Algorithms for Quantitative Pedology
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Documentation for package ‘aqp’ version 2.0.3
- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.
Help Pages
A B C D E F G H I J L M N O P Q R S T U V W X misc
| aqp-package | Algorithms for Quantitative Pedology |
-- A --
| 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 | Algorithms for Quantitative Pedology |
| aqp.env | Algorithms for Quantitative Pedology |
| aqp_df_class | Get aqp_df_class entry from metadata or return a safe value. |
| aqp_df_class-method | Get aqp_df_class entry from metadata or return a safe value. |
| aqp_df_class<- | Get aqp_df_class entry from metadata or return a safe value. |
| aqp_df_class<--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()' |
| as-method | Coerce SoilProfileCollection with 'as()' |
| as.data.frame-method | Coerce SoilProfileCollection with 'as()' |
-- B --
| 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 --
| c | Combine SoilProfileCollection objects |
| c-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 |
| 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 |
| combine | Combine SoilProfileCollection objects |
| combine-method | Combine SoilProfileCollection objects |
| compareSites | Compare Site Level Attributes of a SoilProfileCollection |
| compositeSPC | Return a list representation of site and horizon level data |
| compositeSPC-method | Return a list representation of site and horizon level data |
| confusionIndex | Confusion Index |
| contrastChart | Color Contrast Chart |
| contrastClass | Soil Color Contrast |
| coordinates | Initialize Spatial Data in a SoilProfileCollection |
| coordinates-method | Initialize Spatial Data in a SoilProfileCollection |
| coordinates<- | Initialize Spatial Data in a SoilProfileCollection |
| coordinates<--method | Initialize Spatial Data in a SoilProfileCollection |
| correctAWC | Apply rock fragment or salt correction to available water content |
| crit.clay.argillic | Determines threshold (minimum) clay content for argillic upper bound |
-- D --
| 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 |
| depths | Initialize a SoilProfileCollection from data.frame |
| depths-method | Initialize a SoilProfileCollection from data.frame |
| depths<- | Initialize a SoilProfileCollection from data.frame |
| depths<--method | Initialize a SoilProfileCollection from data.frame |
| depthWeights | Return a vector of contributing fractions over a depth interval |
| depthWeights-method | Return a vector of contributing fractions over a depth interval |
| depth_units | Get depth units from metadata |
| depth_units-method | Get depth units from metadata |
| depth_units<- | Get depth units from metadata |
| depth_units<--method | Get depth units from metadata |
| diagnostic_hz | Retrieve diagnostic data from SoilProfileCollection |
| diagnostic_hz-method | Retrieve diagnostic data from SoilProfileCollection |
| diagnostic_hz<- | Add Data to Diagnostic Features Slot |
| diagnostic_hz<--method | Add Data to Diagnostic Features Slot |
| dice | Efficient Slicing of 'SoilProfileCollection' Objects |
| dice-method | Efficient Slicing of 'SoilProfileCollection' Objects |
| dissolve_hz | Dissolving horizon boundaries by grouping variables |
| duplicate | Duplicate Profiles of a SoilProfileCollection |
-- E --
| 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' |
-- F --
| 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 |
| fragvol_to_texmod | Textural conversions |
-- G --
| generalize.hz | Generalize Horizon Names |
| generalizeHz | Generalize Horizon Names |
| generalizeHz-method | Generalize Horizon Names |
| genhzTableToAdjMat | Convert cross-tabulation to adjacency matrix. |
| genSlabLabels | Generate Labels for Slabs |
| get.increase.depths | Compute Pair-wise Distances of Soil Properties over Depth |
| get.increase.matrix | Compute Pair-wise Distances of Soil Properties over Depth |
