$                       Get data from column of horizon or site data in
                        a SoilProfileCollection
$<-                     Set data in column of horizon or site data in a
                        SoilProfileCollection
.colorSig2PerceptualDistMat
                        Interpret a color signature containing color
                        groups of CIELAB coordinates using perceptual
                        distance via CIE dE00
.detectColorSpec        Detect color specification from a vector of
                        values, or a matrix of color coordinates
GHL                     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
Ohz.colors              Representative O Horizon Colors
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.
SoilTextureLevels       Ranking Systems for USDA Soil Texture Classes
[,SoilProfileCollection-method
                        Matrix/data.frame-like access to profiles and
                        horizons in a SoilProfileCollection
[[                      Get column of horizon or site data in a
                        SoilProfileCollection
[[<-                    Add or change column of horizon or site data in
                        a SoilProfileCollection
accumulateDepths        Accumulate horizon depths, and reflect reversed
                        depths, relative to new datum
addBracket              Add Depth Brackets
addDiagnosticBracket    Annotate Diagnostic Features
addVolumeFraction       Symbolize Volume Fraction within a Soil Profile
                        Collection Plot
aggregateColor          Summarize Soil Colors
aggregateColorPlot      Plot aggregate soil color data
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             Algorithms for Quantitative Pedology
aqp_df_class,SoilProfileCollection-method
                        Get aqp_df_class entry from metadata or return
                        a safe value.
argillic.clay.increase.depth
                        Return upper boundary of argillic horizon
as                      Coerce SoilProfileCollection with 'as()'
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
c,SoilProfileCollection-method
                        Combine SoilProfileCollection objects
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'
col2Munsell             Convert colors into Munsell Notation
collapseHz              Collapse Horizons within Profiles Based on
                        Pattern Matching
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
colorVariation          Quantitative Description of Color Variation
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                 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-method
                        Get depth units from metadata
depths                  Initialize a SoilProfileCollection from
                        data.frame
diagnostic_hz,SoilProfileCollection-method
                        Get or Set Diagnostic Horizon data in a
                        SoilProfileCollection
dice,SoilProfileCollection-method
                        Efficient Slicing of 'SoilProfileCollection'
                        Objects
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 U.S Soil Taxonomy
                        Particle Size Control Section
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
findOverlap             Find Overlap within a Sequence
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           Generalize Horizon Names
genhzTableToAdjMat      Convert cross-tabulation to adjacency matrix.
get.increase.matrix     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
                        Determine thickness of horizons (continuous
                        from surface) matching a pattern
glom,SoilProfileCollection-method
                        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         Guess Horizon Slot Column Names
harden.melanization     Harden (1982) Melanization
harden.rubification     Harden (1982) Rubification
harmonize,SoilProfileCollection-method
                        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<-         Set horizon depth column names
horizonNames<-          Set horizon column names
horizons,SoilProfileCollection-method
                        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
hzAbove                 Select Horizons Above or Below a Reference
                        Horizon
hzDepthTests            Tests of horizon depth logic
hzDesgn,SoilProfileCollection-method
                        Get horizon designation column name
hzDistinctnessCodeToOffset
                        Convert Horizon Boundary Distinctness to
                        Vertical Offset
hzID<-,SoilProfileCollection-method
                        Set horizon IDs
hzMetadata,SoilProfileCollection-method
                        Get horizon-level metadata
hzTopographyCodeToLineType
                        Convert Horizon Boundary Topography to Line
                        Type
hzTopographyCodeToOffset
                        Convert Horizon Boundary Topography to Vertical
                        Offset
hzTransitionProbabilities
                        Horizon Transition Probabilities
hz_dissolve             Dissolving horizon boundaries by grouping
                        variables
hz_intersect            Intersecting horizon boundaries by horizon
                        depths
hz_lag                  Find lagged horizon values
hz_segment              Segmenting of Soil Horizon Data by Depth
                        Interval
hz_to_taxpartsize       Allocate Particle Size Class for the Control
                        Section.
hzdesgnname             Get or Set Horizon Designation Column Name
hzidname<-              Set horizon ID column name
hzmetaname              Get or Set Horizon Metadata Column Name
hztexclname             Get or Set Horizon Texture Class Column Name
idname,SoilProfileCollection-method
                        Get profile ID column name
initSpatial<-,SoilProfileCollection,ANY,ANY-method
                        Initialize Spatial Data in a
                        SoilProfileCollection
invertLabelColor        Make High Contrast Label Colors
isEmpty,SoilProfileCollection-method
                        Check for "empty" profiles in a
                        SoilProfileCollection
jacobs2000              Soil Morphologic Data from Jacobs et al. 2002.
