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aqp (version 2.3.1)

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

2,462

Version

2.3.1

License

GPL (>= 3)

Homepage

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

Maintainer

Dylan Beaudette

Last Published

March 20th, 2026

Functions in aqp (2.3.1)

Calculate Relative Positions from Transect Data

addDiagnosticBracket

Annotate Diagnostic Features

Summarize Soil Colors

SoilTextureLevels

Ranking Systems for USDA Soil Texture Classes

addVolumeFraction

Symbolize Volume Fraction within a Soil Profile Collection Plot

Add Depth Brackets

accumulateDepths

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

aggregateSoilDepth

Probabilistic Estimation of Soil Depth within Groups

aggregateColorPlot

Plot aggregate soil color data

Create Soil Profile Sketches

barron.torrent.redness.LAB

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

checkHzDepthLogic

Check a SoilProfileCollection object for errors in horizon depths.

Soil Data from the Central Sierra Nevada Region of California

bootstrapSoilTexture

Bootstrap Soil Texture Data

Allocate soil properties within various classification systems.

aqp_df_class,SoilProfileCollection-method

Get aqp_df_class entry from metadata or return a safe value.

Multinominal Brier Score

buntley.westin.index

Buntley-Westin (1965) Index

argillic.clay.increase.depth

Return upper boundary of argillic horizon

Algorithms for Quantitative Pedology

Convert colors into Munsell Notation

c,SoilProfileCollection-method

Combine SoilProfileCollection objects

Collapse Horizons within Profiles Based on Pattern Matching

Quantitative Description of Color Variation

colorContrastPlot

Color Contrast Plot

Soil Color Range via Quantiles

Metrics of Contrast Suitable for Comparing Soil Colors

Coerce SoilProfileCollection with as()

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

Test for a valid SoilProfileCollection

Compare Site Level Attributes of a SoilProfileCollection

Color Contrast Chart

Apply rock fragment or salt correction to available water content

Confusion Index

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

Return a list representation of site and horizon level data

Return a vector of contributing fractions over a depth interval

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

Soil Color Contrast

crit.clay.argillic

Determines threshold (minimum) clay content for argillic upper bound

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

Get column of horizon or site data in a SoilProfileCollection

diagnostic_hz,SoilProfileCollection-method

Get or Set Diagnostic Horizon data in a SoilProfileCollection

dice,SoilProfileCollection-method

Efficient Slicing of SoilProfileCollection Objects

.colorSig2PerceptualDistMat

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

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

.detectColorSpec

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

Initialize a SoilProfileCollection from data.frame

depth_units,SoilProfileCollection-method

Get depth units from metadata

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

electroStatics_1D

Label placement based on a simulation of electrostatic forces

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

equivalentMunsellChips

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

Estimate available water capacity for fine-earth fraction

estimateSoilColor

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

Evaluate Generalized Horizon Labels

estimateSoilDepth

Estimate Soil Depth

evalMissingData

Evaluate Missing Data within a SoilProfileCollection

equivalent_munsell

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

Duplicate Profiles of a SoilProfileCollection

Fix Overlap within a Sequence

fragmentClasses

Coarse Fragment Class Labels and Diameter

Find and Fill Horizon Gaps

flagOverlappingHz

Flag perfectly overlapping horizons within a SoilProfileCollection

Sieve the Coarse Fraction of Soil

get.increase.matrix

Compute Pair-wise Distances of Soil Properties over Depth

Generate Labels for Slabs

genhzTableToAdjMat

Convert cross-tabulation to adjacency matrix.

Generalize Horizon Names

Visual Explanation for plotSPC

Determine ML Horizon Boundaries

getArgillicBounds

Estimate upper and lower boundary of argillic diagnostic subsurface horizon

getSurfaceHorizonDepth

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

getLastHorizonID

Get IDs of Deepest Horizons by Profile

glom,SoilProfileCollection-method

Subset soil horizon data using a depth or depth interval

getClosestMunsellChip

Get Approximate Munsell Chip

getCambicBounds

Find all intervals that are potentially part of a Cambic horizon

getSoilDepthClass

Generate Soil Depth Class Matrix

Subset SPC with pattern-matching for text-based attributes

Subset an SPC by applying glom to each profile

horizonDepths<-

Set horizon depth column names

guessGenHzLevels

Guess Appropriate Ordering for Generalized Horizon Labels

Store groupings within a profile collection.

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

harden.rubification

Harden (1982) Rubification

horizonColorIndices

Horizon Color Indices

harden.melanization

Harden (1982) Melanization

harmonize,SoilProfileCollection-method

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

guessHzAttrName

Guess Horizon Slot Column Names

groupedProfilePlot

Grouped Soil Profile Plot

hzMetadata,SoilProfileCollection-method

Get horizon-level metadata

huePositionCircle

Visual Description of Munsell Hue Ordering

Tests of horizon depth logic

Munsell Hue Reference and Position Searching

hzDesgn,SoilProfileCollection-method

Get horizon designation column name

Set horizon column names

hzID<-,SoilProfileCollection-method

Set horizon IDs

horizons,SoilProfileCollection-method

Retrieve horizon data from SoilProfileCollection

Hurst (1977) Redness Index

hzDistinctnessCodeToOffset

Convert Horizon Boundary Distinctness to Vertical Offset

hz_to_taxpartsize

Allocate Particle Size Class for the Control Section.

hzTransitionProbabilities

Horizon Transition Probabilities

Select Horizons Above or Below a Reference Horizon

Find lagged horizon values

Intersecting horizon boundaries by horizon depths

Dissolving horizon boundaries by grouping variables

Get or Set Horizon Designation Column Name

Segmenting of Soil Horizon Data by Depth Interval

hzTopographyCodeToOffset

Convert Horizon Boundary Topography to Vertical Offset

hzTopographyCodeToLineType

Convert Horizon Boundary Topography to Line Type

length,SoilProfileCollection-method

Get the number of profiles in a SoilProfileCollection

invertLabelColor

Make High Contrast Label Colors

idname,SoilProfileCollection-method

Get profile ID column name

Fix Common Errors in Munsell Notation

Set horizon ID column name

Soil Morphologic Data from Jacobs et al. 2002.

