Package: aqp 2.1.0

Dylan Beaudette

aqp: Algorithms for Quantitative Pedology

The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.

Authors:Dylan Beaudette [aut, cre], Pierre Roudier [aut, ctb], Andrew Brown [aut, ctb]

aqp_2.1.0.tar.gz
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aqp.pdf |aqp.html
aqp/json (API)
NEWS

# Install 'aqp' in R:
install.packages('aqp', repos = c('https://ncss-tech.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ncss-tech/aqp/issues

Datasets:
  • ROSETTA.centroids - Average Hydraulic Parameters from the ROSETTA Model by USDA Soil Texture Class
  • SPC.with.overlap - Example SoilProfileCollection with Overlapping Horizons
  • ca630 - Soil Data from the Central Sierra Nevada Region of California
  • equivalent_munsell - Indices of "equivalent" Munsell chips in the 'munsell' data set
  • jacobs2000 - Soil Morphologic Data from Jacobs et al. 2002.
  • munsell - Munsell to sRGB Lookup Table for Common Soil Colors
  • munsell.spectra - Spectral Library of Munsell Colors
  • munsell.spectra.wide - Spectral Library of Munsell Colors
  • munsellHuePosition - Munsell Hue Position Reference
  • osd - Example Output from soilDB::fetchOSD
  • reactionclass - PH Reaction Classes
  • rowley2019 - Soil Morphologic, Geochemical, and Mineralogy Data from Rowley et al. 2019.
  • sierraTransect - Soil Physical and Chemical Data Related to Studies in the Sierra Nevada Mountains, CA, USA.
  • 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
  • spectral.reference - Standard Illuminants and Observers
  • traditionalColorNames - Traditional Soil Color Names
  • us.state.soils - US State Soils
  • wilson2022 - Example Data from Wilson et al. 2022

On CRAN:

digital-soil-mappingncss-technrcspedologypedometricssoilsoil-surveyusda

233 exports 54 stars 11.85 score 12 dependencies 2 dependents 1 mentions 1.3k scripts 2.2k downloads

Last updated 2 days agofrom:32fd050f2b. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 11 2024
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R-4.5-linuxOKOct 11 2024
R-4.4-winOKOct 11 2024
R-4.4-macOKOct 11 2024
R-4.3-winOKOct 11 2024
R-4.3-macOKOct 11 2024

Exports:accumulateDepthsaddBracketaddDiagnosticBracketaddVolumeFractionaggregateColoraggregateSoilDepthalignTransectallocateaqp_df_classaqp_df_class<-aqp.envargillic.clay.increase.depthas.data.framebarron.torrent.redness.LABbootstrapSoilTexturebrierScorebuntley.westin.indexcheckHzDepthLogiccheckSPCcol2MunsellcolorChartcolorContrastcolorContrastPlotcolorQuantilescombinecompareSitescompositeSPCconfusionIndexcontrastChartcontrastClasscoordinatescoordinates<-correctAWCcrit.clay.argillicdenormalizedepth_unitsdepth_units<-depthOfdepthsdepths<-depthWeightsdiagnostic_hzdiagnostic_hz<-dicedissolve_hzduplicateelectroStatics_1DequivalentMunsellChipsestimateAWCestimatePSCSestimateSoilColorestimateSoilDepthevalGenHZevalMissingDataexplainPlotSPCfillHzGapsfindOverlapfixOverlapflagOverlappingHzfragmentClassesfragmentSievefragvol_to_texmodgeneralize.hzgeneralizeHzgenhzTableToAdjMatgenSlabLabelsget.increase.depthsget.increase.matrixget.ml.hzget.slicegetArgillicBoundsgetCambicBoundsgetClosestMunsellChipgetLastHorizonIDgetMineralSoilSurfaceDepthgetPlowLayerDepthgetSoilDepthClassgetSpatialgetSurfaceHorizonDepthGHLGHL<-glomglomApplygrepSPCgroupedProfilePlotgroupSPCguessGenHzLevelsguessHzAttrNameguessHzDesgnNameguessHzTexClNameharden.melanizationharden.rubificationharmonizehasDarkColorshorizonColorIndiceshorizonDepthshorizonDepths<-horizonNameshorizonNames<-horizonshorizons<-huePositionhuePositionCirclehurst.rednesshz_dissolvehz_intersecthz_laghz_segmenthz_to_taxpartsizehzAbovehzBelowHzDepthLogicSubsethzDepthTestshzDesgnhzdesgnnamehzdesgnname<-hzDistinctnessCodeToOffsethzIDhzID<-hzidnamehzidname<-hzMetadatahzmetanamehzmetaname<-hzOffsethztexclnamehztexclname<-hzTopographyCodeToLineTypehzTopographyCodeToOffsethzTransitionProbabilitiesidnameinitSpatial<-invertLabelColorisEmptyL1_profileslookup_taxpartsizeluniquemaxDepthOfmetadatametadata<-minDepthOfmissingDataGridmixMunsellmollic.thickness.requirementmostLikelyHzSequencemunsell2rgbmunsell2spcmutate_profileNCSPnrowoverlapMetricspanel.depth_functionparseMunsellpbindlistpcpc.SPCperturbph_to_rxnclassplotplot_distance_graphplotColorMixtureplotColorQuantilesplotMultipleSPCplotSPCprepanel.depth_functionpreviewColorsprjprj<-profile_compareprofile_idprofile_id<-profileApplyprofileGroupLabelsprofileInformationIndexproj4stringproj4string<-quickSPCrandom_profileReactionClassLevelsrebuildSPCreduceSPCreorderHorizonsrepairMissingHzDepthsreplaceHorizons<-restrictionsrestrictions<-rgb2munsellrxnclass_to_phSANN_1DsegmentshannonEntropysimsimulateColorsitesite<-siteNamessiteNames<-slabslab_functionsliceslice.fastslicedHSDsoilColorSignaturesoilPaletteSoilProfileCollectionsoilTextureColorPalSoilTextureLevelsspc_in_syncspc2mpsplinespec2MunsellsplitsplitLogicErrorsssc_to_texclsubApplysubsetsubsetHzsubsetProfilessummarizeSPCsummaryTauWtauWtexcl_to_ssctexmod_to_fragvoltottexture_to_taxpartsizetexture_to_texmodtextureTriangleSummarythicknessOfthompson.bell.darknesstransformuniqueunrollvalidSpatialDatawarpHorizonsxtableTauW

