An Overview of the aqp Package"

In aqp: Algorithms for Quantitative Pedology

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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.

Related Tutorials by Topic

Soil Morphology

• Soil Profile Sketches
• Visualization of Horizon Boundaries
• Assigning Generalized Horizon Labels
• Dealing With Troublesome Data
• Simulation of Soil Morphology by Perturbation
• Soil Texture Visualization Ideas
• SPC Sketch Tips
• Vertical vs. Perpendicular Horizon Depths

Soil Color

• Mixing Munsell Colors
• Soil Color Contrast
• Some ideas on summarizing soil color
• Soil Color Tiles
• Investigating Soil Color
• Some Ideas on Soil Color Signatures
• Soil Color Transition Probability

Numerical Classification

• Pair-Wise Distances by Generalized Horizon Labels
• Pair-Wise Distance Between Profiles and Mixed Variable Types

Soil Hydrology

• Theoretical Water Retention Curves
• Water Retention Curve Development from KSSL Data

Geomorphology

• Hydrologic Ordering of Geomorphic Proportions
• Exploring Geomorphic Summaries

Soil Taxonomy

• What does a subgroup look like?
• Querying Soil Series Data

Multivariate Summaries of Soil Property Data

• L1 Profiles
• Getting and Comparing KSSL Data

Soil Spectroscopy

• Soil Colors from VNIR Spectra

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

• plotSPC(): create sketches of soil profiles from an SPC
• explainPlotSPC(): explain various elements of a soil profile sketch
• groupedProfilePlot(): create grouped sketches of soil profiles
• plotMultipleSPC(): create sketches from multiple, possibly non-conformal SPCs
• addBracket(): add vertical brackets beside soil profile sketches
• addDiagnosticBracket(): add vertical brackets beside soil profile sketches based on diagnostic features
• addVolumeFraction(): add visual explanation of coarse fragment volume to soil profile sketches
• alignTransect(): align soil profiles to an external gradient such as topographic sequence

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

• NCSP(): numerical classification of soil profiles, within a SoilProfileCollection
• compareSites(): pair-wise comparison of site-level data from a SoilProfileCollection

Pedology

• allocate(): perform one of several classification systems to soil property data
• estimateAWC(): estimate plant-available water holding capacity
• correctAWC(): apply rock fragment or soluble salt corrections to AWC estimates
• hzDistinctnessCodeToOffset(): convert horizon boundary distinctness codes to vertical offset
• hzTopographyCodeToLineType(): convert horizon boundary topography codes to line types
• hzTopographyCodeToOffset(): convert horizon boundary topography codes to offset
• ph_to_rxnclass(): convert pH to reaction class
• rxnclass_to_ph(): convert reaction class to pH range
• ReactionClassLevels(): ordered factor of reaction classes
• horizonColorIndices(): compute various soil color-based indices to horizons within an SPC

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.

• invertLabelColor(): automatic adjustment of label color for maximum contrast, based on specified background color
• hzTransitionProbabilities(): derive transition probability matrix from horizon level data
• mostLikelyHzSequence(): use Markov Chains to predict the most likely sequence of horizons

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

• sp1
• sp2
• sp3
• sp4
• sp5
• sp6
• sierraTransect
• wilson2022
• rowley2019
• jacobs2000
• osd
• SPC.with.overlap
• us.state.soils
• soil_minerals
• munsell
• equivalent_munsell
• munsellHuePosition
• munsell.spectra
• spectral.reference
• ROSETTA.centroids
• reactionclass
• soiltexture

aqp documentation built on Oct. 19, 2024, 5:06 p.m.