Get or Set Horizon Metadata Column Name

isEmpty,SoilProfileCollection-method

Check for "empty" profiles in a SoilProfileCollection

Get or Set Horizon Texture Class Column Name

initSpatial<-,SoilProfileCollection,ANY,ANY-method

Initialize Spatial Data in a SoilProfileCollection

mu_confusion_matrix

Map unit confusion matrix and other classification measures

min,SoilProfileCollection-method

Get the minimum bottom depth in a SoilProfileCollection

lookup_taxpartsize

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

max,SoilProfileCollection-method

Get the maximum bottom depth in a SoilProfileCollection

metadata,SoilProfileCollection-method

Retrieve metadata from SoilProfileCollection

Munsell to sRGB Lookup Table for Common Soil Colors

Eliminate duplicate instances of profile IDs in a list of SoilProfileCollections

Mix Munsell Colors via Spectral Library

mollic.thickness.requirement

Calculate the minimum thickness requirement for Mollic epipedon

missingDataGrid

Missing Data Grid

Example Output from soilDB::fetchOSD()

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

Find Overlap within a Sequence

nrow,SoilProfileCollection-method

Get the number of horizons in a SoilProfileCollection

munsell.spectra

Spectral Library of Munsell Colors

panel.depth_function

Lattice Panel Function for Soil Profiles

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

names,SoilProfileCollection-method

Get names of columns in site and horizons table

munsellHuePosition

Munsell Hue Position Reference

munsell2spc,SoilProfileCollection-method

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

Perturb soil horizon depths using boundary distinctness

Parse Munsell Color Notation

Iterate over profiles in a SoilProfileCollection

Combine a list of SoilProfileCollection objects

plotColorMixture

Visualize Spectral Mixing of Munsell Colors

plotProfileDendrogram

Plot soil profiles below a dendrogram or cladogram

plotColorQuantiles

Visualize Color Quantiles

plot_distance_graph

Between Individual Distance Plot

plotMultipleSPC

Plot Multiple SoilProfileCollection Objects

pH Reaction Classes

reorderHorizons

Re-order corrupted horizon data

Select a subset of columns from a SoilProfileCollection

Rebuild a SoilProfileCollection object

Convert pH to/from Reaction Classes

profileGroupLabels

Soil Profile Group Labels

Quickly Assemble a SoilProfileCollection

Set profile IDs

profileInformationIndex

Soil Profile Information Index

repairMissingHzDepths

Repair Problematic Lower Horizon Depths

Generate a SoilProfileCollection of random profiles

Shannon Entropy

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

sRGB to Munsell Color Conversion

replaceHorizons<-

Replace Data in Horizon Slot

restrictions,SoilProfileCollection-method

Get or Set Restriction data in a SoilProfileCollection

Shuffle Horizons of a SoilProfileCollection

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

SoilProfileCollection show method

Soil Color Palette

[,SoilProfileCollection-method

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

Set site column names

Simulate Soil Colors

site,SoilProfileCollection-method

Retrieve site data from SoilProfileCollection

soilColorSignature

Soil Profile Color Signatures

Tukey's HSD Over Slices

Slab-Wise Aggregation of SoilProfileCollection Objects

DEPRECATED Simulate Soil Profiles

Slicing of SoilProfileCollection Objects

Sample Soil Database #5

soilTextureColorPal

Soil Texture Color Palettes

spc2mpspline,SoilProfileCollection-method

SoilProfileCollection wrapper for mpspline2::mpspline()

Soil Profile Data Example 3

Soil Chemical Data from Serpentinitic Soils of California

Soil Profile Data Example 1

Honcut Creek Soil Profile Data

Munsell Colors of Common Soil Minerals

Soil Physical and Chemical Data from Manganiferous Soils

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

Subset SPC based on result of performing function on each profile

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

Quickly assess relative state of site and horizon slots

subset,SoilProfileCollection-method

Subset a SoilProfileCollection with logical expressions

subsetHz,SoilProfileCollection-method

Subset the horizons in a SoilProfileCollection using logical criteria

splitLogicErrors

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

split,SoilProfileCollection-method

Split a SoilProfileCollection object into a list of SoilProfileCollection objects.

Convert reflectance spectra to closest Munsell chip

DEPRECATED use subset

spectral.reference

Standard Illuminants and Observers

textureTriangleSummary

Soil Texture Low-RV-High as Defined by Quantiles

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

validSpatialData,SoilProfileCollection-method

Check for valid spatial reference of profiles

thompson.bell.darkness

Thompson-Bell (1996) Index

Calculate Thickness of Horizons Matching Logical Criteria

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

Textural conversions

traditionalColorNames

Traditional Soil Color Names

validateMunsell

Validate Standard Munsell Notation

Inflate / Deflate Horizon Thickness

Example Data from Wilson et al. 2022

Format a LaTeX table with results