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aqp (version 2.0.3)

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

2.0.3

License

GPL (>= 3)

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Maintainer

Dylan Beaudette

Last Published

April 18th, 2024

Functions in aqp (2.0.3)

prj,SoilProfileCollection-method

Get or Set Coordinate Reference System for SoilProfileCollection
SoilProfileCollection

An S4 object representation of a group of soil profiles.
ROSETTA.centroids

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

Subset SoilProfileCollection Objects or Horizons via checkHzDepthLogic
SANN_1D

Fix Overlap within a Sequence via Simulated Annealing
GHL

Get or Set Generalized Horizon Label (GHL) Column Name
L1_profiles

Create Representative Soil Profiles via L1 Estimator
SPC.with.overlap

Example SoilProfileCollection with Overlapping Horizons
plotSPC

Create Soil Profile Sketches
NCSP

Numerical Classification of Soil Profiles
aggregateSoilDepth

Probabilistic Estimation of Soil Depth within Groups
SoilTextureLevels

Ranking Systems for USDA Soil Texture Classes
allocate

Allocate soil properties within various classification systems.
aqp-package

Algorithms for Quantitative Pedology
brierScore

Multinominal Brier Score
barron.torrent.redness.LAB

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

Calculate Relative Positions from Transect Data
buntley.westin.index

Buntley-Westin (1965) Index
aqp_df_class,SoilProfileCollection-method

Get aqp_df_class entry from metadata or return a safe value.
argillic.clay.increase.depth

Return upper boundary of argillic horizon
as

Coerce SoilProfileCollection with as()
accumulateDepths

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

Test for a valid SoilProfileCollection
bootstrapSoilTexture

Bootstrap Soil Texture Data
compositeSPC

Return a list representation of site and horizon level data
compareSites

Compare Site Level Attributes of a SoilProfileCollection
colorQuantiles

Soil Color Range via Quantiles
c,SoilProfileCollection-method

Combine SoilProfileCollection objects
confusionIndex

Confusion Index
contrastChart

Color Contrast Chart
colorChart

Visualize soil colors in Munsell notation according to within-group frequency.
col2Munsell

Convert colors into Munsell Notation
diagnostic_hz<-

Add Data to Diagnostic Features Slot
diagnostic_hz,SoilProfileCollection-method

Retrieve diagnostic data from SoilProfileCollection
contrastClass

Soil Color Contrast
correctAWC

Apply rock fragment or salt correction to available water content
denormalize

Create a (redundant) horizon-level attribute from a site-level attribute
crit.clay.argillic

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

Check a SoilProfileCollection object for errors in horizon depths.
aggregateColor

Summarize Soil Colors
addVolumeFraction

Symbolize Volume Fraction on a Soil Profile Collection Plot
depthOf

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

Return a vector of contributing fractions over a depth interval
ca630

Soil Data from the Central Sierra Nevada Region of California
electroStatics_1D

Label placement based on a simulation of electrostatic forces
duplicate

Duplicate Profiles of a SoilProfileCollection
addBracket

Add Depth Brackets
depth_units,SoilProfileCollection-method

Get depth units from metadata
addDiagnosticBracket

Annotate Diagnostic Features
colorContrastPlot

Color Contrast Plot
colorContrast

Metrics of Contrast Suitable for Comparing Soil Colors
[[

Get column of horizon or site data in a SoilProfileCollection
[[<-

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

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

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

Dissolving horizon boundaries by grouping variables
dice,SoilProfileCollection-method

Efficient Slicing of SoilProfileCollection Objects
depths

Initialize a SoilProfileCollection from data.frame
estimateAWC

Estimate available water capacity for fine-earth fraction
evalGenHZ

Evaluate Generalized Horizon Labels
$<-

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

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

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

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

Fix Overlap within a Sequence
flagOverlappingHz

Flag perfectly overlapping horizons within a SoilProfileCollection
fillHzGaps

Find and Fill Horizon Gaps
explainPlotSPC

Visual Explanation for plotSPC
getArgillicBounds

Estimate upper and lower boundary of argillic diagnostic subsurface horizon
getCambicBounds

Find all intervals that are potentially part of a Cambic horizon
getClosestMunsellChip

