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aqp (version 1.29)

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

install.packages('aqp')

Monthly Downloads

2,080

Version

1.29

License

GPL (>= 3)

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Repository

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

Maintainer

Dylan Beaudette

Last Published

April 7th, 2021

Functions in aqp (1.29)

Add Depth Brackets

addVolumeFraction

Symbolize Volume Fraction on a Soil Profile Collection Plot

Create Soil Profile Sketches

SoilTextureLevels

Ranking Systems for USDS Soil Texture Classes

Summarize Soil Colors

Create Representative Soil Profiles via L1 Estimator

HzDepthLogicSubset

Subset SoilProfileCollection Objects or Horizons via checkHzDepthLogic

addDiagnosticBracket

Annotate Diagnostic Features

ROSETTA.centroids

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

barron.torrent.redness.LAB

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

aggregateSoilDepth

Probabalistic Estimation of Soil Depth within Groups

Multinominal Brier Score

Calculate Relative Positions from Transect Data

buntley.westin.index

Buntley-Westin (1965) Index

colorContrastPlot

Color Contrast Plot

Metrics of Contrast Suitable for Comparing Soil Colors

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

Return a vector of contributing fractions over a depth interval

Soil Data from the Central Sierra Nevada Region of California

checkHzDepthLogic

Check a SoilProfileCollection object for errors in horizon depths.

Get aqp_df_class entry from metadata or return a safe value.

bootstrapSoilTexture

Bootstrap Soil Texture Data

Get depth units from metadata

depths<-,SoilProfileCollection-method

Initialize a SoilProfileCollection from a data.frame object

argillic.clay.increase.depth

Return upper boundary of argillic horizon

diagnostic_hz<-

Add data to the diagnostic slot

SoilProfileCollection

An S4 object representation of a group of soil profiles.

Coerce SoilProfileCollection with as()

Soil Color Contrast

Test for a valid SoilProfileCollection

Confusion Index

Return a list representation of site and horizon level data

Color Contrast Chart

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

Efficient Slicing of SoilProfileCollection Objects

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

Get coordinates from spatial slot

Apply rock fragment or salt correction to available water content

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

Allocate soil properties within various classification systems.

Visual Explanation for plotSPC

estimateSoilDepth

Estimate Soil Depth

Algorithms for Quantitative Pedology

Soil Color Range via Quantiles

getLastHorizonID

Get IDs of Deepest Horizons by Profile

getArgillicBounds

Estimate upper and lower boundary of argillic diagnostic subsurface horizon

Retrieve diagnostic data from SoilProfileCollection

Duplicte Profiles of a SoilProfileCollection

equivalentMunsellChips

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

c,SoilProfileCollection-method

Combine SoilProfileCollection objects

Determine ML Horizon Boundaries

crit.clay.argillic

Determines threshold (minimum) clay content for argillic upper bound

.as.data.frame.aqp

Wrapper method for data.frame subclass conversion

.makeEquivalentMunsellLUT

.makeEquivalentMunsellLUT

Example Objective Function for Full-Pattern Matching

get.increase.depths

Return the horizon top depths from a call to get.increase.matrix()

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

Get column of horizon or site data in a SoilProfileCollection

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

Subset an SPC by applying glom to each profile

get.increase.matrix

compute pair-wise distances to determine where an attribute increases within a vertical distance specified

Set horizon IDs

(EXPERIMENTAL) Store groupings within a profile collection.

