Man pages for aqp
Algorithms for Quantitative Pedology

accumulateDepthsAccumulate horizon depths, and reflect reversed depths,...
addBracketAdd Depth Brackets
addDiagnosticBracketAnnotate Diagnostic Features
addVolumeFractionSymbolize Volume Fraction on a Soil Profile Collection Plot
aggregateColorSummarize Soil Colors
aggregateSoilDepthProbabalistic Estimation of Soil Depth within Groups
alignTransectCalculate Relative Positions from Transect Data
allocateAllocate soil properties within various classification...
aqp_df_classGet aqp_df_class entry from metadata or return a safe value.
aqp-packageAlgorithms for Quantitative Pedology
argillic.clay.increase.depthReturn upper boundary of argillic horizon
barron.torrent.redness.LABBarron & Torrent (1986) Redness Index in LAB color space
bootstrapSoilTextureBootstrap Soil Texture Data
brierScoreMultinominal Brier Score
buntley.westin.indexBuntley-Westin (1965) Index
ca630Soil Data from the Central Sierra Nevada Region of California
checkHzDepthLogicCheck a SoilProfileCollection object for errors in horizon...
checkSPCTest for a valid SoilProfileCollection
coercion-methodsCoerce SoilProfileCollection with 'as()'
colorChartVisualize soil colors in Munsell notation according to...
colorContrastMetrics of Contrast Suitable for Comparing Soil Colors
colorContrastPlotColor Contrast Plot
colorQuantilesSoil Color Range via Quantiles
combine-SoilProfileCollection-methodCombine SoilProfileCollection objects
compareSitesCompare Site Level Attributes of a SoilProfileCollection
compositeSPCReturn a list representation of site and horizon level data
confusionIndexConfusion Index
contrastChartColor Contrast Chart
contrastClassSoil Color Contrast
correctAWCApply rock fragment or salt correction to available water...
crit.clay.argillicDetermines threshold (minimum) clay content for argillic...
denormalizeCreate a (redundant) horizon-level attribute from a...
depthOfGet top or bottom depths of horizons matching a regular...
depthsInitialize a SoilProfileCollection from data.frame
depth_unitsGet depth units from metadata
depthWeightsReturn a vector of contributing fractions over a depth...
diagnostic_hzRetrieve diagnostic data from SoilProfileCollection
diagnostic_hz-setAdd Data to Diagnostic Features Slot
dice-SoilProfileCollection-methodEfficient Slicing of 'SoilProfileCollection' Objects
dissolve_hzDissolving horizon boundaries by grouping variables
dollarsignGet data from column of horizon or site data in a...
dollarsign-setSet data in column of horizon or site data in a...
doublebracketGet column of horizon or site data in a SoilProfileCollection
doublebracket-setAdd or change column of horizon or site data in a...
duplicateDuplicate Profiles of a SoilProfileCollection
electroStatics_1DLabel placement based on a simulation of electrostatic forces
equivalent_munsellIndices of "equivalent" Munsell chips in the 'munsell' data...
equivalentMunsellChipsIdentify "equivalent" (whole number value/chroma) Munsell...
estimateAWCEstimate available water capacity for fine-earth fraction
estimatePSCSEstimate boundaries of the particle size control section (U.S...
estimateSoilColorEstimate dry soil colors from moist soil colors and vice...
estimateSoilDepthEstimate Soil Depth
evalGenHZEvaluate Generalized Horizon Labels
evalMissingDataEvaluate Missing Data
explainPlotSPCVisual Explanation for 'plotSPC'
fillHzGapsFind and Fill Horizon Gaps
fixOverlapFix Overlap within a Sequence
flagOverlappingHzFlag perfectly overlapping horizons within a...
fragmentClassesCoarse Fragment Class Labels and Diameter
fragmentSieveSieve the Coarse Fraction of Soil
generalize.hzGeneralize Horizon Names
genSlabLabelsGenerate Labels for Slabs
getArgillicBoundsEstimate upper and lower boundary of argillic diagnostic...
getCambicBoundsFind all intervals that are potentially part of a Cambic...
getClosestMunsellChipGet Approximate Munsell Chip
get.increase.matrixCompute Pair-wise Distances of Soil Properties over Depth
getLastHorizonIDGet IDs of Deepest Horizons by Profile ML Horizon Boundaries
getSoilDepthClassGenerate Soil Depth Class Matrix
getSurfaceHorizonDepthDetermine thickness of horizons (continuous from surface)...
