Function reference • aqp

All functions
`GHL(<SoilProfileCollection>)` `GHL<-`(<SoilProfileCollection>)	Get or Set Generalized Horizon Label (GHL) Column Name
`HzDepthLogicSubset()`	Subset `SoilProfileCollection` Objects or Horizons via `checkHzDepthLogic`
`L1_profiles()`	Create Representative Soil Profiles via L1 Estimator
`NCSP()`	Numerical Classification of Soil Profiles
`ROSETTA.centroids`	Average Hydraulic Parameters from the ROSETTA Model by USDA Soil Texture Class
`SANN_1D()`	Fix Overlap within a Sequence via Simulated Annealing
`SPC.with.overlap`	Example SoilProfileCollection with Overlapping Horizons
`SoilProfileCollection()`	An S4 object representation of a group of soil profiles.
`prj(<SoilProfileCollection>)` `prj<-`(<SoilProfileCollection>) `proj4string(<SoilProfileCollection>)` `proj4string<-`(<SoilProfileCollection>,<ANY>)	Get or Set Coordinate Reference System for SoilProfileCollection
`plotSPC()` `plot(<SoilProfileCollection>,<ANY>)`	Create Soil Profile Sketches
`SoilTextureLevels()`	Ranking Systems for USDA Soil Texture Classes
`accumulateDepths()`	Accumulate horizon depths, and reflect reversed depths, relative to new datum
`addBracket()`	Add Depth Brackets
`addDiagnosticBracket()`	Annotate Diagnostic Features
`addVolumeFraction()`	Symbolize Volume Fraction on a Soil Profile Collection Plot
`aggregateColor()`	Summarize Soil Colors
`aggregateSoilDepth()`	Probabilistic Estimation of Soil Depth within Groups
`alignTransect()`	Calculate Relative Positions from Transect Data
`allocate()`	Allocate soil properties within various classification systems.
`aqp-package` `aqp` `aqp.env`	Algorithms for Quantitative Pedology
`aqp_df_class(<SoilProfileCollection>)` `aqp_df_class<-`(<SoilProfileCollection>)	Get aqp_df_class entry from metadata or return a safe value.
`argillic.clay.increase.depth()`	Return upper boundary of argillic horizon
`barron.torrent.redness.LAB()`	Barron & Torrent (1986) Redness Index in LAB color space
`bootstrapSoilTexture()`	Bootstrap Soil Texture Data
`brierScore()`	Multinominal Brier Score
`buntley.westin.index()`	Buntley-Westin (1965) Index
`ca630`	Soil Data from the Central Sierra Nevada Region of California
`checkHzDepthLogic()`	Check a SoilProfileCollection object for errors in horizon depths.
`checkSPC()`	Test for a valid `SoilProfileCollection`
`as.data.frame(<SoilProfileCollection>)`	Coerce SoilProfileCollection with `as()`
`col2Munsell()`	Convert colors into Munsell Notation
`colorChart()`	Visualize soil colors in Munsell notation according to within-group frequency.
`colorContrast()`	Metrics of Contrast Suitable for Comparing Soil Colors
`colorContrastPlot()`	Color Contrast Plot
`colorQuantiles()`	Soil Color Range via Quantiles
`c(<SoilProfileCollection>)` `combine(<SoilProfileCollection>)` `combine(<list>)`	Combine SoilProfileCollection objects
`compareSites()`	Compare Site Level Attributes of a SoilProfileCollection
`compositeSPC()`	Return a list representation of site and horizon level data
`confusionIndex()`	Confusion Index
`contrastChart()`	Color Contrast Chart
`contrastClass()`	Soil Color Contrast
`correctAWC()`	Apply rock fragment or salt correction to available water content
`crit.clay.argillic()`	Determines threshold (minimum) clay content for argillic upper bound
`denormalize()`	Create a (redundant) horizon-level attribute from a site-level attribute
`depthOf()` `maxDepthOf()` `minDepthOf()`	Get top or bottom depths of horizons matching a regular expression pattern
`depthWeights()`	Return a vector of contributing fractions over a depth interval
`depth_units(<SoilProfileCollection>)` `depth_units<-`(<SoilProfileCollection>)	Get depth units from metadata
`depths(<SoilProfileCollection>)` `depths<-`(<SoilProfileCollection>) `depths<-`(<data.frame>)	Initialize a SoilProfileCollection from data.frame
`diagnostic_hz<-`(<SoilProfileCollection>)	Add Data to Diagnostic Features Slot
`diagnostic_hz(<SoilProfileCollection>)`	Retrieve diagnostic data from SoilProfileCollection
`dice(<SoilProfileCollection>)`	Efficient Slicing of `SoilProfileCollection` Objects
`dissolve_hz()`	Dissolving horizon boundaries by grouping variables
`$<-`(<SoilProfileCollection>)	Set data in column of horizon or site data in a SoilProfileCollection
`$`(<SoilProfileCollection>)	Get data from column of horizon or site data in a SoilProfileCollection
`[[<-`(<SoilProfileCollection>,<ANY>,<ANY>)	Add or change column of horizon or site data in a SoilProfileCollection
`[[`(<SoilProfileCollection>,<ANY>,<ANY>)	Get column of horizon or site data in a SoilProfileCollection
`duplicate()`	Duplicate Profiles of a SoilProfileCollection
`electroStatics_1D()`	Label placement based on a simulation of electrostatic forces
`equivalentMunsellChips()`	Identify "equivalent" (whole number value/chroma) Munsell chips
`equivalent_munsell`	Indices of "equivalent" Munsell chips in the `munsell` data set
`estimateAWC()`	Estimate available water capacity for fine-earth fraction
`estimatePSCS()`	Estimate boundaries of the particle size control section (U.S Soil Taxonomy; 12th edition)
`estimateSoilColor()`	Estimate dry soil colors from moist soil colors and vice versa.
