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aqp (version 2.3)

Algorithms for Quantitative Pedology

Description

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 . 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 . 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.

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Version

Install

install.packages('aqp')

Monthly Downloads

3,409

Version

2.3

License

GPL (>= 3)

Homepage

https://ncss-tech.github.io/aqp/

Maintainer

Dylan Beaudette

Last Published

January 17th, 2026

Functions in aqp (2.3)

SPC.with.overlap

Example SoilProfileCollection with Overlapping Horizons

Create Representative Soil Profiles via L1 Estimator

prj,SoilProfileCollection-method

Get or Set Coordinate Reference System for SoilProfileCollection

Get or Set Generalized Horizon Label (GHL) Column Name

Create Soil Profile Sketches

Numerical Classification of Soil Profiles

SoilTextureLevels

Ranking Systems for USDA Soil Texture Classes

Calculate Relative Positions from Transect Data

Add Depth Brackets

Summarize Soil Colors

addVolumeFraction

Symbolize Volume Fraction within a Soil Profile Collection Plot

accumulateDepths

Accumulate horizon depths, and reflect reversed depths, relative to new datum

aggregateSoilDepth

Probabilistic Estimation of Soil Depth within Groups

Allocate soil properties within various classification systems.

aggregateColorPlot

Plot aggregate soil color data

addDiagnosticBracket

Annotate Diagnostic Features

checkHzDepthLogic

Check a SoilProfileCollection object for errors in horizon depths.

Algorithms for Quantitative Pedology

bootstrapSoilTexture

Bootstrap Soil Texture Data

argillic.clay.increase.depth

Return upper boundary of argillic horizon

aqp_df_class,SoilProfileCollection-method

Get aqp_df_class entry from metadata or return a safe value.

Test for a valid SoilProfileCollection

colorContrastPlot

Color Contrast Plot

Coerce SoilProfileCollection with as()

Convert colors into Munsell Notation

Multinominal Brier Score

Compare Site Level Attributes of a SoilProfileCollection

c,SoilProfileCollection-method

Combine SoilProfileCollection objects

Metrics of Contrast Suitable for Comparing Soil Colors

barron.torrent.redness.LAB

Barron & Torrent (1986) Redness Index in LAB color space

Visualize soil colors in Munsell notation according to within-group frequency.

Collapse Horizons within Profiles Based on Pattern Matching

Soil Color Range via Quantiles

Quantitative Description of Color Variation

Soil Data from the Central Sierra Nevada Region of California

depth_units,SoilProfileCollection-method

Get depth units from metadata

Return a vector of contributing fractions over a depth interval

buntley.westin.index

Buntley-Westin (1965) Index

Soil Color Contrast

Create a (redundant) horizon-level attribute from a site-level attribute

Color Contrast Chart

dice,SoilProfileCollection-method

Efficient Slicing of SoilProfileCollection Objects

Set data in column of horizon or site data in a SoilProfileCollection

Apply rock fragment or salt correction to available water content

crit.clay.argillic

Determines threshold (minimum) clay content for argillic upper bound

estimateSoilColor

Estimate dry soil colors from moist soil colors and vice versa.

.colorSig2PerceptualDistMat

Interpret a color signature containing color groups of CIELAB coordinates using perceptual distance via CIE dE00

Evaluate Generalized Horizon Labels

Get data from column of horizon or site data in a SoilProfileCollection

Get top or bottom depths of horizons matching a regular expression pattern

estimateSoilDepth

Estimate Soil Depth

Estimate boundaries of the U.S Soil Taxonomy Particle Size Control Section

Get column of horizon or site data in a SoilProfileCollection

Duplicate Profiles of a SoilProfileCollection

equivalent_munsell

Indices of "equivalent" Munsell chips in the munsell data set

Estimate available water capacity for fine-earth fraction

Initialize a SoilProfileCollection from data.frame

Sieve the Coarse Fraction of Soil

Find and Fill Horizon Gaps

Fix Overlap within a Sequence

Generate Labels for Slabs

get.increase.matrix

Compute Pair-wise Distances of Soil Properties over Depth

Return a list representation of site and horizon level data

equivalentMunsellChips

Identify "equivalent" (whole number value/chroma) Munsell chips

fragmentClasses

Coarse Fragment Class Labels and Diameter

Confusion Index

flagOverlappingHz

Flag perfectly overlapping horizons within a SoilProfileCollection

electroStatics_1D

Label placement based on a simulation of electrostatic forces

.detectColorSpec

Detect color specification from a vector of values, or a matrix of color coordinates