GHLGet or Set Generalized Horizon Label (GHL) Column Name
glomSubset soil horizon data using a depth or depth interval
glomApplySubset an SPC by applying glom to each profile
grepSPCSubset SPC with pattern-matching for text-based attributes
groupedProfilePlotGrouped Soil Profile Plot
groupSPCStore groupings within a profile collection.
guessGenHzLevelsGuess Appropriate Ordering for Generalized Horizon Labels
guessHzAttrNameGuess Horizon Slot Column Names
harden.melanizationHarden (1982) Melanization
harden.rubificationHarden (1982) Rubification
harmonize-SoilProfileCollection-methodHarmonize a property by profile-level denormalization for...
hasDarkColorsFind horizons with colors darker than a Munsell hue, value,...
horizonColorIndicesHorizon Color Indices
horizonDepthsSet horizon depth column names
horizonNamesSet horizon column names
horizonsRetrieve horizon data from SoilProfileCollection
huePositionMunsell Hue Reference and Position Searching
huePositionCircleVisual Description of Munsell Hue Ordering
hurst.rednessHurst (1977) Redness Index
HzDepthLogicSubsetSubset 'SoilProfileCollection' Objects or Horizons via...
hzDepthTestsTests of horizon depth logic
hzDesgnGet horizon designation column name
hzdesgnnameGet or Set Horizon Designation Column Name
hzDistinctnessCodeToOffsetConvert Horizon Boundary Distinctness to Vertical Offset
hzIDSet horizon IDs
hzidnameSet horizon ID column name
hzMetadataGet horizon-level metadata
hzOffsetHorizons Above or Below
hztexclnameGet or Set Horizon Texture Class Column Name
hzTopographyCodeToLineTypeConvert Horizon Boundary Topography to Line Type
hzTopographyCodeToOffsetConvert Horizon Boundary Topography to Vertical Offset
hzTransitionProbabilitiesConvert cross-tabulation to adjacency matrix.
idnameGet profile ID column name
initSpatialInitialize Spatial Data in a SoilProfileCollection
invertLabelColorMake High Contrast Label Colors
isEmptyCheck for "empty" profiles in a SoilProfileCollection
jacobs2000Soil Morphologic Data from Jacobs et al. 2002.
L1_profilesCreate Representative Soil Profiles via L1 Estimator
lengthGet the number of profiles in a SoilProfileCollection
luniqueEliminate duplicate instances of profile IDs in a list of...
maxGet the maximum bottom depth in a SoilProfileCollection
metadataRetrieve metadata from SoilProfileCollection
minGet the minimum bottom depth in a SoilProfileCollection
missingDataGridMissing Data Grid
mixMunsellMix Munsell Colors via Spectral Library
mollic.thickness.requirementCalculate the minimum thickness requirement for Mollic...
munsellMunsell to sRGB Lookup Table for Common Soil Colors
munsell2rgbConvert Munsell Color Notation to other Color Space...
munsell2spc-SoilProfileCollection-methodMerge Munsell Hue, Value, Chroma converted to sRGB & CIELAB...