| get.ml.hz | Determine ML Horizon Boundaries |
| get.slice | Slicing of SoilProfileCollection Objects |
| 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 |
| getMineralSoilSurfaceDepth | Determine thickness of horizons (continuous from surface) matching a pattern |
| getPlowLayerDepth | Determine thickness of horizons (continuous from surface) matching a pattern |
| getSoilDepthClass | Generate Soil Depth Class Matrix |
| getSpatial | Initialize Spatial Data in a SoilProfileCollection |
| getSpatial-method | Initialize Spatial Data in a SoilProfileCollection |
| getSurfaceHorizonDepth | Determine thickness of horizons (continuous from surface) matching a pattern |
| GHL | Get or Set Generalized Horizon Label (GHL) Column Name |
| GHL-method | Get or Set Generalized Horizon Label (GHL) Column Name |
| GHL<- | Get or Set Generalized Horizon Label (GHL) Column Name |
| GHL<--method | Get or Set Generalized Horizon Label (GHL) Column Name |
| glom | Subset soil horizon data using a depth or depth interval |
| glom-method | Subset soil horizon data using a depth or depth interval |
| glomApply | Subset an SPC by applying glom to each profile |
| glomApply-method | Subset an SPC by applying glom to each profile |
| grepSPC | Subset SPC with pattern-matching for text-based attributes |
| grepSPC-method | Subset SPC with pattern-matching for text-based attributes |
| groupedProfilePlot | Grouped Soil Profile Plot |
| groupSPC | Store groupings within a profile collection. |
| guessGenHzLevels | Guess Appropriate Ordering for Generalized Horizon Labels |
| guessHzAttrName | Guess Horizon Slot Column Names |
| guessHzDesgnName | Guess Horizon Slot Column Names |
| guessHzTexClName | Guess Horizon Slot Column Names |
-- H --
| harden.melanization | Harden (1982) Melanization |
| harden.rubification | Harden (1982) Rubification |
| harmonize | Harmonize a property by profile-level denormalization for convenient visualization or analysis of ranges |
| harmonize-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 |
| horizonDepths-method | Set horizon depth column names |
| horizonDepths<- | Set horizon depth column names |
| horizonDepths<--method | Set horizon depth column names |
| horizonNames | Set horizon column names |
| horizonNames-method | Set horizon column names |
| horizonNames<- | Set horizon column names |
| horizonNames<--method | Set horizon column names |
| horizons | Retrieve horizon data from SoilProfileCollection |
| horizons-method | Retrieve horizon data from SoilProfileCollection |
| horizons<- | Retrieve horizon data from SoilProfileCollection |
| horizons<--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 | Horizons Above or Below |
| hzBelow | Horizons Above or Below |
| HzDepthLogicSubset | Subset 'SoilProfileCollection' Objects or Horizons via 'checkHzDepthLogic' |
| hzDepthTests | Tests of horizon depth logic |
| hzDesgn | Get horizon designation column name |
| hzDesgn-method | Get horizon designation column name |
| hzdesgnname | Get or Set Horizon Designation Column Name |
| hzdesgnname-method | Get or Set Horizon Designation Column Name |
| hzdesgnname<- | Get or Set Horizon Designation Column Name |
| hzdesgnname<--method | Get or Set Horizon Designation Column Name |
| hzDistinctnessCodeToOffset | Convert Horizon Boundary Distinctness to Vertical Offset |
| hzID | Set horizon IDs |
| hzID-method | Set horizon IDs |
| hzID<- | Set horizon IDs |
| hzID<--method | Set horizon IDs |
| hzidname | Set horizon ID column name |
| hzidname-method | Set horizon ID column name |
| hzidname<- | Set horizon ID column name |
| hzidname<--method | Set horizon ID column name |
| hzMetadata | Get horizon-level metadata |
| hzMetadata-method | Get horizon-level metadata |
| hzOffset | Horizons Above or Below |
| hztexclname | Get or Set Horizon Texture Class Column Name |