Dependencies:cliclusterdata.tablefarvergluelatticelifecyclemagrittrrlangstringistringrvctrs

An Overview of the aqp Package

Rendered fromaqp-overview.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-02-20
Started: 2023-12-27

Introduction to SoilProfileCollection Objects

Rendered fromIntroduction-to-SoilProfileCollection-Objects.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2023-12-29
Started: 2022-08-29

Missing Data

Rendered frommissing-data.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2023-11-28
Started: 2023-11-18

Munsell Color Conversion

Rendered fromMunsell-color-conversion.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-04-17
Started: 2023-11-29

Numerical Classification of Soil Profiles

Rendered fromNCSP.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2023-08-25
Started: 2023-03-20

Overlapping Annotation

Rendered fromlabel-placement.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2023-08-28
Started: 2023-06-07

What is new in aqp 2.x?

Rendered fromnew-in-aqp-2.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-03-12
Started: 2023-08-15

Readme and manuals

Help Manual

Help pageTopics
Algorithms for Quantitative Pedologyaqp-package aqp aqp.env
Matrix/data.frame-like access to profiles and horizons in a SoilProfileCollection[,SoilProfileCollection-method
Get column of horizon or site data in a SoilProfileCollection[[ [[,SoilProfileCollection,ANY,ANY-method [[,SoilProfileCollection,ANY-method [[,SoilProfileCollection-method
Add or change column of horizon or site data in a SoilProfileCollection[[<- [[<-,SoilProfileCollection,ANY,ANY-method [[<-,SoilProfileCollection-method
Get data from column of horizon or site data in a SoilProfileCollection$ $,SoilProfileCollection-method
Set data in column of horizon or site data in a SoilProfileCollection$<- $<-,SoilProfileCollection-method
Accumulate horizon depths, and reflect reversed depths, relative to new datumaccumulateDepths
Add Depth BracketsaddBracket
Annotate Diagnostic FeaturesaddDiagnosticBracket
Symbolize Volume Fraction on a Soil Profile Collection PlotaddVolumeFraction
Summarize Soil ColorsaggregateColor
Probabilistic Estimation of Soil Depth within GroupsaggregateSoilDepth
Calculate Relative Positions from Transect DataalignTransect
Allocate soil properties within various classification systems.allocate
Get aqp_df_class entry from metadata or return a safe value.aqp_df_class aqp_df_class,SoilProfileCollection-method aqp_df_class<- aqp_df_class<-,SoilProfileCollection-method
Return upper boundary of argillic horizonargillic.clay.increase.depth
Coerce SoilProfileCollection with 'as()'as as,SoilProfileCollection-method as.data.frame,SoilProfileCollection-method
Barron & Torrent (1986) Redness Index in LAB color spacebarron.torrent.redness.LAB
Bootstrap Soil Texture DatabootstrapSoilTexture
Multinominal Brier ScorebrierScore
Buntley-Westin (1965) Indexbuntley.westin.index
Combine SoilProfileCollection objectsc c,SoilProfileCollection-method combine combine,list-method combine,SoilProfileCollection-method
Soil Data from the Central Sierra Nevada Region of Californiaca630
Check a SoilProfileCollection object for errors in horizon depths.checkHzDepthLogic
Test for a valid 'SoilProfileCollection'checkSPC
Convert colors into Munsell Notationcol2Munsell
Visualize soil colors in Munsell notation according to within-group frequency.colorChart
Metrics of Contrast Suitable for Comparing Soil ColorscolorContrast
Color Contrast PlotcolorContrastPlot
Soil Color Range via QuantilescolorQuantiles
Compare Site Level Attributes of a SoilProfileCollectioncompareSites
