L1 estimator)slicedHSD(): apply Tukey’s HSD over groups within a
“dice()-ed” SPCaccumulateDepths(): fix horizon depths when old-style O
horizon notation has been usedfillHzGaps(): fill topological gaps in horizon
depthrepairMissingHzDepths(): attempt fixing missing or
duplicated horizon bottom depthsflagOverlappingHz(): flag horizons with perfect
overlapcheckHzDepthLogic(): apply battery of horizon depth
topological testssplitLogicErrors(): split an SPC according to variety
of possibly horizon depth errorsHzDepthLogicSubset(): remove profiles from an SPC if
any depth logic errors are presentevalMissingData(): report metrics of missing data by
profile within SPCmissingDataGrid(): visual indication of missing
dataprofileInformationIndex(): experimental indices of
“information content” by profileas(SPC, 'list'): convert SPC to listas(SPC, 'data.frame'): convert site and horizon data to
data.frameas(SPC, 'sf'): convert site and spatial data to sf
objectprj(): get/set coordinate reference system (CRS)
metadatainitSpatial(): set (site-level) column names containing
coordinatesgetSpatial(): get spatial data (site + coordinates)
from an SPCcheckSPC(): check SPC for internal consistencyrebuildSPC(): re-make an SPC from a previous version of
aqp (rarely required)plotSPC(): create sketches of soil profiles from an
SPCexplainPlotSPC(): explain various elements of a soil
profile sketchgroupedProfilePlot(): create grouped sketches of soil
profilesplotMultipleSPC(): create sketches from multiple,
possibly non-conformal SPCsaddBracket(): add vertical brackets beside soil profile
sketchesaddDiagnosticBracket(): add vertical brackets beside
soil profile sketches based on diagnostic featuresaddVolumeFraction(): add visual explanation of coarse
fragment volume to soil profile sketchesalignTransect(): align soil profiles to an external
gradient such as topographic sequencecol2Munsell(): convert various color notations to
Munsell notationmunsell2rgb(): convert Munsell notation to sRGB or
CIELAB color coordinatesparseMunsell(): parse and optionally convert a munsell
colorspec2Munsell(): estimate the closest Munsell color
given reflectance spectra in the visible rangegetClosestMunsellChip(): estimate a reasonably close
Munsell color given non-standard notationestimateSoilColor(): estimate moist soil color from dry
soil color (and vice versa)colorContrast(): pair-wise color contrast and CIE2000
(dE00) based on colors in Munsell notationcolorContrastPlot(): visual explanation of soil color
contrast and dE00contrastChart(): Munsell color book style explanation
of soil color contrast and dE00soilColorSignature(): derive soil color signatures for
profiles within an SPCcolorChart(): Munsell color book representation of
color frequencyaggregateColor(): estimate color proportions within an
SPC according within groups of horizonscolorQuantiles(): marginal and L1 quantiles of color in
CIELAB coordinateshuePosition(): generate an ordered factor of the
standard Munsell hueshuePositionCircle(): graphical representation of the
standard Munsell hues, with optional simulation of common color vision
deficiencysimulateColor(): simulate a range of Munsell colors
given measures of central tendency and spreadpreviewColors(): graphical preview of colors as a grid
or via nMDSsoilPalette(): generate swatch-like arrangements of
colors and labelsequivalentMunsellChips(): for a specified Munsell
color, identify other Munsell colors with a very lower CIE2000 color
contrast differencemixMunsell(): simulate an subtractive mixture of
pigments specified in Munsell notationplotColorMixture(): simulate a subtractive mixture of
pigments, display reflectance spectraNCSP(): numerical classification of soil profiles,
within a SoilProfileCollectioncompareSites(): pair-wise comparison of site-level data
from a SoilProfileCollectionallocate(): perform one of several classification
systems to soil property dataestimateAWC(): estimate plant-available water holding
capacitycorrectAWC(): apply rock fragment or soluble salt
corrections to AWC estimateshzDistinctnessCodeToOffset(): convert horizon boundary
distinctness codes to vertical offsethzTopographyCodeToLineType(): convert horizon boundary
topography codes to line typeshzTopographyCodeToOffset(): convert horizon boundary
topography codes to offsetph_to_rxnclass(): convert pH to reaction classrxnclass_to_ph(): convert reaction class to pH
rangeReactionClassLevels(): ordered factor of reaction
classeshorizonColorIndices(): compute various soil color-based
indices to horizons within an SPCtextureTriangleSummary(): graphical summary of sand,
silt, clay fractions on a soil texture trianglebootstrapSoilTexture(): simulation of realistic
compositions (sand, silt, clay) from a small set of example dataSoilTextureLevels(): ordered factor of soil texture
classestexcl_to_ssc(): convert soil texture classes to sand,
silt, clay centroidsssc_to_texcl(): convert sand, silt, clay values to soil
texture classtexture_to_taxpartsize(): convert soil texture to Soil
Taxonomy particle size classfragmentSieve(): classify coarse fragments by fragment
diametertexmod_to_fragvoltot(): estimate ranges in coarse
fragment volume based on a soil texture modifiertexture_to_texmod()fragvol_to_texmod()fragmentClasses(): coarse fragment diameter thresholds
used by USDA-NRCSgetArgillicBounds(): estimate the upper and lower
boundaries of an argillic horizongetCambicBounds(): estimate the upper and lower
boundaries of a cambic horizongetSurfaceHorizonDepth()getMineralSoilSurfaceDepth()getPlowLayerDepth()hasDarkColors()estimatePSCS()generalize.hz(): apply REGEX rules to group horizon
designations into a reduced set of “generalized horizon labels”evalGenHZ(): evaluate internal consistency of assigned
GHLgenhzTableToAdjMat(): convert a cross-tabulation of GHL
vs. original horizon designations to adjacency matrixget.ml.hz(): extract most likely horizon boundary
depths from probability depth functionsguessGenHzLevels(): estimate the correct ordering of
GHL given horizon depthsGHL(): get/set GHL metadata for a
SoilProfileCollectioninvertLabelColor(): automatic adjustment of label color
for maximum contrast, based on specified background colorhzTransitionProbabilities(): derive transition
probability matrix from horizon level datamostLikelyHzSequence(): use Markov Chains to predict
the most likely sequence of horizonsshannonEntropy(): Shannon entropybrierScore(): Brier’s scoretauW(): weighted tau statisticfindOverlap(): identify overlap within a vector of
positions based on a given thresholdoverlapMetrics(): metrics of overlap within a vector or
positions based on a given thresholdfixOverlap(): attempt the minimum of adjustments to
vector of positions such that a given distance threshold is
enforcedsp1sp2sp3sp4sp5sp6sierraTransectwilson2022rowley2019jacobs2000osdSPC.with.overlapus.state.soilssoil_mineralsmunsellequivalent_munsellmunsellHuePositionmunsell.spectraspectral.referenceROSETTA.centroidsreactionclasssoiltexture