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aqp (version 1.25)

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

2,609

Version

1.25

License

GPL (>= 3)

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Repository

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

Maintainer

Dylan Beaudette

Last Published

October 19th, 2020

Functions in aqp (1.25)

addVolumeFraction

Symbolize Volume Fraction on a Soil Profile Collection Plot

SoilProfileCollection

An S4 object representation of a group of soil profiles.

Add Depth Brackets

aggregateSoilDepth

Probabalistic Estimation of Soil Depth

ROSETTA.centroids

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

Summarize Soil Colors

SoilTextureLevels

Generate a vector of USDA soil texture codes or class names, sorted according to approximate particle size

Slicing of SoilProfilecollection Objects

Create Soil Profile Sketches

Slab-Wise Aggregation of SoilProfileCollection Objects

barron.torrent.redness.LAB

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

argillic.clay.increase.depth

Return upper boundary of argillic horizon

Algorithms for Quantitative Pedology

Get aqp_df_class entry from metadata or return a safe value.

combine,SoilProfileCollection-method

Combine SoilProfileCollection objects

Return a list representation of site and horizon level data

Coerce SoilProfileCollection with as()

Color Contrast Chart

Confusion Index

Metrics of Contrast Suitable for Comparing Soil Colors

buntley.westin.index

Buntley-Westin (1965) Index

Soil Data from the Central Sierra Nevada Region of California

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

crit.clay.argillic

Determines threshold (minimum) clay content for argillic upper bound

colorContrastPlot

Color Contrast Plot

Test for a valid SoilProfileCollection

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

Soil Color Contrast

checkHzDepthLogic

Check a SoilProfileCollection object for errors in horizon depths.

Return a vector of contributing fractions over a depth interval

Get coordinates from spatial slot

Soil Color Range via Quantiles

Multinominal Brier score

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

bootstrapSoilTexture

Bootstrap Soil Texture Data

Get depth units from metadata

Duplicte Profiles of a SoilProfileColection

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

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

getArgillicBounds

Estimate upper and lower boundary of argillic diagnostic subsurface horizon

Visual Explanation for plotSPC

evalMissingData

Evaluate Missing Data

getSurfaceHorizonDepth

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

getSoilDepthClass

Generate Soil Depth Class Matrix

Example Objective Function for Full-Pattern Matching

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

Get column of horizon or site data in a SoilProfileCollection

Attempt to fix overlapping sketches when using relative horizontal spacing.

Subset SPC with pattern-matching for text-based attributes

[EXPERIMENTAL] Store groupings within a profile collection.

getCambicBounds

Find all intervals that are potentially part of a Cambic horizon

guessHzDesgnName

Guess Horizon Designation Column Name

guessHzAttrName

Guess Arbitrary Horizon Column Name

diagnostic_hz<-

Add data to the diagnostic slot

Generalize Horizon Names

Retrieve diagnostic data from SoilProfileCollection

glom,SoilProfileCollection-method

Subset soil horizon data using a depth or depth interval

Subset an SPC by applying glom to each profile

estimateSoilDepth

Estimate Soil Depth

get.increase.depths

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

Evaluate Generalized Horizon Labels

harden.rubification

Harden (1982) Rubification

groupedProfilePlot

Grouped Soil Profile Plot

guessGenHzLevels

Guess Appropriate Ordering for Generalized Horizon Labels

Hurst (1977) Redness Index

Tests of horizon depth logic

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

Set horizon texture class column name

Get horizon texture class column name

Set horizon ID column name

Get profile ID column name

horizonColorIndices

Horizon Color Indices

depths<-,SoilProfileCollection-method

Initialize a SoilProfileCollection from a data.frame object

Munsell Hue Position for Soil Color Description

Retrieve horizon data from SoilProfileCollection

harmonize,SoilProfileCollection-method

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

harden.melanization

Harden (1982) Melanization

.parseHSD_formula

.parseHSD_formula

Determine ML Horizon Boundaries

guessHzTexClName

Guess Horizon Texture Class Column Name

get.increase.matrix

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

invertLabelColor

Make High Contrast Label Colors

hzTopographyCodeToLineType

Convert Horizon Boundary Topography Distinctness to Line Type

Soil Morphologic Data from Jacobs et al. 2002.

