# Algorithms for Quantitative Pedology

## Documentation for package ‘aqp’ version 1.19

- DESCRIPTION file.
- Code demos. Use demo() to run them.

## Help Pages

A B C D E F G H I J L M N P R S T U V X misc

aqp-package | Algorithms for Quantitative Pedology

## -- A --

addBracket | Add Depth Brackets
addDiagnosticBracket | Add Depth Brackets
addVolumeFraction | Symbolize Volume Fraction on a Soil Profile Collection Plot
aggregateColor | Summarize Soil Colors
aggregateSoilDepth | Probabalistic Estimation of Soil Depth
aqp | Algorithms for Quantitative Pedology
aqp.env | Algorithms for Quantitative Pedology
argillic.clay.increase.depth | Return upper boundary of argillic horizon

## -- B --

barron.torrent.redness.LAB | Barron & Torrent (1986) Redness Index in LAB color space
brierScore | Multinominal Brier score
buntley.westin.index | Buntley-Westin (1965) Index

## -- C --

ca630 | Soil Data from the Central Sierra Nevada Region of California
checkHzDepthLogic | Check a 'SoilProfileCollection' object for errors in horizon depths.
checkSPC | Test for a valid SoilProfileCollection
clod.hz.ids | Return the unique horizon IDs within a "depth-clod"
colorContrast | Metrics of Contrast Suitable for Comparing Soil Colors
colorContrastPlot | Color Contrast Plot
colorQuantiles | Soil Color Range via Quantiles
confusionIndex | Confusion Index
contrastChart | Color Contrast Chart
contrastClass | Soil Color Contrast
coordinates-method | SoilProfileCollection Class
coordinates<--method | SoilProfileCollection Class
crit.clay.argillic | Determines threshold (minimum) clay content for argillic upper bound

## -- D --

denormalize | Create a (redundant) horizon-level attribute from a site-level attribute
depths<- | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
depths<--method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
depth_units | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
depth_units-method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
depth_units<- | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
depth_units<--method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
diagnostic_hz | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
diagnostic_hz-method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
diagnostic_hz<- | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
diagnostic_hz<--method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects

## -- E --

estimatePSCS | Estimate boundaries of the particle size control section (U.S Soil Taxonomy; 12th edition)
estimateSoilDepth | Estimate Soil Depth
evalGenHZ | Evaluate Generalized Horizon Labels
evalMissingData | Evaluate Missing Data
explainPlotSPC | Profile Plot

## -- F --

f.noise | Example Objective Function for Full-Pattern Matching
findOverlap | Attempt to fix overlapping sketches when using relative horizontal spacing.
fixOverlap | Attempt to fix overlapping sketches when using relative horizontal spacing.

## -- G --

generalize.hz | Generalize Horizon Names
genhzTableToAdjMat | Horizon Transition Probabilities
genSlabLabels | Slab-Wise Aggregation of SoilProfileCollection Objects
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
get.ml.hz | Determine ML Horizon Boundaries
get.slice | Slicing of SoilProfilecollection Objects
getArgillicBounds | getArgillicBounds
getClosestMunsellChip | Convert Munsell Notation to and from sRGB color coordinates
getMineralSoilSurfaceDepth | Determine thickness of horizons (continuous from surface) matching a pattern
getPlowLayerDepth | Determine thickness of horizons (continuous from surface) matching a pattern
getSoilDepthClass | Generate Soil Depth Class Matrix
getSurfaceHorizonDepth | Determine thickness of horizons (continuous from surface) matching a pattern
glom | Return a "ragged" group of horizons selected from SoilProfileCollection
groupedProfilePlot | Grouped Soil Profile Plot
guessGenHzLevels | Guess Appropriate Ordering for Generalized Horizon Labels

## -- H --

harden.melanization | Harden (1982) Melanization
harden.rubification | Harden (1982) Rubification
horizonColorIndices | Horizon Color Indices
horizonDepths | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
horizonDepths-method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
horizonDepths<- | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
horizonDepths<--method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
horizonNames | SoilProfileCollection Class
horizonNames-method | SoilProfileCollection Class
horizonNames<- | SoilProfileCollection Class
horizonNames<--method | SoilProfileCollection Class
horizons | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
horizons-method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
horizons<- | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
horizons<--method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
huePosition | Munsell Hue Position for Soil Color Description
hurst.redness | Hurst (1977) Redness Index
hzDepthTests | Tests of horizon depth logic
hzDesgn | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hzDesgn-method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hzdesgnname | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hzdesgnname-method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hzdesgnname<- | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hzdesgnname<--method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hzDistinctnessCodeToOffset | Convert Horizon Distinctness Codes
hzID | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hzID-method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hzID<- | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hzID<--method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hzidname | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hzidname-method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hzidname<- | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hzidname<--method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hztexclname | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hztexclname-method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hztexclname<- | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hztexclname<--method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
hzTransitionProbabilities | Horizon Transition Probabilities

## -- I --

idname | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
idname-method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects

## -- J --

jacobs2000 | Soil Morphologic Data from Jacobs et al. 2002.