| hztexclname-method | Get or Set Horizon Texture Class Column Name |
| hztexclname<- | Get or Set Horizon Texture Class Column Name |
| hztexclname<--method | Get or Set Horizon Texture Class Column Name |
| hzTopographyCodeToLineType | Convert Horizon Boundary Topography to Line Type |
| hzTopographyCodeToOffset | Convert Horizon Boundary Topography to Vertical Offset |
| hzTransitionProbabilities | Horizon Transition Probabilities |
-- I --
| idname | Get profile ID column name |
| idname-method | Get profile ID column name |
| initSpatial<- | Initialize Spatial Data in a SoilProfileCollection |
| initSpatial<--method | Initialize Spatial Data in a SoilProfileCollection |
| invertLabelColor | Make High Contrast Label Colors |
| isEmpty | Check for "empty" profiles in a SoilProfileCollection |
| isEmpty-method | Check for "empty" profiles in a SoilProfileCollection |
-- J --
| jacobs2000 | Soil Morphologic Data from Jacobs et al. 2002. |
-- L --
| L1_profiles | Create Representative Soil Profiles via L1 Estimator |
| length | Get the number of profiles in a SoilProfileCollection |
| length-method | Get the number of profiles in a SoilProfileCollection |
| lunique | Eliminate duplicate instances of profile IDs in a list of SoilProfileCollections |
-- M --
| max | Get the maximum bottom depth in a SoilProfileCollection |
| max-method | Get the maximum bottom depth in a SoilProfileCollection |
| maxDepthOf | Get top or bottom depths of horizons matching a regular expression pattern |
| metadata | Retrieve metadata from SoilProfileCollection |
| metadata-method | Retrieve metadata from SoilProfileCollection |
| metadata<- | Retrieve metadata from SoilProfileCollection |
| metadata<--method | Retrieve metadata from SoilProfileCollection |
| min | Get the minimum bottom depth in a SoilProfileCollection |
| min-method | Get the minimum bottom depth in a SoilProfileCollection |
| minDepthOf | Get top or bottom depths of horizons matching a regular expression pattern |
| missingDataGrid | Missing Data Grid |
| mixMunsell | Mix Munsell Colors via Spectral Library |
| mollic.thickness.requirement | Calculate the minimum thickness requirement for Mollic epipedon |
| mostLikelyHzSequence | Horizon Transition Probabilities |
| 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 |
| munsell2rgb | Convert Munsell Color Notation to other Color Space Coordinates (sRGB and CIELAB) |
| munsell2spc | Merge Munsell Hue, Value, Chroma converted to sRGB & CIELAB into a SoilProfileCollection |
| munsell2spc-method | Merge Munsell Hue, Value, Chroma converted to sRGB & CIELAB into a SoilProfileCollection |
| munsellHuePosition | Munsell Hue Position Reference |
| mutate | Transform a SPC with expressions based on site or horizon level attributes |
| mutate-method | Transform a SPC with expressions based on site or horizon level attributes |
| mutate_profile | Transform a SPC (by profile) with a set of expressions |
| mutate_profile-method | Transform a SPC (by profile) with a set of expressions |
-- N --
| names | Get names of columns in site and horizons table |
| names-method | Get names of columns in site and horizons table |
| NCSP | Numerical Classification of Soil Profiles |
| nrow | Get the number of horizons in a SoilProfileCollection |
| nrow-method | Get the number of horizons in a SoilProfileCollection |
-- O --
| osd | Example Output from soilDB::fetchOSD() |
| overlapMetrics | Find Overlap within a Sequence |
-- P --
| panel.depth_function | Lattice Panel Function for Soil Profiles |
| parseMunsell | Parse Munsell Color Notation |
| pbindlist | Combine a list of SoilProfileCollection objects |
| pc | Deprecated: Numerical Soil Profile Comparison |
| pc.SPC | Deprecated: Numerical Soil Profile Comparison |
| permute_profile | Perturb soil horizon depths using boundary distinctness |
| perturb | Perturb soil horizon depths using boundary distinctness |
| ph_to_rxnclass | Convert pH to/from Reaction Classes |