`estimateSoilDepth()`	Estimate Soil Depth
`evalGenHZ()`	Evaluate Generalized Horizon Labels
`evalMissingData()`	Evaluate Missing Data within a SoilProfileCollection
`explainPlotSPC()`	Visual Explanation for `plotSPC`
`fillHzGaps()`	Find and Fill Horizon Gaps
`fixOverlap()`	Fix Overlap within a Sequence
`flagOverlappingHz()`	Flag perfectly overlapping horizons within a SoilProfileCollection
`fragmentClasses()`	Coarse Fragment Class Labels and Diameter
`fragmentSieve()`	Sieve the Coarse Fraction of Soil
`genSlabLabels()`	Generate Labels for Slabs
`generalize.hz()` `generalizeHz(<character>)` `generalizeHz(<SoilProfileCollection>)`	Generalize Horizon Names
`genhzTableToAdjMat()`	Convert cross-tabulation to adjacency matrix.
`get.increase.matrix()` `get.increase.depths()`	Compute Pair-wise Distances of Soil Properties over Depth
`get.ml.hz()`	Determine ML Horizon Boundaries
`getArgillicBounds()`	Estimate upper and lower boundary of argillic diagnostic subsurface horizon
`getCambicBounds()`	Find all intervals that are potentially part of a Cambic horizon
`getClosestMunsellChip()`	Get Approximate Munsell Chip
`getLastHorizonID()`	Get IDs of Deepest Horizons by Profile
`getSoilDepthClass()`	Generate Soil Depth Class Matrix
`getSurfaceHorizonDepth()` `getMineralSoilSurfaceDepth()` `getPlowLayerDepth()`	Determine thickness of horizons (continuous from surface) matching a pattern
`glom(<SoilProfileCollection>)` `trunc(<SoilProfileCollection>)`	Subset soil horizon data using a depth or depth interval
`glomApply()`	Subset an SPC by applying glom to each profile
`grepSPC()`	Subset SPC with pattern-matching for text-based attributes
`groupSPC()`	Store groupings within a profile collection.
`groupedProfilePlot()`	Grouped Soil Profile Plot
`guessGenHzLevels()`	Guess Appropriate Ordering for Generalized Horizon Labels
`guessHzAttrName()` `guessHzDesgnName()` `guessHzTexClName()`	Guess Horizon Slot Column Names
`harden.melanization()`	Harden (1982) Melanization
`harden.rubification()`	Harden (1982) Rubification
`harmonize(<SoilProfileCollection>)`	Harmonize a property by profile-level denormalization for convenient visualization or analysis of ranges
`hasDarkColors()`	Find horizons with colors darker than a Munsell hue, value, chroma threshold
`horizonColorIndices()`	Horizon Color Indices
`horizonDepths<-`(<SoilProfileCollection>) `horizonDepths(<SoilProfileCollection>)`	Set horizon depth column names
`horizonNames<-`(<SoilProfileCollection>) `horizonNames(<SoilProfileCollection>)`	Set horizon column names
`horizons(<SoilProfileCollection>)` `horizons<-`(<SoilProfileCollection>)	Retrieve horizon data from SoilProfileCollection
`huePosition()`	Munsell Hue Reference and Position Searching
`huePositionCircle()`	Visual Description of Munsell Hue Ordering
`hurst.redness()`	Hurst (1977) Redness Index
`hzDepthTests()`	Tests of horizon depth logic
`hzDesgn(<SoilProfileCollection>)`	Get horizon designation column name
`hzDistinctnessCodeToOffset()`	Convert Horizon Boundary Distinctness to Vertical Offset
`hzID<-`(<SoilProfileCollection>) `hzID(<SoilProfileCollection>)`	Set horizon IDs
`hzMetadata(<SoilProfileCollection>)`	Get horizon-level metadata
`hzAbove()` `hzBelow()` `hzOffset()`	Horizons Above or Below
`hzTopographyCodeToLineType()`	Convert Horizon Boundary Topography to Line Type
`hzTopographyCodeToOffset()`	Convert Horizon Boundary Topography to Vertical Offset
`hzTransitionProbabilities()` `mostLikelyHzSequence()`	Horizon Transition Probabilities
`hzdesgnname(<SoilProfileCollection>)` `hzdesgnname<-`(<SoilProfileCollection>)	Get or Set Horizon Designation Column Name
`hzidname<-`(<SoilProfileCollection>) `hzidname(<SoilProfileCollection>)`	Set horizon ID column name
`hztexclname(<SoilProfileCollection>)` `hztexclname<-`(<SoilProfileCollection>)	Get or Set Horizon Texture Class Column Name