Return a list representation of site and horizon level datacompositeSPC compositeSPC,SoilProfileCollection-method
Confusion IndexconfusionIndex
Color Contrast ChartcontrastChart
Soil Color ContrastcontrastClass
Apply rock fragment or salt correction to available water contentcorrectAWC
Determines threshold (minimum) clay content for argillic upper boundcrit.clay.argillic
Create a (redundant) horizon-level attribute from a site-level attributedenormalize
Get depth units from metadatadepth_units depth_units,SoilProfileCollection-method depth_units<- depth_units<-,SoilProfileCollection-method
Get top or bottom depths of horizons matching a regular expression patterndepthOf maxDepthOf minDepthOf
Initialize a SoilProfileCollection from data.framedepths depths,SoilProfileCollection-method depths<- depths<-,data.frame-method depths<-,SoilProfileCollection-method
Return a vector of contributing fractions over a depth intervaldepthWeights depthWeights,SoilProfileCollection-method
Get or Set Diagnostic Horizon data in a SoilProfileCollectiondiagnostic_hz diagnostic_hz,SoilProfileCollection-method diagnostic_hz<- diagnostic_hz<-,SoilProfileCollection-method
Efficient Slicing of 'SoilProfileCollection' Objectsdice dice,SoilProfileCollection-method
Duplicate Profiles of a SoilProfileCollectionduplicate
Label placement based on a simulation of electrostatic forceselectroStatics_1D
Indices of "equivalent" Munsell chips in the 'munsell' data setequivalent_munsell
Identify "equivalent" (whole number value/chroma) Munsell chipsequivalentMunsellChips
Estimate available water capacity for fine-earth fractionestimateAWC
Estimate boundaries of the U.S Soil Taxonomy Particle Size Control SectionestimatePSCS
Estimate dry soil colors from moist soil colors and vice versa.estimateSoilColor
Estimate Soil DepthestimateSoilDepth
Evaluate Generalized Horizon LabelsevalGenHZ
Evaluate Missing Data within a SoilProfileCollectionevalMissingData
Visual Explanation for 'plotSPC'explainPlotSPC
Find and Fill Horizon GapsfillHzGaps
Find Overlap within a SequencefindOverlap overlapMetrics
Fix Overlap within a SequencefixOverlap
Flag perfectly overlapping horizons within a SoilProfileCollectionflagOverlappingHz
Coarse Fragment Class Labels and DiameterfragmentClasses
Sieve the Coarse Fraction of SoilfragmentSieve
Generalize Horizon Namesgeneralize.hz generalizeHz generalizeHz,character-method generalizeHz,SoilProfileCollection-method
Convert cross-tabulation to adjacency matrix.genhzTableToAdjMat
Generate Labels for SlabsgenSlabLabels
Compute Pair-wise Distances of Soil Properties over Depthget.increase.depths get.increase.matrix
Determine ML Horizon Boundariesget.ml.hz
Estimate upper and lower boundary of argillic diagnostic subsurface horizongetArgillicBounds
Find all intervals that are potentially part of a Cambic horizongetCambicBounds
Get Approximate Munsell ChipgetClosestMunsellChip
Get IDs of Deepest Horizons by ProfilegetLastHorizonID
Generate Soil Depth Class MatrixgetSoilDepthClass
Determine thickness of horizons (continuous from surface) matching a patterngetMineralSoilSurfaceDepth getPlowLayerDepth getSurfaceHorizonDepth
Get or Set Generalized Horizon Label (GHL) Column NameGHL GHL,SoilProfileCollection-method GHL<- GHL<-,SoilProfileCollection-method
Subset soil horizon data using a depth or depth intervalglom glom,SoilProfileCollection-method trunc,SoilProfileCollection-method
Subset an SPC by applying glom to each profileglomApply glomApply,SoilProfileCollection-method
Subset SPC with pattern-matching for text-based attributesgrepSPC grepSPC,SoilProfileCollection-method
Grouped Soil Profile PlotgroupedProfilePlot
Store groupings within a profile collection.groupSPC