| plot | Create Soil Profile Sketches |
| plot,SoilProfileCollection,ANY-method,plot.SoilProfileCollection | Create Soil Profile Sketches |
| plot-method | Create Soil Profile Sketches |
| plotColorMixture | Visualize Spectral Mixing of Munsell Colors |
| plotColorQuantiles | Visualize Color Quantiles |
| plotMultipleSPC | Plot Multiple 'SoilProfileCollection' Objects |
| plotSPC | Create Soil Profile Sketches |
| plot_distance_graph | Between Individual Distance Plot |
| prepanel.depth_function | Lattice Panel Function for Soil Profiles |
| previewColors | Preview Colors |
| prj | Get or Set Coordinate Reference System for SoilProfileCollection |
| prj-method | Get or Set Coordinate Reference System for SoilProfileCollection |
| prj<- | Get or Set Coordinate Reference System for SoilProfileCollection |
| prj<--method | Get or Set Coordinate Reference System for SoilProfileCollection |
| profileApply | Iterate over profiles in a SoilProfileCollection |
| profileApply-method | Iterate over profiles in a SoilProfileCollection |
| profileGroupLabels | Soil Profile Group Labels |
| profileInformationIndex | Soil Profile Information Index |
| profile_compare | Deprecated: Numerical Soil Profile Comparison |
| profile_compare-method | Deprecated: Numerical Soil Profile Comparison |
| profile_id | Set profile IDs |
| profile_id-method | Set profile IDs |
| profile_id<- | Set profile IDs |
| profile_id<--method | Set profile IDs |
| proj4string-method | Get or Set Coordinate Reference System for SoilProfileCollection |
| proj4string<--method | Get or Set Coordinate Reference System for SoilProfileCollection |
-- Q --
| quickSPC | Quickly Assemble a SoilProfileCollection |
-- R --
| random_profile | Random Profile |
| reactionclass | pH Reaction Classes |
| ReactionClassLevels | Convert pH to/from Reaction Classes |
| rebuildSPC | Rebuild a SoilProfileCollection object |
| reduceSPC | Select a subset of columns from a SoilProfileCollection |
| reorderHorizons | Re-order corrupted horizon data |
| reorderHorizons-method | Re-order corrupted horizon data |
| repairMissingHzDepths | Repair Problematic Lower Horizon Depths |
| replaceHorizons<- | Replace Data in Horizon Slot |
| replaceHorizons<--method | Replace Data in Horizon Slot |
| restrictions | Retrieve restriction data from SoilProfileCollection |
| restrictions-method | Retrieve restriction data from SoilProfileCollection |
| restrictions<- | Add Data to Restrictions Slot |
| restrictions<--method | Add Data to Restrictions Slot |
| rgb2munsell | sRGB to Munsell Color Conversion |
| ROSETTA.centroids | Average Hydraulic Parameters from the ROSETTA Model by USDA Soil Texture Class |
| rowley2019 | Soil Morphologic, Geochemical, and Mineralogy Data from Rowley et al. 2019. |
| rxnclass_to_ph | Convert pH to/from Reaction Classes |
-- S --
| SANN_1D | Fix Overlap within a Sequence via Simulated Annealing |
| 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 |
| site | Retrieve site data from SoilProfileCollection |
| site-method | Retrieve site data from SoilProfileCollection |
| site<- | Retrieve site data from SoilProfileCollection |
| site<--method | Retrieve site data from SoilProfileCollection |
| siteNames | Set site column names |
| siteNames-method | Set site column names |
| siteNames<- | Set site column names |
| siteNames<--method | Set site column names |
| slab | Slab-Wise Aggregation of SoilProfileCollection Objects |
| slab-method | Slab-Wise Aggregation of SoilProfileCollection Objects |
| slab_function | Slab-Wise Aggregation of SoilProfileCollection Objects |
| slice | Slicing of SoilProfileCollection Objects |
| slice-method | Slicing of SoilProfileCollection Objects |
| slice-methods | Slicing of SoilProfileCollection Objects |
| slice.fast | Slicing of SoilProfileCollection Objects |
| slicedHSD | Tukey's HSD Over Slices |
| soilColorSignature | Soil Profile Color Signatures |