getSoilDepthClass

Generate Soil Depth Class Matrix

hzDistinctnessCodeToOffset

Convert Horizon Boundary Distinctness to Vertical Offset

Set horizon designation column name

equivalent_munsell

Indices of "equivalent" Munsell chips in munsell data set

Fix Overlap within a Sequence via Simulated Annealing

Estimate available water capacity for fine-earth fraction

Make a data.frame from non-standard expressions evaluated in a data environment

getSurfaceHorizonDepth

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

.parseGrouped_formula

.parseHSD_formula

harmonize,SoilProfileCollection-method

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

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

groupedProfilePlot

Grouped Soil Profile Plot

Find and Fill Horizon Gaps

Subset SPC with pattern-matching for text-based attributes

Mix Munsell Colors via Spectral Library

Get horizon designation column name

Evaluate Generalized Horizon Labels

evalMissingData

Evaluate Missing Data

Tests of horizon depth logic

mollic.thickness.requirement

Calculate the minimum thickness requirement for Mollic epipedon

Combine a list of SoilProfileCollection objects

Generalize Horizon Names

guessGenHzLevels

Guess Appropriate Ordering for Generalized Horizon Labels

horizonDepths<-

Set horizon depth column names

hzTopographyCodeToLineType

Convert Horizon Boundary Topography to Line Type

horizonColorIndices

Horizon Color Indices

Get horizon IDs

guessHzAttrName

Guess Arbitrary Horizon Column Name

Hurst (1977) Redness Index

Munsell Hue Position for Soil Color Description

hzTopographyCodeToOffset

Convert Horizon Boundary Topography to Vertical Offset

hzTransitionProbabilities

Horizon Transition Probabilities

Find Overlap within a Sequence

Numerical Soil Profile Comparison

Retrieve metadata from SoilProfileCollection

Get the maximum bottom depth in a SoilProfileCollection

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

glom,SoilProfileCollection-method

Subset soil horizon data using a depth or depth interval

guessHzDesgnName

Guess Horizon Designation Column Name

plot_distance_graph

Between Individual Distance Plot

invertLabelColor

Make High Contrast Label Colors

pms.munsell.lut

Pantone Colors / Munsell Lookup Table

munsell.spectra

Spectral Library of Munsell Colors

Munsell to sRGB Lookup Table for Common Soil Colors

Soil Morphologic Data from Jacobs et al. 2002.

Get horizon designation column name

proj4string<-,SoilProfileCollection,ANY-method

Set PROJ4 string for the SoilProfileCollection

proj4string,SoilProfileCollection-method

Set PROJ4 string for the SoilProfileCollection

soilColorSignature

Soil Profile Color Signatures

Soil Color Palette

textureTriangleSummary

Soil Texture Low-RV-High as Defined by Quantiles

panel.depth_function

Lattice Panel Function for Soil Profiles

thompson.bell.darkness

Thompson-Bell (1996) Index

Get profile ID column name

Get horizon texture class column name

Get the minimum bottom depth in a SoilProfileCollection

Find and Quantify Overlap within a 1D Sequence

Get the number of horizons in a SoilProfileCollection

missingDataGrid

Missing Data Grid

getClosestMunsellChip

Get Approximate Munsell Chip

getCambicBounds

Find all intervals that are potentially part of a Cambic horizon

harden.melanization

Harden (1982) Melanization

guessHzTexClName

Guess Horizon Texture Class Column Name

Set horizon column names

Parse Munsell Color Notation

Retrieve horizon data from SoilProfileCollection

munsell2spc,SoilProfileCollection-method

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

profileGroupLabels

Soil Profile Group Labels

harden.rubification

Harden (1982) Rubification

Rebuild a SoilProfileCollection object

Set profile IDs

Set horizon texture class column name

Get the number of profiles in a SoilProfileCollection

Set horizon ID column name

plotColorQuantiles

Visualize Color Quantiles

Eliminate duplicate instances of profile IDs in a list of SoilProfileCollections

[,SoilProfileCollection-method

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

Iterate over profiles in a SoilProfileCollection

DEPRECATED Simulate Soil Profiles

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

replaceHorizons<-

Replace data in the horizon slot

reorderHorizons

Re-order corrupted horizon data

plotMultipleSPC

Plot Multiple SoilProfileCollection Objects

resample.twotheta

Resample an XRD Pattern

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

Munsell Colors of Common Soil Minerals

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

Perturb soil horizon depths using boundary distinctness

plotColorMixture

Visualize Spectral Mixing of Munsell Colors

Get names of columns in site and horizons table

Add data to the restrictions slot

Shannon Entropy

Slicing of SoilProfileCollection Objects

SoilProfileCollection show method

repairMissingHzDepths

Repair Problematic Lower Horizon Depths

Sample Soil Database #5

Soil Physical and Chemical Data from Manganiferous Soils

Tukey's HSD Over Slices

Retrieve site data from SoilProfileCollection

Soil Profile Data Example 1

Retrieve restriction data from SoilProfileCollection

Soil Profile Data Example 3

Set site column names

sRGB to Munsell Color Conversion

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

Sample XRD Patterns

transform,SoilProfileCollection-method

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

trunc,SoilProfileCollection-method

Truncate a SoilProfileCollection to specified top and bottom depth

Slab-Wise Aggregation of SoilProfileCollection Objects

split,SoilProfileCollection-method

Split a SoilProfileCollection object into a list of SoilProfileCollection objects.

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

Soil Chemical Data from Serpentinitic Soils of California

splitLogicErrors

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

Honcut Creek Soil Profile Data

Textural conversions

Segmenting of Soil Horizon Data by Depth Interval

Format a LaTeX table with results

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

Subset SPC based on result of performing function on each profile

validSpatialData

Get names of columns in site table

subset,SoilProfileCollection-method

Subset a SoilProfileCollection with logical expressions

DEPRECATED use subset

Get the indexes of unique profiles in a SoilProfileCollection

Quickly assess relative state of site and horizon slots

spc2mpspline,SoilProfileCollection-method

Missing-data-safe, SPC-wide wrapper around mpspline2::mpspline "continuous" 1cm output

Unroll Genetic Horizons