launderMunsell          Fix Common Errors in Munsell Notation
length,SoilProfileCollection-method
                        Get the number of profiles in a
                        SoilProfileCollection
lookup_taxpartsize      Ranking Systems for USDA Taxonomic
                        Particle-Size and Substitute Classes of Mineral
                        Soils
lunique                 Eliminate duplicate instances of profile IDs in
                        a list of SoilProfileCollections
max,SoilProfileCollection-method
                        Get the maximum bottom depth in a
                        SoilProfileCollection
metadata,SoilProfileCollection-method
                        Retrieve metadata from SoilProfileCollection
min,SoilProfileCollection-method
                        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
mu_confusion_matrix     Map unit confusion matrix and other
                        classification measures
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-method
                        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-method
                        Get names of columns in site and horizons table
nrow,SoilProfileCollection-method
                        Get the number of horizons in a
                        SoilProfileCollection
osd                     Example Output from soilDB::fetchOSD()
panel.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
ph_to_rxnclass          Convert pH to/from Reaction Classes
plotColorMixture        Visualize Spectral Mixing of Munsell Colors
plotColorQuantiles      Visualize Color Quantiles
plotMultipleSPC         Plot Multiple 'SoilProfileCollection' Objects
plotProfileDendrogram   Plot soil profiles below a dendrogram or
                        cladogram
plotSPC                 Create Soil Profile Sketches
plot_distance_graph     Between Individual Distance Plot
previewColors           Preview Colors
prj,SoilProfileCollection-method
                        Get or Set Coordinate Reference System for
                        SoilProfileCollection
profileApply            Iterate over profiles in a
                        SoilProfileCollection
profileGroupLabels      Soil Profile Group Labels
profileInformationIndex
                        Soil Profile Information Index
profile_id<-            Set profile IDs
quickSPC                Quickly Assemble a SoilProfileCollection
random_profile          Random Profile
reactionclass           pH Reaction Classes
rebuildSPC              Rebuild a SoilProfileCollection object
reduceSPC               Select a subset of columns from a
                        SoilProfileCollection
reorderHorizons         Re-order corrupted horizon data
repairMissingHzDepths   Repair Problematic Lower Horizon Depths
replaceHorizons<-       Replace Data in Horizon Slot
restrictions,SoilProfileCollection-method
                        Get or Set Restriction data in a
                        SoilProfileCollection
rgb2munsell             sRGB to Munsell Color Conversion
rowley2019              Soil Morphologic, Geochemical, and Mineralogy
                        Data from Rowley et al. 2019.
rp                      Generate a 'SoilProfileCollection' of random
                        profiles
shannonEntropy          Shannon Entropy
shuffle                 Shuffle Horizons of a SoilProfileCollection
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
site,SoilProfileCollection-method
                        Retrieve site data from SoilProfileCollection
siteNames<-             Set site column names
slab                    Slab-Wise Aggregation of SoilProfileCollection
                        Objects
slice-methods           Slicing of SoilProfileCollection Objects
slicedHSD               Tukey's HSD Over Slices
soilColorSignature      Soil Profile Color Signatures
soilPalette             Soil Color Palette
soilTextureColorPal     Soil Texture Color Palettes
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-method
                        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-method
                        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-method
                        Subset a SoilProfileCollection with logical
                        expressions
subsetHz,SoilProfileCollection-method
                        Subset the horizons in a SoilProfileCollection
                        using logical criteria
subsetProfiles          DEPRECATED use subset
summarizeSPC            Perform summaries on groups (from 'group_by')
                        and create new site or horizon level attributes
tauW                    Compute weighted naive and _tau_ statistics for
                        a cross-classification matrix
texcl_to_ssc            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-method
                        Transform a SPC with expressions based on site
                        or horizon level attributes
unique,SoilProfileCollection-method
                        Uniqueness within a 'SoilProfileCollection' via
                        MD5 Hash
us.state.soils          US State Soils
validSpatialData,SoilProfileCollection-method
                        Check for valid spatial reference of profiles
validateMunsell         Validate Standard Munsell Notation
warpHorizons            Inflate / Deflate Horizon Thickness
wilson2022              Example Data from Wilson et al. 2022
xtableTauW              Format a LaTeX table with results