munsellHuePositionMunsell Hue Position Reference
munsell.spectraSpectral Library of Munsell Colors
mutate_profileTransform a SPC (by profile) with a set of expressions
namesGet names of columns in site and horizons table
NCSPNumerical Classification of Soil Profiles
nrowGet the number of horizons in a SoilProfileCollection
osdExample Output from soilDB::fetchOSD()
overlapMetricsFind Overlap within a Sequence
panel.depth_functionLattice Panel Function for Soil Profiles
parseMunsellParse Munsell Color Notation
pbindlistCombine a list of SoilProfileCollection objects
perturbPerturb soil horizon depths using boundary distinctness
plotColorMixtureVisualize Spectral Mixing of Munsell Colors
plotColorQuantilesVisualize Color Quantiles
plot_distance_graphBetween Individual Distance Plot
plotMultipleSPCPlot Multiple 'SoilProfileCollection' Objects
previewColorsPreview Colors
profileApplyIterate over profiles in a SoilProfileCollection
profile_compareDeprecated: Numerical Soil Profile Comparison
profileGroupLabelsSoil Profile Group Labels
profile_idSet profile IDs
profileInformationIndexSoil Profile Information Index
quickSPCQuickly Assemble a SoilProfileCollection
random_profileRandom Profile
reactionConvert pH to/from Reaction Classes
reactionclasspH Reaction Classes
rebuildSPCRebuild a SoilProfileCollection object
reduceSPCSelect a subset of columns from a SoilProfileCollection
reorderHorizonsRe-order corrupted horizon data
repairMissingHzDepthsRepair Problematic Lower Horizon Depths
replaceHorizonsReplace Data in Horizon Slot
restrictionsRetrieve restriction data from SoilProfileCollection
restrictions-setAdd Data to Restrictions Slot
rgb2munsellsRGB to Munsell Color Conversion
ROSETTA.centroidsAverage Hydraulic Parameters from the ROSETTA Model by USDA...
rowley2019Soil Morphologic, Geochemical, and Mineralogy Data from...
SANN_1DFix Overlap within a Sequence via Simulated Annealing
segmentSegmenting of Soil Horizon Data by Depth Interval
shannonEntropyShannon Entropy
showSoilProfileCollection show method
sierraTransectSoil Physical and Chemical Data Related to Studies in the...
simDEPRECATED Simulate Soil Profiles
simulateColorSimulate Soil Colors
singlebracketMatrix/data.frame-like access to profiles and horizons in a...
siteRetrieve site data from SoilProfileCollection
siteNamesSet site column names
slabSlab-Wise Aggregation of SoilProfileCollection Objects
sliceSlicing of SoilProfileCollection Objects
slicedHSDTukey's HSD Over Slices
soilColorSignatureSoil Profile Color Signatures
soil_mineralsMunsell Colors of Common Soil Minerals
soilPaletteSoil Color Palette
SoilProfileCollection-classAn S4 object representation of a group of soil profiles.
SoilProfileCollection-crsGet or Set Coordinate Reference System for...
SoilProfileCollection-plotting-methodsCreate Soil Profile Sketches
soiltextureLookup tables for sand, silt, clay, texture class, and...
SoilTextureLevelsRanking Systems for USDA Soil Texture Classes
sp1Soil Profile Data Example 1
sp2Honcut Creek Soil Profile Data
sp3Soil Profile Data Example 3
sp4Soil Chemical Data from Serpentinitic Soils of California
sp5Sample Soil Database #5
sp6Soil Physical and Chemical Data from Manganiferous Soils
spc2mpspline-SoilProfileCollection-methodSoilProfileCollection wrapper for 'mpspline2::mpspline()'
spc_in_syncQuickly assess relative state of site and horizon slots
SPC.with.overlapExample SoilProfileCollection with Overlapping Horizons
spec2MunsellConvert reflectance spectra to closest Munsell chip
spectral.referenceStandard Illuminants and Observers
splitLogicErrorsSplit a SoilProfileCollection into a list based on types of...
split-SoilProfileCollection-methodSplit a SoilProfileCollection object into a list of...
subApplySubset SPC based on result of performing function on each...
subsetHz-SoilProfileCollection-methodSubset the horizons in a SoilProfileCollection using logical...
subsetProfilesDEPRECATED use subset
subset-SoilProfileCollection-methodSubset a SoilProfileCollection with logical expressions
summarizeSPCPerform summaries on groups (from 'group_by') and create new...
tauWCompute weighted naive and _tau_ statistics for a...
textureTextural conversions
textureTriangleSummarySoil Texture Low-RV-High as Defined by Quantiles
thompson.bell.darknessThompson-Bell (1996) Index
traditionalColorNamesTraditional Soil Color Names
transformTransform a SPC with expressions based on site or horizon...
uniqueUniqueness within a 'SoilProfileCollection' via MD5 Hash
unrollUnroll Genetic Horizons
us.state.soilsUS State Soils
validSpatialDataCheck for valid spatial reference of profiles
wilson2022Example Data from Wilson et al. 2022
xtableTauWFormat a LaTeX table with results
aqp documentation built on Sept. 8, 2023, 5:45 p.m.