Algorithms for Quantitative Pedology

Documentation for package ‘aqp’ version 1.19

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

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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