R: Algorithms for Quantitative Pedology

# Algorithms for Quantitative Pedology

## Documentation for package ‘aqp’ version 2.2

- 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 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 | 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
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
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 | Get or Set Diagnostic Horizon data in a SoilProfileCollection
diagnostic_hz-method | Get or Set Diagnostic Horizon data in a SoilProfileCollection
diagnostic_hz<- | Get or Set Diagnostic Horizon data in a SoilProfileCollection
diagnostic_hz<--method | Get or Set Diagnostic Horizon data in a SoilProfileCollection
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 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'

## -- 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
hzmetaname | Get or Set Horizon Metadata Column Name
hzmetaname-method | Get or Set Horizon Metadata Column Name
hzmetaname<- | Get or Set Horizon Metadata Column Name
hzmetaname<--method | Get or Set Horizon Metadata Column Name
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
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.

## -- 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
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

## -- 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
mutate_profile_raw | 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
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
plotProfileDendrogram | Plot soil profiles below a dendrogram
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_id | Set profile IDs
profile_id-method | Set profile IDs
profile_id<- | Set profile IDs
profile_id<--method | Set profile IDs
proj4string | Get or Set Coordinate Reference System for SoilProfileCollection
proj4string-method | Get or Set Coordinate Reference System for SoilProfileCollection
proj4string<- | 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 | Get or Set Restriction data in a SoilProfileCollection
restrictions-method | Get or Set Restriction data in a SoilProfileCollection
restrictions<- | Get or Set Restriction data in a SoilProfileCollection
restrictions<--method | Get or Set Restriction data in a SoilProfileCollection
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.
soilTextureColorPal | Soil Texture Color Palettes
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