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