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aqp (version 2.1.0)

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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install.packages('aqp')

Monthly Downloads

2,181

Version

2.1.0

License

GPL (>= 3)

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Repository

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

Homepage

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

Maintainer

Dylan Beaudette

Last Published

October 19th, 2024

Functions in aqp (2.1.0)

SoilProfileCollection

An S4 object representation of a group of soil profiles.

HzDepthLogicSubset

Subset SoilProfileCollection Objects or Horizons via checkHzDepthLogic

SPC.with.overlap

Example SoilProfileCollection with Overlapping Horizons

Fix Overlap within a Sequence via Simulated Annealing

prj,SoilProfileCollection-method

Get or Set Coordinate Reference System for SoilProfileCollection

Get or Set Generalized Horizon Label (GHL) Column Name

ROSETTA.centroids

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

Numerical Classification of Soil Profiles

Create Soil Profile Sketches

addVolumeFraction

Symbolize Volume Fraction within a Soil Profile Collection Plot

Summarize Soil Colors

addDiagnosticBracket

Annotate Diagnostic Features

aggregateSoilDepth

Probabilistic Estimation of Soil Depth within Groups

SoilTextureLevels

Ranking Systems for USDA Soil Texture Classes

Algorithms for Quantitative Pedology

accumulateDepths

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

Calculate Relative Positions from Transect Data

Add Depth Brackets

Allocate soil properties within various classification systems.

buntley.westin.index

Buntley-Westin (1965) Index

checkHzDepthLogic

Check a SoilProfileCollection object for errors in horizon depths.

bootstrapSoilTexture

Bootstrap Soil Texture Data

barron.torrent.redness.LAB

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

Soil Data from the Central Sierra Nevada Region of California

aqp_df_class,SoilProfileCollection-method

Get aqp_df_class entry from metadata or return a safe value.

Test for a valid SoilProfileCollection

Coerce SoilProfileCollection with as()

Multinominal Brier Score

argillic.clay.increase.depth

Return upper boundary of argillic horizon

colorContrastPlot

Color Contrast Plot

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

Metrics of Contrast Suitable for Comparing Soil Colors

Collapse Horizons within Profiles Based on Pattern Matching

Convert colors into Munsell Notation

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

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

diagnostic_hz,SoilProfileCollection-method

Get or Set Diagnostic Horizon data in a SoilProfileCollection

Initialize a SoilProfileCollection from data.frame

Return a list representation of site and horizon level data

Confusion Index

Apply rock fragment or salt correction to available water content

crit.clay.argillic

Determines threshold (minimum) clay content for argillic upper bound

electroStatics_1D

Label placement based on a simulation of electrostatic forces

Estimate available water capacity for fine-earth fraction

equivalent_munsell

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

dice,SoilProfileCollection-method

Efficient Slicing of SoilProfileCollection Objects

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

Soil Color Range via Quantiles

Soil Color Contrast

Return a vector of contributing fractions over a depth interval

depth_units,SoilProfileCollection-method

Get depth units from metadata

flagOverlappingHz

Flag perfectly overlapping horizons within a SoilProfileCollection

equivalentMunsellChips

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

Color Contrast Chart

c,SoilProfileCollection-method

Combine SoilProfileCollection objects

Compare Site Level Attributes of a SoilProfileCollection

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

evalMissingData

Evaluate Missing Data within a SoilProfileCollection

Visual Explanation for plotSPC

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

Find and Fill Horizon Gaps

Fix Overlap within a Sequence

getArgillicBounds

Estimate upper and lower boundary of argillic diagnostic subsurface horizon

Evaluate Generalized Horizon Labels

estimateSoilDepth

Estimate Soil Depth

Determine ML Horizon Boundaries

get.increase.matrix

Compute Pair-wise Distances of Soil Properties over Depth

getClosestMunsellChip

Get Approximate Munsell Chip

getLastHorizonID

Get IDs of Deepest Horizons by Profile

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

Sieve the Coarse Fraction of Soil

Get column of horizon or site data in a SoilProfileCollection

Generate Labels for Slabs

estimateSoilColor

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

getCambicBounds

Find all intervals that are potentially part of a Cambic horizon

Duplicate Profiles of a SoilProfileCollection

Generalize Horizon Names

genhzTableToAdjMat

Convert cross-tabulation to adjacency matrix.

glom,SoilProfileCollection-method

Subset soil horizon data using a depth or depth interval

Subset an SPC by applying glom to each profile

guessHzAttrName

Guess Horizon Slot Column Names

harden.melanization

Harden (1982) Melanization

Store groupings within a profile collection.

fragmentClasses

Coarse Fragment Class Labels and Diameter

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

Subset SPC with pattern-matching for text-based attributes

getSoilDepthClass

Generate Soil Depth Class Matrix

getSurfaceHorizonDepth

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

Munsell Hue Reference and Position Searching

horizons,SoilProfileCollection-method

Retrieve horizon data from SoilProfileCollection

Set horizon column names

horizonDepths<-

Set horizon depth column names

hzTopographyCodeToOffset

Convert Horizon Boundary Topography to Vertical Offset

hzTopographyCodeToLineType

Convert Horizon Boundary Topography to Line Type

guessGenHzLevels

Guess Appropriate Ordering for Generalized Horizon Labels

groupedProfilePlot

Grouped Soil Profile Plot

Dissolving horizon boundaries by grouping variables

Tests of horizon depth logic

hzDesgn,SoilProfileCollection-method

Get horizon designation column name

horizonColorIndices

Horizon Color Indices

hzTransitionProbabilities

Horizon Transition Probabilities

harden.rubification

Harden (1982) Rubification

harmonize,SoilProfileCollection-method

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

huePositionCircle

Visual Description of Munsell Hue Ordering

idname,SoilProfileCollection-method

Get profile ID column name

Horizons Above or Below

Get or Set Horizon Designation Column Name

Intersecting horizon boundaries by horizon depths

hzMetadata,SoilProfileCollection-method

Get horizon-level metadata

Find lagged horizon values

Hurst (1977) Redness Index

hzID<-,SoilProfileCollection-method

Set horizon IDs

Soil Morphologic Data from Jacobs et al. 2002.