`idname(<SoilProfileCollection>)`	Get profile ID column name
`initSpatial<-`(<SoilProfileCollection>,<ANY>,<ANY>) `initSpatial<-`(<SoilProfileCollection>,<ANY>,<character>) `getSpatial(<SoilProfileCollection>)` `coordinates(<SoilProfileCollection>)` `coordinates<-`(<SoilProfileCollection>,<ANY>) `coordinates<-`(<SoilProfileCollection>,<character>)	Initialize Spatial Data in a SoilProfileCollection
`invertLabelColor()`	Make High Contrast Label Colors
`isEmpty(<SoilProfileCollection>)`	Check for "empty" profiles in a SoilProfileCollection
`jacobs2000`	Soil Morphologic Data from Jacobs et al. 2002.
`length(<SoilProfileCollection>)`	Get the number of profiles in a SoilProfileCollection
`lunique()`	Eliminate duplicate instances of profile IDs in a list of SoilProfileCollections
`max(<SoilProfileCollection>)`	Get the maximum bottom depth in a SoilProfileCollection
`metadata(<SoilProfileCollection>)` `metadata<-`(<SoilProfileCollection>)	Retrieve metadata from SoilProfileCollection
`min(<SoilProfileCollection>)`	Get the minimum bottom depth in a SoilProfileCollection
`missingDataGrid()`	Missing Data Grid
`mixMunsell()`	Mix Munsell Colors via Spectral Library
`mollic.thickness.requirement()`	Calculate the minimum thickness requirement for Mollic epipedon
`munsell`	Munsell to sRGB Lookup Table for Common Soil Colors
`munsell.spectra`	Spectral Library of Munsell Colors
`munsell2rgb()`	Convert Munsell Color Notation to other Color Space Coordinates (sRGB and CIELAB)
`munsell2spc(<SoilProfileCollection>)`	Merge Munsell Hue, Value, Chroma converted to sRGB & CIELAB into a SoilProfileCollection
`munsellHuePosition`	Munsell Hue Position Reference
`mutate_profile()`	Transform a SPC (by profile) with a set of expressions
`names(<SoilProfileCollection>)`	Get names of columns in site and horizons table
`nrow(<SoilProfileCollection>)`	Get the number of horizons in a SoilProfileCollection
`osd`	Example Output from soilDB::fetchOSD()
`findOverlap()` `overlapMetrics()`	Find Overlap within a Sequence
`panel.depth_function()` `prepanel.depth_function()`	Lattice Panel Function for Soil Profiles
`parseMunsell()`	Parse Munsell Color Notation
`pbindlist()`	Combine a list of SoilProfileCollection objects
`perturb()`	Perturb soil horizon depths using boundary distinctness
`plotColorMixture()`	Visualize Spectral Mixing of Munsell Colors
`plotColorQuantiles()`	Visualize Color Quantiles
`plotMultipleSPC()`	Plot Multiple `SoilProfileCollection` Objects
`plot_distance_graph()`	Between Individual Distance Plot
`previewColors()`	Preview Colors
`profileApply(<SoilProfileCollection>)`	Iterate over profiles in a SoilProfileCollection
`profileGroupLabels()`	Soil Profile Group Labels
`profileInformationIndex()`	Soil Profile Information Index
`pc()` `pc.SPC()` `profile_compare(<SoilProfileCollection>)` `profile_compare(<data.frame>)`	Deprecated: Numerical Soil Profile Comparison
`profile_id<-`(<SoilProfileCollection>) `profile_id(<SoilProfileCollection>)`	Set profile IDs
`quickSPC()`	Quickly Assemble a SoilProfileCollection
`random_profile()`	Random Profile
`ph_to_rxnclass()` `rxnclass_to_ph()` `ReactionClassLevels()`	Convert pH to/from Reaction Classes
`reactionclass`	pH Reaction Classes
`rebuildSPC()`	Rebuild a SoilProfileCollection object
`reduceSPC()`	Select a subset of columns from a SoilProfileCollection
`reorderHorizons(<SoilProfileCollection>)`	Re-order corrupted horizon data
`repairMissingHzDepths()`	Repair Problematic Lower Horizon Depths
`replaceHorizons<-`(<SoilProfileCollection>)	Replace Data in Horizon Slot
`restrictions<-`(<SoilProfileCollection>)	Add Data to Restrictions Slot
`restrictions(<SoilProfileCollection>)`	Retrieve restriction data from SoilProfileCollection
`rgb2munsell()`	sRGB to Munsell Color Conversion
`rowley2019`	Soil Morphologic, Geochemical, and Mineralogy Data from Rowley et al. 2019.
