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aqp (version 1.19)

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

2,609

Version

1.19

License

GPL (>= 3)

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Maintainer

Dylan Beaudette

Last Published

January 24th, 2020

Functions in aqp (1.19)

aggregateColor

Summarize Soil Colors
checkSPC

Test for a valid SoilProfileCollection
SoilProfileCollection-plotting-methods

Profile Plot
checkHzDepthLogic

Check a SoilProfileCollection object for errors in horizon depths.
slab-methods

Slab-Wise Aggregation of SoilProfileCollection Objects
aggregateSoilDepth

Probabalistic Estimation of Soil Depth
clod.hz.ids

Return the unique horizon IDs within a "depth-clod"
colorContrastPlot

Color Contrast Plot
confusionIndex

Confusion Index
SPC-utils

Getters, Setters, and Utility Methods for SoilProfileCollection Objects
getArgillicBounds

getArgillicBounds
get.ml.hz

Determine ML Horizon Boundaries
colorContrast

Metrics of Contrast Suitable for Comparing Soil Colors
harden.rubification

Harden (1982) Rubification
hzDepthTests

Tests of horizon depth logic
slice-methods

Slicing of SoilProfilecollection Objects
addBracket

Add Depth Brackets
horizonColorIndices

Horizon Color Indices
fixOverlap

Attempt to fix overlapping sketches when using relative horizontal spacing.
buntley.westin.index

Buntley-Westin (1965) Index
generalize.hz

Generalize Horizon Names
plotMultipleSPC

Plot Multiple SoilProfileCollection Objects
colorQuantiles

Soil Color Range via Quantiles
hzDistinctnessCodeToOffset

Convert Horizon Distinctness Codes
barron.torrent.redness.LAB

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

Soil Profile Group Labels
SoilProfileCollection-class

SoilProfileCollection Class
addVolumeFraction

Symbolize Volume Fraction on a Soil Profile Collection Plot
plot_distance_graph

Between Individual Distance Plot
ca630

Soil Data from the Central Sierra Nevada Region of California
aqp-package

Algorithms for Quantitative Pedology
contrastClass

Soil Color Contrast
contrastChart

Color Contrast Chart
estimateSoilDepth

Estimate Soil Depth
rebuildSPC

Rebuild a SoilProfileCollection object
brierScore

Multinominal Brier score
sp1

Soil Profile Data Example 1
denormalize

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

Get Indices to Unique Soil Profiles Within a Collection
profile_compare-methods

Numerical Soil Profile Comparison
munsell

Munsell to sRGB Lookup Table for Common Soil Colors
estimatePSCS

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

Return upper boundary of argillic horizon
sp3

Soil Profile Data Example 3
sp2

Honcut Creek Soil Profile Data
f.noise

Example Objective Function for Full-Pattern Matching
evalGenHZ

Evaluate Generalized Horizon Labels
crit.clay.argillic

Determines threshold (minimum) clay content for argillic upper bound
missingDataGrid

Missing Data Grid
evalMissingData

Evaluate Missing Data
get.increase.depths

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

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

Random Profile
sp4

Soil Chemical Data from Serpentinitic Soils of California
thompson.bell.darkness

Thompson-Bell (1996) Index
huePosition

Munsell Hue Position for Soil Color Description
getSoilDepthClass

Generate Soil Depth Class Matrix
textureTriangleSummary

Soil Texture Low-RV-High as Defined by Quantiles
hurst.redness

Hurst (1977) Redness Index
getSurfaceHorizonDepth

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

Guess Appropriate Ordering for Generalized Horizon Labels
soilColorSignature

Soil Profile Color Signatures
glom

Return a "ragged" group of horizons selected from SoilProfileCollection
previewColors

Preview Colors
harden.melanization

Harden (1982) Melanization
groupedProfilePlot

Grouped Soil Profile Plot
sim

Simulate Soil Profiles
soilPalette

Sol Color Palette
hzTransitionProbabilities

Horizon Transition Probabilities
panel.depth_function

Lattice Panel Function for Soil Profiles
munsell2rgb

Convert Munsell Notation to and from sRGB color coordinates
soil_minerals

Munsell Colors of Common Soil Minerals
rruff.sample

Sample XRD Patterns
profileApply-methods

Apply a function to soil profiles within a SoilProfileCollection object.
sp5

Sample Soil Database #5
resample.twotheta

Resample an XRD Pattern
jacobs2000

Soil Morphologic Data from Jacobs et al. 2002.
rowley2019

Soil Morphologic, Geochemical, and Mineralogy Data from Rowley et al. 2019.
sp6

Soil Physical and Chemical Data from Manganiferous Soils
tau

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

Shannon Entropy
unroll

Unroll Genetic Horizons
union

Combine Multiple SoilProfileCollection Objects
subsetProfiles-methods

Subset SoilProfileCollection Objects.