Algorithms for Quantitative Pedology


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Documentation for package ‘aqp’ version 2.0.4

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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 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 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
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

-- 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 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.
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