Guess Appropriate Ordering for Generalized Horizon LabelsguessGenHzLevels
Guess Horizon Slot Column NamesguessHzAttrName guessHzDesgnName guessHzTexClName
Harden (1982) Melanizationharden.melanization
Harden (1982) Rubificationharden.rubification
Harmonize a property by profile-level denormalization for convenient visualization or analysis of rangesharmonize harmonize,SoilProfileCollection-method
Find horizons with colors darker than a Munsell hue, value, chroma thresholdhasDarkColors
Horizon Color IndiceshorizonColorIndices
Set horizon depth column nameshorizonDepths horizonDepths,SoilProfileCollection-method horizonDepths<- horizonDepths<-,SoilProfileCollection-method
Set horizon column nameshorizonNames horizonNames,SoilProfileCollection-method horizonNames<- horizonNames<-,SoilProfileCollection-method
Retrieve horizon data from SoilProfileCollectionhorizons horizons,SoilProfileCollection-method horizons<- horizons<-,SoilProfileCollection-method
Munsell Hue Reference and Position SearchinghuePosition
Visual Description of Munsell Hue OrderinghuePositionCircle
Hurst (1977) Redness Indexhurst.redness
Dissolving horizon boundaries by grouping variablesdissolve_hz hz_dissolve
Intersecting horizon boundaries by horizon depthshz_intersect
Find lagged horizon valueshz_lag
Segmenting of Soil Horizon Data by Depth Intervalhz_segment segment
Allocate Particle Size Class for the Control Section.hz_to_taxpartsize
Horizons Above or BelowhzAbove hzBelow hzOffset
Subset 'SoilProfileCollection' Objects or Horizons via 'checkHzDepthLogic'HzDepthLogicSubset
Tests of horizon depth logichzDepthTests
Get horizon designation column namehzDesgn hzDesgn,SoilProfileCollection-method
Get or Set Horizon Designation Column Namehzdesgnname hzdesgnname,SoilProfileCollection-method hzdesgnname<- hzdesgnname<-,SoilProfileCollection-method
Convert Horizon Boundary Distinctness to Vertical OffsethzDistinctnessCodeToOffset
Set horizon IDshzID hzID,SoilProfileCollection-method hzID<- hzID<-,SoilProfileCollection-method
Set horizon ID column namehzidname hzidname,SoilProfileCollection-method hzidname<- hzidname<-,SoilProfileCollection-method
Get horizon-level metadatahzMetadata hzMetadata,SoilProfileCollection-method
Get or Set Horizon Metadata Column Namehzmetaname hzmetaname,SoilProfileCollection-method hzmetaname<- hzmetaname<-,SoilProfileCollection-method
Get or Set Horizon Texture Class Column Namehztexclname hztexclname,SoilProfileCollection-method hztexclname<- hztexclname<-,SoilProfileCollection-method
Convert Horizon Boundary Topography to Line TypehzTopographyCodeToLineType
Convert Horizon Boundary Topography to Vertical OffsethzTopographyCodeToOffset
Horizon Transition ProbabilitieshzTransitionProbabilities mostLikelyHzSequence
Get profile ID column nameidname idname,SoilProfileCollection-method
Initialize Spatial Data in a SoilProfileCollectioncoordinates coordinates,SoilProfileCollection-method coordinates<- coordinates<-,SoilProfileCollection,ANY-method coordinates<-,SoilProfileCollection,character-method getSpatial getSpatial,SoilProfileCollection-method initSpatial<- initSpatial<-,SoilProfileCollection,ANY,ANY-method initSpatial<-,SoilProfileCollection,ANY,character-method
Make High Contrast Label ColorsinvertLabelColor
Check for "empty" profiles in a SoilProfileCollectionisEmpty isEmpty,SoilProfileCollection-method
Soil Morphologic Data from Jacobs et al. 2002.jacobs2000
Create Representative Soil Profiles via L1 EstimatorL1_profiles
Get the number of profiles in a SoilProfileCollectionlength length,SoilProfileCollection-method
Ranking Systems for USDA Taxonomic Particle-Size and Substitute Classes of Mineral Soilslookup_taxpartsize