Get Approximate Munsell Chip
estimateSoilDepth

Estimate Soil Depth
get.ml.hz

Determine ML Horizon Boundaries
genhzTableToAdjMat

Convert cross-tabulation to adjacency matrix.
fragmentClasses

Coarse Fragment Class Labels and Diameter
fragmentSieve

Sieve the Coarse Fraction of Soil
get.increase.matrix

Compute Pair-wise Distances of Soil Properties over Depth
evalMissingData

Evaluate Missing Data within a SoilProfileCollection
glomApply

Subset an SPC by applying glom to each profile
getSurfaceHorizonDepth

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

Guess Appropriate Ordering for Generalized Horizon Labels
generalize.hz

Generalize Horizon Names
genSlabLabels

Generate Labels for Slabs
getLastHorizonID

Get IDs of Deepest Horizons by Profile
glom,SoilProfileCollection-method

Subset soil horizon data using a depth or depth interval
guessHzAttrName

Guess Horizon Slot Column Names
groupSPC

Store groupings within a profile collection.
getSoilDepthClass

Generate Soil Depth Class Matrix
groupedProfilePlot

Grouped Soil Profile Plot
grepSPC

Subset SPC with pattern-matching for text-based attributes
harden.rubification

Harden (1982) Rubification
harden.melanization

Harden (1982) Melanization
harmonize,SoilProfileCollection-method

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

Munsell Hue Reference and Position Searching
horizonNames<-

Set horizon column names
horizonColorIndices

Horizon Color Indices
horizons,SoilProfileCollection-method

Retrieve horizon data from SoilProfileCollection
huePositionCircle

Visual Description of Munsell Hue Ordering
hzTopographyCodeToLineType

Convert Horizon Boundary Topography to Line Type
hzMetadata,SoilProfileCollection-method

Get horizon-level metadata
hzDepthTests

Tests of horizon depth logic
hurst.redness

Hurst (1977) Redness Index
hzID<-,SoilProfileCollection-method

Set horizon IDs
hzAbove

Horizons Above or Below
hzDesgn,SoilProfileCollection-method

Get horizon designation column name
horizonDepths<-

Set horizon depth column names
hzDistinctnessCodeToOffset

Convert Horizon Boundary Distinctness to Vertical Offset
hasDarkColors

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

Horizon Transition Probabilities
hztexclname

Get or Set Horizon Texture Class Column Name
length,SoilProfileCollection-method

Get the number of profiles in a SoilProfileCollection
hzTopographyCodeToOffset

Convert Horizon Boundary Topography to Vertical Offset
lunique

Eliminate duplicate instances of profile IDs in a list of SoilProfileCollections
idname,SoilProfileCollection-method

Get profile ID column name
hzdesgnname

Get or Set Horizon Designation Column Name
jacobs2000

Soil Morphologic Data from Jacobs et al. 2002.
isEmpty,SoilProfileCollection-method

Check for "empty" profiles in a SoilProfileCollection
max,SoilProfileCollection-method

Get the maximum bottom depth in a SoilProfileCollection
metadata,SoilProfileCollection-method

Retrieve metadata from SoilProfileCollection
mixMunsell

Mix Munsell Colors via Spectral Library
mollic.thickness.requirement

Calculate the minimum thickness requirement for Mollic epipedon
munsell

Munsell to sRGB Lookup Table for Common Soil Colors
munsell.spectra

Spectral Library of Munsell Colors
names,SoilProfileCollection-method

Get names of columns in site and horizons table
panel.depth_function

Lattice Panel Function for Soil Profiles
parseMunsell

Parse Munsell Color Notation
hzidname<-

Set horizon ID column name
nrow,SoilProfileCollection-method

Get the number of horizons in a SoilProfileCollection
munsellHuePosition

Munsell Hue Position Reference
munsell2rgb

Convert Munsell Color Notation to other Color Space Coordinates (sRGB and CIELAB)
munsell2spc,SoilProfileCollection-method