length,SoilProfileCollection-method

Get the number of profiles in a SoilProfileCollection

isEmpty,SoilProfileCollection-method

Check for "empty" profiles in a SoilProfileCollection

Segmenting of Soil Horizon Data by Depth Interval

invertLabelColor

Make High Contrast Label Colors

hz_to_taxpartsize

Allocate Particle Size Class for the Control Section.

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

Set horizon ID column name

mollic.thickness.requirement

Calculate the minimum thickness requirement for Mollic epipedon

Mix Munsell Colors via Spectral Library

lookup_taxpartsize

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

Eliminate duplicate instances of profile IDs in a list of SoilProfileCollections

hzDistinctnessCodeToOffset

Convert Horizon Boundary Distinctness to Vertical Offset

Get or Set Horizon Metadata Column Name

panel.depth_function

Lattice Panel Function for Soil Profiles

Parse Munsell Color Notation

min,SoilProfileCollection-method

Get the minimum bottom depth in a SoilProfileCollection

Example Output from soilDB::fetchOSD()

munsell2spc,SoilProfileCollection-method

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

Get or Set Horizon Texture Class Column Name

Munsell to sRGB Lookup Table for Common Soil Colors

munsell.spectra

Spectral Library of Munsell Colors

missingDataGrid

Missing Data Grid

Find Overlap within a Sequence

Combine a list of SoilProfileCollection objects

Perturb soil horizon depths using boundary distinctness

Initialize Spatial Data in a SoilProfileCollection

profileGroupLabels

Soil Profile Group Labels

Quickly Assemble a SoilProfileCollection

Set profile IDs

munsellHuePosition

Munsell Hue Position Reference

sRGB to Munsell Color Conversion

Convert pH to/from Reaction Classes

Deprecated: Numerical Soil Profile Comparison

replaceHorizons<-

Replace Data in Horizon Slot

max,SoilProfileCollection-method

Get the maximum bottom depth in a SoilProfileCollection

restrictions,SoilProfileCollection-method

Get or Set Restriction data in a SoilProfileCollection

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

pH Reaction Classes

metadata,SoilProfileCollection-method

Retrieve metadata from SoilProfileCollection

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

Slab-Wise Aggregation of SoilProfileCollection Objects

Slicing of SoilProfileCollection Objects

Tukey's HSD Over Slices

names,SoilProfileCollection-method

Get names of columns in site and horizons table

nrow,SoilProfileCollection-method

Get the number of horizons in a SoilProfileCollection

plotColorMixture

Visualize Spectral Mixing of Munsell Colors

Subset SPC based on result of performing function on each profile

site,SoilProfileCollection-method

Retrieve site data from SoilProfileCollection

Set site column names

Soil Chemical Data from Serpentinitic Soils of California

plotColorQuantiles

Visualize Color Quantiles

soilColorSignature

Soil Profile Color Signatures

subset,SoilProfileCollection-method

Subset a SoilProfileCollection with logical expressions

Soil Profile Data Example 3

spectral.reference

Standard Illuminants and Observers

plotMultipleSPC

Plot Multiple SoilProfileCollection Objects

Calculate Thickness of Horizons Matching Logical Criteria

Convert reflectance spectra to closest Munsell chip

profileInformationIndex

Soil Profile Information Index

repairMissingHzDepths

Repair Problematic Lower Horizon Depths

thompson.bell.darkness

Thompson-Bell (1996) Index

plot_distance_graph

Between Individual Distance Plot

reorderHorizons

Re-order corrupted horizon data

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

transform,SoilProfileCollection-method

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

Soil Profile Data Example 1

Iterate over profiles in a SoilProfileCollection

soilTextureColorPal

Soil Texture Color Palettes

Soil Color Palette

Soil Physical and Chemical Data from Manganiferous Soils

subsetHz,SoilProfileCollection-method

Subset the horizons in a SoilProfileCollection using logical criteria

DEPRECATED Simulate Soil Profiles

DEPRECATED use subset

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

Honcut Creek Soil Profile Data

Sample Soil Database #5

traditionalColorNames

Traditional Soil Color Names

validSpatialData,SoilProfileCollection-method

Check for valid spatial reference of profiles

Format a LaTeX table with results

spc2mpspline,SoilProfileCollection-method

SoilProfileCollection wrapper for mpspline2::mpspline()

Quickly assess relative state of site and horizon slots

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

Select a subset of columns from a SoilProfileCollection

Shannon Entropy

Textural conversions

Rebuild a SoilProfileCollection object

split,SoilProfileCollection-method

Split a SoilProfileCollection object into a list of SoilProfileCollection objects.

Inflate / Deflate Horizon Thickness

SoilProfileCollection show method

Example Data from Wilson et al. 2022

splitLogicErrors

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

unique,SoilProfileCollection-method

Uniqueness within a SoilProfileCollection via MD5 Hash

Unroll Genetic Horizons

textureTriangleSummary

Soil Texture Low-RV-High as Defined by Quantiles

Simulate Soil Colors

Munsell Colors of Common Soil Minerals

[,SoilProfileCollection-method

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

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

Create Representative Soil Profiles via L1 Estimator