Eliminate duplicate instances of profile IDs in a list of SoilProfileCollectionslunique
Get the maximum bottom depth in a SoilProfileCollectionmax max,SoilProfileCollection-method
Retrieve metadata from SoilProfileCollectionmetadata metadata,SoilProfileCollection-method metadata<- metadata<-,SoilProfileCollection-method
Get the minimum bottom depth in a SoilProfileCollectionmin min,SoilProfileCollection-method
Missing Data GridmissingDataGrid
Mix Munsell Colors via Spectral LibrarymixMunsell
Calculate the minimum thickness requirement for Mollic epipedonmollic.thickness.requirement
Munsell to sRGB Lookup Table for Common Soil Colorsmunsell
Spectral Library of Munsell Colorsmunsell.spectra munsell.spectra.wide
Convert Munsell Color Notation to other Color Space Coordinates (sRGB and CIELAB)munsell2rgb
Merge Munsell Hue, Value, Chroma converted to sRGB & CIELAB into a SoilProfileCollectionmunsell2spc munsell2spc,SoilProfileCollection-method
Munsell Hue Position ReferencemunsellHuePosition
Transform a SPC (by profile) with a set of expressionsmutate_profile mutate_profile,SoilProfileCollection-method
Get names of columns in site and horizons tablenames names,SoilProfileCollection-method
Numerical Classification of Soil ProfilesNCSP
Get the number of horizons in a SoilProfileCollectionnrow nrow,SoilProfileCollection-method
Example Output from soilDB::fetchOSD()osd
Lattice Panel Function for Soil Profilespanel.depth_function prepanel.depth_function
Parse Munsell Color NotationparseMunsell
Combine a list of SoilProfileCollection objectspbindlist
Deprecated: Numerical Soil Profile Comparisonpc pc.SPC profile_compare profile_compare,data.frame-method profile_compare,SoilProfileCollection-method
Perturb soil horizon depths using boundary distinctnesspermute_profile perturb
Convert pH to/from Reaction Classesph_to_rxnclass ReactionClassLevels rxnclass_to_ph
Between Individual Distance Plotplot_distance_graph
Visualize Spectral Mixing of Munsell ColorsplotColorMixture
Visualize Color QuantilesplotColorQuantiles
Plot Multiple 'SoilProfileCollection' ObjectsplotMultipleSPC
Create Soil Profile Sketchesplot plot,SoilProfileCollection,ANY-method plot,SoilProfileCollection,ANY-method,plot.SoilProfileCollection plot,SoilProfileCollection-method plotSPC
Preview ColorspreviewColors
Get or Set Coordinate Reference System for SoilProfileCollectionprj prj,SoilProfileCollection-method prj<- prj<-,SoilProfileCollection-method proj4string proj4string,SoilProfileCollection-method proj4string<- proj4string<-,SoilProfileCollection-method
Set profile IDsprofile_id profile_id,SoilProfileCollection-method profile_id<- profile_id<-,SoilProfileCollection-method
Iterate over profiles in a SoilProfileCollectionprofileApply profileApply,SoilProfileCollection-method
Soil Profile Group LabelsprofileGroupLabels
Soil Profile Information IndexprofileInformationIndex
Quickly Assemble a SoilProfileCollectionquickSPC
Random Profile.lpp random_profile
pH Reaction Classesreactionclass
Rebuild a SoilProfileCollection objectrebuildSPC
Select a subset of columns from a SoilProfileCollectionreduceSPC
Re-order corrupted horizon datareorderHorizons reorderHorizons,SoilProfileCollection-method
Repair Problematic Lower Horizon DepthsrepairMissingHzDepths
Replace Data in Horizon SlotreplaceHorizons<- replaceHorizons<-,SoilProfileCollection-method
Get or Set Restriction data in a SoilProfileCollectionrestrictions restrictions,SoilProfileCollection-method restrictions<- restrictions<-,SoilProfileCollection-method
sRGB to Munsell Color Conversionrgb2munsell
Average Hydraulic Parameters from the ROSETTA Model by USDA Soil Texture ClassROSETTA.centroids