Add or change column of horizon or site data in a SoilProfileCollection

Determine ML Horizon Boundaries

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

glom,SoilProfileCollection-method

Subset soil horizon data using a depth or depth interval

groupedProfilePlot

Grouped Soil Profile Plot

Subset an SPC by applying glom to each profile

Subset SPC with pattern-matching for text-based attributes

guessHzAttrName

Guess Horizon Slot Column Names

Store groupings within a profile collection.

harden.melanization

Harden (1982) Melanization

guessGenHzLevels

Guess Appropriate Ordering for Generalized Horizon Labels

Visual Explanation for plotSPC

genhzTableToAdjMat

Convert cross-tabulation to adjacency matrix.

diagnostic_hz,SoilProfileCollection-method

Get or Set Diagnostic Horizon data in a SoilProfileCollection

Generalize Horizon Names

getSoilDepthClass

Generate Soil Depth Class Matrix

evalMissingData

Evaluate Missing Data within a SoilProfileCollection

Hurst (1977) Redness Index

huePositionCircle

Visual Description of Munsell Hue Ordering

horizonDepths<-

Set horizon depth column names

hzDesgn,SoilProfileCollection-method

Get horizon designation column name

getSurfaceHorizonDepth

Determine thickness of horizons (continuous from surface) matching a pattern

hzTransitionProbabilities

Horizon Transition Probabilities

harden.rubification

Harden (1982) Rubification

Tests of horizon depth logic

harmonize,SoilProfileCollection-method

Harmonize a property by profile-level denormalization for convenient visualization or analysis of ranges

Get or Set Horizon Designation Column Name

hzID<-,SoilProfileCollection-method

Set horizon IDs

hzDistinctnessCodeToOffset

Convert Horizon Boundary Distinctness to Vertical Offset

Set horizon column names

hzTopographyCodeToLineType

Convert Horizon Boundary Topography to Line Type

Segmenting of Soil Horizon Data by Depth Interval

Eliminate duplicate instances of profile IDs in a list of SoilProfileCollections

hzTopographyCodeToOffset

Convert Horizon Boundary Topography to Vertical Offset

lookup_taxpartsize

Ranking Systems for USDA Taxonomic Particle-Size and Substitute Classes of Mineral Soils

hz_to_taxpartsize

Allocate Particle Size Class for the Control Section.

metadata,SoilProfileCollection-method

Retrieve metadata from SoilProfileCollection

max,SoilProfileCollection-method

Get the maximum bottom depth in a SoilProfileCollection

Set horizon ID column name

munsell.spectra

Spectral Library of Munsell Colors

Get or Set Horizon Metadata Column Name

Get or Set Horizon Texture Class Column Name

Dissolving horizon boundaries by grouping variables

Convert Munsell Color Notation to other Color Space Coordinates (sRGB and CIELAB)

min,SoilProfileCollection-method

Get the minimum bottom depth in a SoilProfileCollection

nrow,SoilProfileCollection-method

Get the number of horizons in a SoilProfileCollection

missingDataGrid

Missing Data Grid

Combine a list of SoilProfileCollection objects

Parse Munsell Color Notation

horizons,SoilProfileCollection-method

Retrieve horizon data from SoilProfileCollection

Find horizons with colors darker than a Munsell hue, value, chroma threshold

horizonColorIndices

Horizon Color Indices

Find Overlap within a Sequence

panel.depth_function

Lattice Panel Function for Soil Profiles

Example Output from soilDB::fetchOSD()

plotColorQuantiles

Visualize Color Quantiles

Initialize Spatial Data in a SoilProfileCollection

Horizons Above or Below

mu_confusion_matrix

Map unit confusion matrix and other classification measures

idname,SoilProfileCollection-method

Get profile ID column name

hzMetadata,SoilProfileCollection-method

Get horizon-level metadata

Find lagged horizon values

Intersecting horizon boundaries by horizon depths

plotColorMixture

Visualize Spectral Mixing of Munsell Colors

Perturb soil horizon depths using boundary distinctness

Munsell to sRGB Lookup Table for Common Soil Colors

plotMultipleSPC

Plot Multiple SoilProfileCollection Objects

profileInformationIndex

Soil Profile Information Index

replaceHorizons<-

Replace Data in Horizon Slot

profileGroupLabels

Soil Profile Group Labels

repairMissingHzDepths

Repair Problematic Lower Horizon Depths

Transform a SPC (by profile) with a set of expressions

munsell2spc,SoilProfileCollection-method

Merge Munsell Hue, Value, Chroma converted to sRGB & CIELAB into a SoilProfileCollection

length,SoilProfileCollection-method

Get the number of profiles in a SoilProfileCollection

Soil Morphologic Data from Jacobs et al. 2002.

