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aqp (version 2.0.2)

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

2,337

Version

2.0.2

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

November 28th, 2023

Functions in aqp (2.0.2)

SoilTextureLevels

Ranking Systems for USDA Soil Texture Classes

addVolumeFraction

Symbolize Volume Fraction on a Soil Profile Collection Plot

accumulateDepths

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

Allocate soil properties within various classification systems.

aggregateSoilDepth

Probabalistic Estimation of Soil Depth within Groups

Multinominal Brier Score

Test for a valid SoilProfileCollection

Calculate Relative Positions from Transect Data

addDiagnosticBracket

Annotate Diagnostic Features

Add Depth Brackets

Summarize Soil Colors

Algorithms for Quantitative Pedology

aqp_df_class,SoilProfileCollection-method

Get aqp_df_class entry from metadata or return a safe value.

buntley.westin.index

Buntley-Westin (1965) Index

barron.torrent.redness.LAB

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

Coerce SoilProfileCollection with as()

checkHzDepthLogic

Check a SoilProfileCollection object for errors in horizon depths.

bootstrapSoilTexture

Bootstrap Soil Texture Data

argillic.clay.increase.depth

Return upper boundary of argillic horizon

Soil Data from the Central Sierra Nevada Region of California

c,SoilProfileCollection-method

Combine SoilProfileCollection objects

Soil Color Range via Quantiles

Compare Site Level Attributes of a SoilProfileCollection

Return a list representation of site and horizon level data

diagnostic_hz<-

Add Data to Diagnostic Features Slot

diagnostic_hz,SoilProfileCollection-method

Retrieve diagnostic data from SoilProfileCollection

Confusion Index

Convert colors into Munsell Notation

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

equivalentMunsellChips

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

equivalent_munsell

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

dice,SoilProfileCollection-method

Efficient Slicing of SoilProfileCollection Objects

Dissolving horizon boundaries by grouping variables

Apply rock fragment or salt correction to available water content

Soil Color Contrast

Initialize a SoilProfileCollection from data.frame

Get column of horizon or site data in a SoilProfileCollection

estimateSoilColor

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

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

electroStatics_1D

Label placement based on a simulation of electrostatic forces

depth_units,SoilProfileCollection-method

Get depth units from metadata

Metrics of Contrast Suitable for Comparing Soil Colors

colorContrastPlot

Color Contrast Plot

Evaluate Generalized Horizon Labels

Duplicate Profiles of a SoilProfileCollection

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

estimateSoilDepth

Estimate Soil Depth

Color Contrast Chart

Fix Overlap within a Sequence

genhzTableToAdjMat

Convert cross-tabulation to adjacency matrix.

flagOverlappingHz

Flag perfectly overlapping horizons within a SoilProfileCollection

evalMissingData

Evaluate Missing Data within a SoilProfileCollection

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

crit.clay.argillic

Determines threshold (minimum) clay content for argillic upper bound

getClosestMunsellChip

Get Approximate Munsell Chip

Determine ML Horizon Boundaries

getCambicBounds

Find all intervals that are potentially part of a Cambic horizon

getLastHorizonID

Get IDs of Deepest Horizons by Profile

getSoilDepthClass

Generate Soil Depth Class Matrix

get.increase.matrix

Compute Pair-wise Distances of Soil Properties over Depth

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

Find and Fill Horizon Gaps

fragmentClasses

Coarse Fragment Class Labels and Diameter

Visual Explanation for plotSPC

harden.melanization

Harden (1982) Melanization

Return a vector of contributing fractions over a depth interval

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

Sieve the Coarse Fraction of Soil

harden.rubification

Harden (1982) Rubification

Store groupings within a profile collection.

getArgillicBounds

Estimate upper and lower boundary of argillic diagnostic subsurface horizon

Estimate available water capacity for fine-earth fraction

groupedProfilePlot

Grouped Soil Profile Plot

Horizons Above or Below

Hurst (1977) Redness Index

hzTopographyCodeToLineType

Convert Horizon Boundary Topography to Line Type

getSurfaceHorizonDepth

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

Generalize Horizon Names

Generate Labels for Slabs

Estimate boundaries of the particle size control section (U.S Soil Taxonomy; 12th edition)

Tests of horizon depth logic

length,SoilProfileCollection-method

Get the number of profiles in a SoilProfileCollection

harmonize,SoilProfileCollection-method

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

hzTransitionProbabilities

Horizon Transition Probabilities

glom,SoilProfileCollection-method

Subset soil horizon data using a depth or depth interval

Mix Munsell Colors via Spectral Library

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

Eliminate duplicate instances of profile IDs in a list of SoilProfileCollections

guessHzAttrName

Guess Horizon Slot Column Names

guessGenHzLevels

Guess Appropriate Ordering for Generalized Horizon Labels

hzTopographyCodeToOffset

Convert Horizon Boundary Topography to Vertical Offset

Set horizon ID column name

Get or Set Horizon Designation Column Name

Munsell to sRGB Lookup Table for Common Soil Colors

Set horizon column names

horizons,SoilProfileCollection-method

Retrieve horizon data from SoilProfileCollection

munsell2spc,SoilProfileCollection-method

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

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

Example Output from soilDB::fetchOSD()