`segment()`	Segmenting of Soil Horizon Data by Depth Interval
`shannonEntropy()`	Shannon Entropy
`sierraTransect`	Soil Physical and Chemical Data Related to Studies in the Sierra Nevada Mountains, CA, USA.
`sim()`	DEPRECATED Simulate Soil Profiles
`simulateColor()`	Simulate Soil Colors
`[`(<SoilProfileCollection>)	Matrix/data.frame-like access to profiles and horizons in a SoilProfileCollection
`site(<SoilProfileCollection>)` `site<-`()	Retrieve site data from SoilProfileCollection
`siteNames<-`(<SoilProfileCollection>) `siteNames(<SoilProfileCollection>)`	Set site column names
`slab(<SoilProfileCollection>)` `slab_function()`	Slab-Wise Aggregation of SoilProfileCollection Objects
`slice.fast()` `slice(<SoilProfileCollection>)` `get.slice()`	Slicing of SoilProfileCollection Objects
`slicedHSD()`	Tukey's HSD Over Slices
`soilColorSignature()`	Soil Profile Color Signatures
`soilPalette()`	Soil Color Palette
`soil_minerals`	Munsell Colors of Common Soil Minerals
`soiltexture`	Lookup tables for sand, silt, clay, texture class, and textural modifiers.
`sp1`	Soil Profile Data Example 1
`sp2`	Honcut Creek Soil Profile Data
`sp3`	Soil Profile Data Example 3
`sp4`	Soil Chemical Data from Serpentinitic Soils of California
`sp5`	Sample Soil Database #5
`sp6`	Soil Physical and Chemical Data from Manganiferous Soils
`spc2mpspline(<SoilProfileCollection>)`	SoilProfileCollection wrapper for `mpspline2::mpspline()`
`spc_in_sync()`	Quickly assess relative state of site and horizon slots
`spec2Munsell()`	Convert reflectance spectra to closest Munsell chip
`spectral.reference`	Standard Illuminants and Observers
`split(<SoilProfileCollection>)`	Split a SoilProfileCollection object into a list of SoilProfileCollection objects.
`splitLogicErrors()`	Split a `SoilProfileCollection` into a list based on types of horizon logic errors
`subApply()`	Subset SPC based on result of performing function on each profile
`subset(<SoilProfileCollection>)`	Subset a SoilProfileCollection with logical expressions
`subsetHz(<SoilProfileCollection>)`	Subset the horizons in a SoilProfileCollection using logical criteria
`subsetProfiles(<SoilProfileCollection>)`	DEPRECATED use subset
`summarizeSPC()`	Perform summaries on groups (from `group_by`) and create new site or horizon level attributes
`tauW()` `summaryTauW()`	Compute weighted naive and tau statistics for a cross-classification matrix
`texcl_to_ssc()` `ssc_to_texcl()` `texmod_to_fragvoltot()` `texture_to_taxpartsize()` `texture_to_texmod()` `fragvol_to_texmod()`	Textural conversions
`textureTriangleSummary()`	Soil Texture Low-RV-High as Defined by Quantiles
`thicknessOf()`	Calculate Thickness of Horizons Matching Logical Criteria
`thompson.bell.darkness()`	Thompson-Bell (1996) Index
`traditionalColorNames`	Traditional Soil Color Names
`transform(<SoilProfileCollection>)`	Transform a SPC with expressions based on site or horizon level attributes
`unique(<SoilProfileCollection>)`	Uniqueness within a `SoilProfileCollection` via MD5 Hash
`unroll()`	Unroll Genetic Horizons
`us.state.soils`	US State Soils
`validSpatialData(<SoilProfileCollection>)`	Check for valid spatial reference of profiles
`warpHorizons()`	Inflate / Deflate Horizon Thickness
`wilson2022`	Example Data from Wilson et al. 2022
`xtableTauW()`	Format a LaTeX table with results

Reference

All functions