plotProfileDendrogram

Plot soil profiles below a dendrogram or cladogram

restrictions,SoilProfileCollection-method

Get or Set Restriction data in a SoilProfileCollection

sRGB to Munsell Color Conversion

Convert pH to/from Reaction Classes

DEPRECATED Simulate Soil Profiles

munsellHuePosition

Munsell Hue Position Reference

Rebuild a SoilProfileCollection object

soilColorSignature

Soil Profile Color Signatures

pH Reaction Classes

Soil Color Palette

names,SoilProfileCollection-method

Get names of columns in site and horizons table

[,SoilProfileCollection-method

Matrix/data.frame-like access to profiles and horizons in a SoilProfileCollection

Set profile IDs

Iterate over profiles in a SoilProfileCollection

site,SoilProfileCollection-method

Retrieve site data from SoilProfileCollection

Quickly Assemble a SoilProfileCollection

Soil Physical and Chemical Data from Manganiferous Soils

Set site column names

Simulate Soil Colors

invertLabelColor

Make High Contrast Label Colors

Soil Chemical Data from Serpentinitic Soils of California

Sample Soil Database #5

Munsell Hue Reference and Position Searching

Lookup tables for sand, silt, clay, texture class, and textural modifiers.

Soil Profile Data Example 1

Slab-Wise Aggregation of SoilProfileCollection Objects

isEmpty,SoilProfileCollection-method

Check for "empty" profiles in a SoilProfileCollection

Compute weighted naive and tau statistics for a cross-classification matrix

spc2mpspline,SoilProfileCollection-method

SoilProfileCollection wrapper for mpspline2::mpspline()

Soil Physical and Chemical Data Related to Studies in the Sierra Nevada Mountains, CA, USA.

soilTextureColorPal

Soil Texture Color Palettes

Shuffle Horizons of a SoilProfileCollection

mollic.thickness.requirement

Calculate the minimum thickness requirement for Mollic epipedon

Soil Morphologic, Geochemical, and Mineralogy Data from Rowley et al. 2019.

Mix Munsell Colors via Spectral Library

Generate a SoilProfileCollection of random profiles

Slicing of SoilProfileCollection Objects

validSpatialData,SoilProfileCollection-method

Check for valid spatial reference of profiles

Tukey's HSD Over Slices

Textural conversions

Honcut Creek Soil Profile Data

Soil Profile Data Example 3

Subset SPC based on result of performing function on each profile

transform,SoilProfileCollection-method

Transform a SPC with expressions based on site or horizon level attributes

unique,SoilProfileCollection-method

Uniqueness within a SoilProfileCollection via MD5 Hash

splitLogicErrors

Split a SoilProfileCollection into a list based on types of horizon logic errors

spectral.reference

Standard Illuminants and Observers

Select a subset of columns from a SoilProfileCollection

reorderHorizons

Re-order corrupted horizon data

plot_distance_graph

Between Individual Distance Plot

subsetHz,SoilProfileCollection-method

Subset the horizons in a SoilProfileCollection using logical criteria

Munsell Colors of Common Soil Minerals

subset,SoilProfileCollection-method

Subset a SoilProfileCollection with logical expressions

Quickly assess relative state of site and horizon slots

Shannon Entropy

SoilProfileCollection show method

split,SoilProfileCollection-method

Split a SoilProfileCollection object into a list of SoilProfileCollection objects.

Calculate Thickness of Horizons Matching Logical Criteria

textureTriangleSummary

Soil Texture Low-RV-High as Defined by Quantiles

thompson.bell.darkness

Thompson-Bell (1996) Index

Convert reflectance spectra to closest Munsell chip

Format a LaTeX table with results

traditionalColorNames

Traditional Soil Color Names

DEPRECATED use subset

Perform summaries on groups (from group_by) and create new site or horizon level attributes

Inflate / Deflate Horizon Thickness

Example Data from Wilson et al. 2022

ROSETTA.centroids

Average Hydraulic Parameters from the ROSETTA Model by USDA Soil Texture Class

HzDepthLogicSubset

Subset SoilProfileCollection Objects or Horizons via checkHzDepthLogic

SoilProfileCollection

An S4 object representation of a group of soil profiles.

Fix Overlap within a Sequence via Simulated Annealing