Get horizon designation column name

hzTransitionProbabilities

Horizon Transition Probabilities

Get the number of horizons in a SoilProfileCollection

plotMultipleSPC

Plot Multiple SoilProfileCollection Objects

Get names of columns in site and horizons table

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

hzDistinctnessCodeToOffset

Convert Horizon Boundary Distinctness to Vertical Offset

horizonDepths<-

Set horizon depth column names

Set horizon column names

Convert Munsell Notation to and from sRGB color coordinates

plot_distance_graph

Between Individual Distance Plot

Retrieve metadata from SoilProfileCollection

Get the maximum bottom depth in a SoilProfileCollection

Set horizon IDs

Set horizon designation column name

Get horizon designation column name

panel.depth_function

Lattice Panel Function for Soil Profiles

munsell2spc,SoilProfileCollection-method

Merge Munsell Hue, Value, Chroma converted to RGB & LAB into a SoilProfileCollection

pms.munsell.lut

Pantone Colors / Munsell Lookup Table

Get the number of profiles in a SoilProfileCollection

Munsell to sRGB Lookup Table for Common Soil Colors

Eliminate duplicate instances of profile IDs in a list of SoilProfileCollections

Get horizon IDs

replaceHorizons<-

Replace data in the horizon slot

reorderHorizons

Re-order corrupted horizon data

proj4string,SoilProfileCollection-method

Set PROJ4 string for the SoilProfileCollection

Retrieve restriction data from SoilProfileCollection

proj4string<-,SoilProfileCollection,ANY-method

Set PROJ4 string for the SoilProfileCollection

Shannon Entropy

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

Tukey's HSD Over Slices

Combine a list of SoilProfileCollection objects

Set profile IDs

Simulate Soil Profiles

Set site column names

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

munsell.spectra

Spectral Library of Munsell Colors

profileGroupLabels

Soil Profile Group Labels

Iterate over profiles in a SoilProfileCollection

profile_compare-methods

Numerical Soil Profile Comparison

Sample XRD Patterns

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

Segmenting of horizon data into depth intervals

SoilProfileCollection show method

Unroll Genetic Horizons

split,SoilProfileCollection-method

Split a SoilProfileCollection object into a list of SoilProfileCollection objects.

Munsell Colors of Common Soil Minerals

Subset SPC based on result of performing function on each profile

Textural conversions

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

textureTriangleSummary

Soil Texture Low-RV-High as Defined by Quantiles

missingDataGrid

Missing Data Grid

mollic.thickness.requirement

Calculate the minimum thickness requirement for Mollic epipedon

Get the minimum bottom depth in a SoilProfileCollection

Mix Munsell Colors via Spectral Library

Soil Profile Data Example 3

subset,SoilProfileCollection-method

Subset a SoilProfileCollection with logical expressions

Rebuild a SoilProfileCollection object

subsetProfiles-methods

Subset SoilProfileCollection Objects.

thompson.bell.darkness

Thompson-Bell (1996) Index

Soil Color Palette

soilColorSignature

Soil Profile Color Signatures

Sample Soil Database #5

Soil Chemical Data from Serpentinitic Soils of California

Soil Physical and Chemical Data from Manganiferous Soils

trunc,SoilProfileCollection-method

Truncate a SoilProfileCollection to specified top and bottom depth

Quickly assess relative state of site and horizon slots

spc2mpspline,SoilProfileCollection-method

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

union,list,missing-method

[DEPRECATED] union

Get the indexes of unique profiles in a SoilProfileCollection

plotColorMixture

Visualize Spectral Mixing of Munsell Colors

Add data to the restrictions slot

Retrieve site data from SoilProfileCollection

Honcut Creek Soil Profile Data

permute_profile

Permute soil horizon depths using boundary distinctness

[,SoilProfileCollection-method

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

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

resample.twotheta

Resample an XRD Pattern

Soil Profile Data Example 1

Compute weighted na<U+00EF>ve and tau statistics for a cross-classification matrix

validSpatialData

Get names of columns in site table