Soil Morphologic, Geochemical, and Mineralogy Data from Rowley et al. 2019.rowley2019
Fix Overlap within a Sequence via Simulated AnnealingSANN_1D
Shannon EntropyshannonEntropy
Soil Physical and Chemical Data Related to Studies in the Sierra Nevada Mountains, CA, USA.sierraTransect
DEPRECATED Simulate Soil Profilessim
Simulate Soil ColorssimulateColor
Retrieve site data from SoilProfileCollectionsite site,SoilProfileCollection-method site<- site<-,SoilProfileCollection-method
Set site column namessiteNames siteNames,SoilProfileCollection-method siteNames<- siteNames<-,SoilProfileCollection-method
Slab-Wise Aggregation of SoilProfileCollection Objectsslab slab,SoilProfileCollection-method slab_function
Slicing of SoilProfileCollection Objectsget.slice slice slice,SoilProfileCollection-method slice-methods slice.fast
Tukey's HSD Over SlicesslicedHSD
Munsell Colors of Common Soil Mineralssoil_minerals
Soil Profile Color SignaturessoilColorSignature
Soil Color PalettesoilPalette
An S4 object representation of a group of soil profiles.SoilProfileCollection SoilProfileCollection-class
Lookup tables for sand, silt, clay, texture class, and textural modifiers.soiltexture
Soil Texture Color PalettessoilTextureColorPal
Ranking Systems for USDA Soil Texture ClassesSoilTextureLevels
Soil Profile Data Example 1sp1
Honcut Creek Soil Profile Datasp2
Soil Profile Data Example 3sp3
Soil Chemical Data from Serpentinitic Soils of Californiasp4
Sample Soil Database #5sp5
Soil Physical and Chemical Data from Manganiferous Soilssp6
Quickly assess relative state of site and horizon slotsspc_in_sync
Example SoilProfileCollection with Overlapping HorizonsSPC.with.overlap
SoilProfileCollection wrapper for 'mpspline2::mpspline()'spc2mpspline spc2mpspline,SoilProfileCollection-method
Convert reflectance spectra to closest Munsell chipspec2Munsell
Standard Illuminants and Observersspectral.reference
Split a SoilProfileCollection object into a list of SoilProfileCollection objects.split,SoilProfileCollection-method
Split a 'SoilProfileCollection' into a list based on types of horizon logic errorssplitLogicErrors
Subset SPC based on result of performing function on each profilesubApply subApply,SoilProfileCollection-method
Subset a SoilProfileCollection with logical expressionssubset subset,SoilProfileCollection-method
Subset the horizons in a SoilProfileCollection using logical criteriasubsetHz subsetHz,SoilProfileCollection-method
DEPRECATED use subsetsubsetProfiles subsetProfiles,SoilProfileCollection-method
Perform summaries on groups (from 'group_by') and create new site or horizon level attributessummarize summarizeSPC summarizeSPC,SoilProfileCollection-method,
Compute weighted naive and _tau_ statistics for a cross-classification matrixsummaryTauW tauW
Textural conversionsfragvol_to_texmod ssc_to_texcl texcl_to_ssc texmod_to_fragvoltot texture_to_taxpartsize texture_to_texmod
Soil Texture Low-RV-High as Defined by QuantilestextureTriangleSummary
Calculate Thickness of Horizons Matching Logical CriteriathicknessOf
Thompson-Bell (1996) Indexthompson.bell.darkness
Traditional Soil Color NamestraditionalColorNames
Transform a SPC with expressions based on site or horizon level attributesmutate mutate,SoilProfileCollection-method transform,SoilProfileCollection-method
Uniqueness within a 'SoilProfileCollection' via MD5 Hashunique unique,SoilProfileCollection-method
Unroll Genetic Horizonsunroll
US State Soilsus.state.soils
Check for valid spatial reference of profilesvalidSpatialData validSpatialData,SoilProfileCollection-method
Inflate / Deflate Horizon ThicknesswarpHorizons
Example Data from Wilson et al. 2022wilson2022
Format a LaTeX table with resultsxtableTauW