| soilPalette | Soil Color Palette |
| SoilProfileCollection | An S4 object representation of a group of soil profiles. |
| SoilProfileCollection-class | An S4 object representation of a group of soil profiles. |
| soiltexture | Lookup tables for sand, silt, clay, texture class, and textural modifiers. |
| SoilTextureLevels | Ranking Systems for USDA Soil Texture Classes |
| soil_minerals | Munsell Colors of Common Soil Minerals |
| 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 |
| SPC.with.overlap | Example SoilProfileCollection with Overlapping Horizons |
| spc2mpspline | SoilProfileCollection wrapper for 'mpspline2::mpspline()' |
| spc2mpspline-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-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 |
| ssc_to_texcl | Textural conversions |
| subApply | Subset SPC based on result of performing function on each profile |
| subApply-method | Subset SPC based on result of performing function on each profile |
| subset | Subset a SoilProfileCollection with logical expressions |
| subset-method | Subset a SoilProfileCollection with logical expressions |
| subsetHz | Subset the horizons in a SoilProfileCollection using logical criteria |
| subsetHz-method | Subset the horizons in a SoilProfileCollection using logical criteria |
| subsetProfiles | DEPRECATED use subset |
| subsetProfiles-method | DEPRECATED use subset |
| summarize | Perform summaries on groups (from 'group_by') and create new site or horizon level attributes |
| summarizeSPC | Perform summaries on groups (from 'group_by') and create new site or horizon level attributes |
| summarizeSPC,SoilProfileCollection-method, | Perform summaries on groups (from 'group_by') and create new site or horizon level attributes |
| summaryTauW | Compute weighted naive and _tau_ statistics for a cross-classification matrix |
-- T --
| tauW | Compute weighted naive and _tau_ statistics for a cross-classification matrix |
| texcl_to_ssc | Textural conversions |
| texmod_to_fragvoltot | Textural conversions |
| textureTriangleSummary | Soil Texture Low-RV-High as Defined by Quantiles |
| texture_to_taxpartsize | Textural conversions |
| texture_to_texmod | Textural conversions |
| thicknessOf | Calculate Thickness of Horizons Matching Logical Criteria |
| thompson.bell.darkness | Thompson-Bell (1996) Index |
| traditionalColorNames | Traditional Soil Color Names |
| transform-method | Transform a SPC with expressions based on site or horizon level attributes |
| trunc-method | Subset soil horizon data using a depth or depth interval |
-- U --
| unique | Uniqueness within a 'SoilProfileCollection' via MD5 Hash |
| unique-method | Uniqueness within a 'SoilProfileCollection' via MD5 Hash |
| unroll | Unroll Genetic Horizons |
| us.state.soils | US State Soils |
-- V --
| validSpatialData | Check for valid spatial reference of profiles |
| validSpatialData-method | Check for valid spatial reference of profiles |
-- W --
| warpHorizons | Inflate / Deflate Horizon Thickness |
| wilson2022 | Example Data from Wilson et al. 2022 |
-- X --
| xtableTauW | Format a LaTeX table with results |
-- misc --
| $ | Get data from column of horizon or site data in a SoilProfileCollection |
| $-method | Get data from column of horizon or site data in a SoilProfileCollection |
| $<- | Set data in column of horizon or site data in a SoilProfileCollection |
| $<--method | Set data in column of horizon or site data in a SoilProfileCollection |
| .lpp | Random Profile |
| [-method | Matrix/data.frame-like access to profiles and horizons in a SoilProfileCollection |
| [[ | Get column of horizon or site data in a SoilProfileCollection |
| [[-method | Get column of horizon or site data in a SoilProfileCollection |
| [[<- | Add or change column of horizon or site data in a SoilProfileCollection |
| [[<--method | Add or change column of horizon or site data in a SoilProfileCollection |