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

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

Perturb soil horizon depths using boundary distinctness
pbindlist

Combine a list of SoilProfileCollection objects
findOverlap

Find Overlap within a Sequence
osd

Example Output from soilDB::fetchOSD()
profileInformationIndex

Soil Profile Information Index
profileGroupLabels

Soil Profile Group Labels
profileApply

Iterate over profiles in a SoilProfileCollection
previewColors

Preview Colors
missingDataGrid

Missing Data Grid
invertLabelColor

Make High Contrast Label Colors
initSpatial<-

Initialize Spatial Data in a SoilProfileCollection
ph_to_rxnclass

Convert pH to/from Reaction Classes
min,SoilProfileCollection-method

Get the minimum bottom depth in a SoilProfileCollection
plotColorQuantiles

Visualize Color Quantiles
plotMultipleSPC

Plot Multiple SoilProfileCollection Objects
reorderHorizons

Re-order corrupted horizon data
replaceHorizons<-

Replace Data in Horizon Slot
plotColorMixture

Visualize Spectral Mixing of Munsell Colors
quickSPC

Quickly Assemble a SoilProfileCollection
plot_distance_graph

Between Individual Distance Plot
repairMissingHzDepths

Repair Problematic Lower Horizon Depths
random_profile

Random Profile
profile_id<-

Set profile IDs
pc

Deprecated: Numerical Soil Profile Comparison
restrictions<-

Add Data to Restrictions Slot
rowley2019

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

Segmenting of Soil Horizon Data by Depth Interval
sierraTransect

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

DEPRECATED Simulate Soil Profiles
reactionclass

pH Reaction Classes
shannonEntropy

Shannon Entropy
show

SoilProfileCollection show method
restrictions,SoilProfileCollection-method

Retrieve restriction data from SoilProfileCollection
rgb2munsell

sRGB to Munsell Color Conversion
rebuildSPC

Rebuild a SoilProfileCollection object
reduceSPC

Select a subset of columns from a SoilProfileCollection
slab

Slab-Wise Aggregation of SoilProfileCollection Objects
siteNames<-

Set site column names
site,SoilProfileCollection-method

Retrieve site data from SoilProfileCollection
[,SoilProfileCollection-method

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

Simulate Soil Colors
slicedHSD

Tukey's HSD Over Slices
soiltexture

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

Soil Color Palette
soil_minerals

Munsell Colors of Common Soil Minerals
soilColorSignature

Soil Profile Color Signatures
slice-methods

Slicing of SoilProfileCollection Objects
sp1

Soil Profile Data Example 1
sp4

Soil Chemical Data from Serpentinitic Soils of California
spectral.reference

Standard Illuminants and Observers
sp2

Honcut Creek Soil Profile Data
split,SoilProfileCollection-method

Split a SoilProfileCollection object into a list of SoilProfileCollection objects.
sp5

Sample Soil Database #5
spc2mpspline,SoilProfileCollection-method

SoilProfileCollection wrapper for mpspline2::mpspline()
sp6

Soil Physical and Chemical Data from Manganiferous Soils
sp3

Soil Profile Data Example 3
subset,SoilProfileCollection-method

Subset a SoilProfileCollection with logical expressions
summarizeSPC

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

DEPRECATED use subset
splitLogicErrors

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

Soil Texture Low-RV-High as Defined by Quantiles
subsetHz,SoilProfileCollection-method

Subset the horizons in a SoilProfileCollection using logical criteria
spec2Munsell

Convert reflectance spectra to closest Munsell chip
subApply

Subset SPC based on result of performing function on each profile
spc_in_sync

Quickly assess relative state of site and horizon slots
thicknessOf

Calculate Thickness of Horizons Matching Logical Criteria
thompson.bell.darkness

Thompson-Bell (1996) Index
xtableTauW

Format a LaTeX table with results
transform,SoilProfileCollection-method

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

Textural conversions
us.state.soils

US State Soils
validSpatialData,SoilProfileCollection-method

Check for valid spatial reference of profiles
traditionalColorNames

Traditional Soil Color Names
unique,SoilProfileCollection-method

Uniqueness within a SoilProfileCollection via MD5 Hash
warpHorizons

Inflate / Deflate Horizon Thickness
wilson2022

Example Data from Wilson et al. 2022
unroll

Unroll Genetic Horizons
tauW

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