munsell.spectra

Spectral Library of Munsell Colors

Combine a list of SoilProfileCollection objects

Perturb soil horizon depths using boundary distinctness

Find Overlap within a Sequence

Get or Set Horizon Texture Class Column Name

plotMultipleSPC

Plot Multiple SoilProfileCollection Objects

Parse Munsell Color Notation

idname,SoilProfileCollection-method

Get profile ID column name

huePositionCircle

Visual Description of Munsell Hue Ordering

plotColorMixture

Visualize Spectral Mixing of Munsell Colors

Munsell Hue Reference and Position Searching

panel.depth_function

Lattice Panel Function for Soil Profiles

plot_distance_graph

Between Individual Distance Plot

mollic.thickness.requirement

Calculate the minimum thickness requirement for Mollic epipedon

Subset SPC with pattern-matching for text-based attributes

Subset an SPC by applying glom to each profile

plotColorQuantiles

Visualize Color Quantiles

Rebuild a SoilProfileCollection object

Select a subset of columns from a SoilProfileCollection

nrow,SoilProfileCollection-method

Get the number of horizons in a SoilProfileCollection

names,SoilProfileCollection-method

Get names of columns in site and horizons table

profileGroupLabels

Soil Profile Group Labels

Soil Morphologic Data from Jacobs et al. 2002.

isEmpty,SoilProfileCollection-method

Check for "empty" profiles in a SoilProfileCollection

horizonColorIndices

Horizon Color Indices

hzDesgn,SoilProfileCollection-method

Get horizon designation column name

min,SoilProfileCollection-method

Get the minimum bottom depth in a SoilProfileCollection

hzMetadata,SoilProfileCollection-method

Get horizon-level metadata

horizonDepths<-

Set horizon depth column names

hzID<-,SoilProfileCollection-method

Set horizon IDs

missingDataGrid

Missing Data Grid

Deprecated: Numerical Soil Profile Comparison

Segmenting of Soil Horizon Data by Depth Interval

hzDistinctnessCodeToOffset

Convert Horizon Boundary Distinctness to Vertical Offset

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

Initialize Spatial Data in a SoilProfileCollection

max,SoilProfileCollection-method

Get the maximum bottom depth in a SoilProfileCollection

site,SoilProfileCollection-method

Retrieve site data from SoilProfileCollection

Convert pH to/from Reaction Classes

DEPRECATED Simulate Soil Profiles

invertLabelColor

Make High Contrast Label Colors

Set site column names

pH Reaction Classes

profileInformationIndex

Soil Profile Information Index

Quickly Assemble a SoilProfileCollection

[,SoilProfileCollection-method

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

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

Tukey's HSD Over Slices

soilColorSignature

Soil Profile Color Signatures

Simulate Soil Colors

Soil Profile Data Example 1

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

Quickly assess relative state of site and horizon slots

Set profile IDs

Convert reflectance spectra to closest Munsell chip

metadata,SoilProfileCollection-method

Retrieve metadata from SoilProfileCollection

Honcut Creek Soil Profile Data

Soil Profile Data Example 3

subset,SoilProfileCollection-method

Subset a SoilProfileCollection with logical expressions

subsetHz,SoilProfileCollection-method

Subset the horizons in a SoilProfileCollection using logical criteria

transform,SoilProfileCollection-method

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

DEPRECATED use subset

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

traditionalColorNames

Traditional Soil Color Names

Add Data to Restrictions Slot

sRGB to Munsell Color Conversion

replaceHorizons<-

Replace Data in Horizon Slot

restrictions,SoilProfileCollection-method

Retrieve restriction data from SoilProfileCollection

Soil Chemical Data from Serpentinitic Soils of California

textureTriangleSummary

Soil Texture Low-RV-High as Defined by Quantiles

Format a LaTeX table with results

Sample Soil Database #5

split,SoilProfileCollection-method

Split a SoilProfileCollection object into a list of SoilProfileCollection objects.

thompson.bell.darkness

Thompson-Bell (1996) Index

Slab-Wise Aggregation of SoilProfileCollection Objects

Slicing of SoilProfileCollection Objects

spectral.reference

Standard Illuminants and Observers

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

Inflate / Deflate Horizon Thickness

Textural conversions

Example Data from Wilson et al. 2022

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

unique,SoilProfileCollection-method

Uniqueness within a SoilProfileCollection via MD5 Hash

Unroll Genetic Horizons

munsellHuePosition

Munsell Hue Position Reference

Iterate over profiles in a SoilProfileCollection

validSpatialData,SoilProfileCollection-method

Check for valid spatial reference of profiles

repairMissingHzDepths

Repair Problematic Lower Horizon Depths

reorderHorizons

Re-order corrupted horizon data

Shannon Entropy

Soil Color Palette

Subset SPC based on result of performing function on each profile

splitLogicErrors

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

spc2mpspline,SoilProfileCollection-method

SoilProfileCollection wrapper for mpspline2::mpspline()

Munsell Colors of Common Soil Minerals

Soil Physical and Chemical Data from Manganiferous Soils

SoilProfileCollection show method

SoilProfileCollection

An S4 object representation of a group of soil profiles.

Create Soil Profile Sketches

prj,SoilProfileCollection-method

Get or Set Coordinate Reference System for SoilProfileCollection

Create Representative Soil Profiles via L1 Estimator

HzDepthLogicSubset

Subset SoilProfileCollection Objects or Horizons via checkHzDepthLogic

Get or Set Generalized Horizon Label (GHL) Column Name

Fix Overlap within a Sequence via Simulated Annealing

ROSETTA.centroids

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

SPC.with.overlap

Example SoilProfileCollection with Overlapping Horizons

Numerical Classification of Soil Profiles