## -- L --

length-method | SoilProfileCollection Class

## -- M --

make.segments | Lattice Panel Function for Soil Profiles
max-method | SoilProfileCollection Class
metadata | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
metadata-method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
metadata<- | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
metadata<--method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
min-method | SoilProfileCollection Class
missingDataGrid | Missing Data Grid
mostLikelyHzSequence | Horizon Transition Probabilities
munsell | Munsell to sRGB Lookup Table for Common Soil Colors
munsell2rgb | Convert Munsell Notation to and from sRGB color coordinates

## -- N --

names | SoilProfileCollection Class
names-method | SoilProfileCollection Class
nrow-method | SoilProfileCollection Class

## -- P --

panel.depth_function | Lattice Panel Function for Soil Profiles
parseMunsell | Convert Munsell Notation to and from sRGB color coordinates
pc | Numerical Soil Profile Comparison
pc.SPC | Numerical Soil Profile Comparison
plot | Profile Plot
plot-method | Profile Plot
plot.SoilProfileCollection | Profile Plot
plotColorQuantiles | Soil Color Range via Quantiles
plotMultipleSPC | Plot Multiple SoilProfileCollection Objects
plotSPC | Profile Plot
plot_distance_graph | Between Individual Distance Plot
prepanel.depth_function | Lattice Panel Function for Soil Profiles
previewColors | Preview Colors
profileApply | Apply a function to soil profiles within a SoilProfileCollection object.
profileApply-method | Apply a function to soil profiles within a SoilProfileCollection object.
profileGroupLabels | Soil Profile Group Labels
profile_compare | Numerical Soil Profile Comparison
profile_compare-method | Numerical Soil Profile Comparison
profile_id | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
profile_id-method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
profile_id<- | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
profile_id<--method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
proj4string-method | SoilProfileCollection Class
proj4string<--method | SoilProfileCollection Class

## -- R --

random_profile | Random Profile
rbind.SoilProfileCollection | SoilProfileCollection Class
rebuildSPC | Rebuild a SoilProfileCollection object
resample.twotheta | Resample an XRD Pattern
restrictions | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
restrictions-method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
restrictions<- | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
restrictions<--method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
rgb2munsell | Convert Munsell Notation to and from sRGB color coordinates
rowley2019 | Soil Morphologic, Geochemical, and Mineralogy Data from Rowley et al. 2019.
rruff.sample | Sample XRD Patterns

## -- S --

shannonEntropy | Shannon Entropy
show-method | SoilProfileCollection Class
sim | Simulate Soil Profiles
site | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
site-method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
site<- | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
site<--method | Getters, Setters, and Utility Methods for SoilProfileCollection Objects
siteNames | SoilProfileCollection Class
siteNames-method | SoilProfileCollection Class
siteNames<- | SoilProfileCollection Class
siteNames<--method | SoilProfileCollection Class
slab | Slab-Wise Aggregation of SoilProfileCollection Objects
slab-method | Slab-Wise Aggregation of SoilProfileCollection Objects
slab2 | Slab-Wise Aggregation of SoilProfileCollection Objects
slice | Slicing of SoilProfilecollection Objects
slice-method | Slicing of SoilProfilecollection Objects
slice.fast | Slicing of SoilProfilecollection Objects
soilColorSignature | Soil Profile Color Signatures
soilPalette | Sol Color Palette
SoilProfileCollection | SoilProfileCollection Class
SoilProfileCollection-class | SoilProfileCollection Class
soil_minerals | Munsell Colors of Common Soil Minerals
sp1 | Soil Profile Data Example 1
sp2 | Honcut Creek Soil Profile Data
sp3 | Soil Profile Data Example 3
sp4 | Soil Chemical Data from Serpentinitic Soils of California
sp5 | Sample Soil Database #5
sp6 | Soil Physical and Chemical Data from Manganiferous Soils
subsetProfiles | Subset SoilProfileCollection Objects.
subsetProfiles-method | Subset SoilProfileCollection Objects.
summaryTauW | Compute weighted naïve and _tau_ statistics for a cross-classification matrix

## -- T --

tauW | Compute weighted naïve and _tau_ statistics for a cross-classification matrix
test_hz_logic | Check a 'SoilProfileCollection' object for errors in horizon depths.
texture.triangle.low.rv.high | Soil Texture Low-RV-High as Defined by Quantiles
textureTriangleSummary | Soil Texture Low-RV-High as Defined by Quantiles
thompson.bell.darkness | Thompson-Bell (1996) Index

## -- U --

union | Combine Multiple SoilProfileCollection Objects
unique | Get Indices to Unique Soil Profiles Within a Collection
unique-method | Get Indices to Unique Soil Profiles Within a Collection
uniqueSPC | Get Indices to Unique Soil Profiles Within a Collection
unroll | Unroll Genetic Horizons

## -- V --

validSpatialData | SoilProfileCollection Class
validSpatialData-method | SoilProfileCollection Class

## -- X --

xtableTauW | Compute weighted naïve and _tau_ statistics for a cross-classification matrix

## -- misc --

$-method | SoilProfileCollection Class
$<--method | SoilProfileCollection Class
.lpp | Random Profile
[-method | SoilProfileCollection Class