Algorithms for Quantitative Pedology


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Documentation for package ‘aqp’ version 1.29

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

aqp-package Algorithms for Quantitative Pedology

-- A --

addBracket Add Depth Brackets
addDiagnosticBracket Annotate Diagnostic Features
addVolumeFraction Symbolize Volume Fraction on a Soil Profile Collection Plot
aggregateColor Summarize Soil Colors
aggregateSoilDepth Probabalistic Estimation of Soil Depth within Groups
alignTransect Calculate Relative Positions from Transect Data
allocate Allocate soil properties within various classification systems.
aqp Algorithms for Quantitative Pedology
aqp.env Algorithms for Quantitative Pedology
aqp_df_class Get aqp_df_class entry from metadata or return a safe value.
aqp_df_class-method Get aqp_df_class entry from metadata or return a safe value.
aqp_df_class<- Get aqp_df_class entry from metadata or return a safe value.
aqp_df_class<--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()'
as-method Coerce SoilProfileCollection with 'as()'

-- B --

barron.torrent.redness.LAB Barron & Torrent (1986) Redness Index in LAB color space
bootstrapSoilTexture Bootstrap Soil Texture Data
brierScore Multinominal Brier Score
buntley.westin.index Buntley-Westin (1965) Index

-- C --

c Combine SoilProfileCollection objects
c-method Combine SoilProfileCollection objects
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
colorContrast Metrics of Contrast Suitable for Comparing Soil Colors
colorContrastPlot Color Contrast Plot
colorQuantiles Soil Color Range via Quantiles
combine Combine SoilProfileCollection objects
combine-method Combine SoilProfileCollection objects
compositeSPC Return a list representation of site and horizon level data
compositeSPC-method Return a list representation of site and horizon level data
confusionIndex Confusion Index
contrastChart Color Contrast Chart
contrastClass Soil Color Contrast
coordinates Get coordinates from spatial slot
coordinates-method Get coordinates from spatial slot
coordinates<--method Get coordinates from spatial slot
correctAWC Apply rock fragment or salt correction to available water content
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
depthOf Get top or bottom depths of horizons matching a regular expression pattern
depths<- Initialize a SoilProfileCollection from a data.frame object
depths<--method Initialize a SoilProfileCollection from a data.frame object
depthWeights Return a vector of contributing fractions over a depth interval
depthWeights-method Return a vector of contributing fractions over a depth interval
depth_units Get depth units from metadata
depth_units-method Get depth units from metadata
depth_units<- Get depth units from metadata
depth_units<--method Get depth units from metadata
diagnostic_hz Retrieve diagnostic data from SoilProfileCollection
diagnostic_hz-method Retrieve diagnostic data from SoilProfileCollection
diagnostic_hz<- Add data to the diagnostic slot
diagnostic_hz<--method Add data to the diagnostic slot
dice Efficient Slicing of 'SoilProfileCollection' Objects
duplicate Duplicte Profiles of a SoilProfileCollection

-- E --

equivalentMunsellChips Identify "equivalent" (whole number value/chroma) Munsell chips
equivalent_munsell Indices of "equivalent" Munsell chips in 'munsell' data set
estimateAWC Estimate available water capacity for fine-earth fraction
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 Visual Explanation for 'plotSPC'

-- F --

f.noise Example Objective Function for Full-Pattern Matching
fillHzGaps Find and Fill Horizon Gaps
filter Subset a SoilProfileCollection with logical expressions
filter-method Subset a SoilProfileCollection with logical expressions
findOverlap Find Overlap within a Sequence
fixOverlap Fix Overlap within a Sequence via Simulated Annealing

-- 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 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
getLastHorizonID Get IDs of Deepest Horizons by Profile
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
getSurfaceHorizon Determine thickness of horizons (continuous from surface) matching a pattern
getSurfaceHorizonDepth Determine thickness of horizons (continuous from surface) matching a pattern
glom Subset soil horizon data using a depth or depth interval
glom-method Subset soil horizon data using a depth or depth interval
glomApply Subset an SPC by applying glom to each profile
glomApply-method Subset an SPC by applying glom to each profile
grepSPC Subset SPC with pattern-matching for text-based attributes
grepSPC-method Subset SPC with pattern-matching for text-based attributes
groupedProfilePlot Grouped Soil Profile Plot
groupSPC (EXPERIMENTAL) Store groupings within a profile collection.
group_by (EXPERIMENTAL) Store groupings within a profile collection.
guessGenHzLevels Guess Appropriate Ordering for Generalized Horizon Labels
guessHzAttrName Guess Arbitrary Horizon Column Name
guessHzDesgnName Guess Horizon Designation Column Name
guessHzTexClName Guess Horizon Texture Class Column Name

-- H --

harden.melanization Harden (1982) Melanization
harden.rubification Harden (1982) Rubification
harmonize Harmonize a property by profile-level denormalization for convenient visualization or analysis of ranges
harmonize-method Harmonize a property by profile-level denormalization for convenient visualization or analysis of ranges
hasDarkColors Find horizons with colors darker than a Munsell hue, value, chroma threshold
horizonColorIndices Horizon Color Indices
horizonDepths Set horizon depth column names
horizonDepths-method Set horizon depth column names
horizonDepths<- Set horizon depth column names
horizonDepths<--method Set horizon depth column names
horizonNames Set horizon column names
horizonNames-method Set horizon column names
horizonNames<- Set horizon column names
horizonNames<--method Set horizon column names
horizons Retrieve horizon data from SoilProfileCollection
horizons-method Retrieve horizon data from SoilProfileCollection
horizons<- Retrieve horizon data from SoilProfileCollection
horizons<--method Retrieve horizon data from SoilProfileCollection
huePosition Munsell Hue Position for Soil Color Description
hurst.redness Hurst (1977) Redness Index
HzDepthLogicSubset Subset 'SoilProfileCollection' Objects or Horizons via 'checkHzDepthLogic'
hzDepthTests Tests of horizon depth logic
hzDesgn Get horizon designation column name
hzDesgn-method Get horizon designation column name
hzdesgnname Get horizon designation column name
hzdesgnname-method Get horizon designation column name
hzdesgnname<- Set horizon designation column name
hzdesgnname<--method Set horizon designation column name
hzDistinctnessCodeToOffset Convert Horizon Boundary Distinctness to Vertical Offset
hzID Get horizon IDs
hzID-method Get horizon IDs
hzID<- Set horizon IDs
hzID<--method Set horizon IDs
hzidname Set horizon ID column name
hzidname-method Set horizon ID column name
hzidname<- Set horizon ID column name
hzidname<--method Set horizon ID column name
hztexclname Get horizon texture class column name
hztexclname-method Get horizon texture class column name
hztexclname<- Set horizon texture class column name
hztexclname<--method Set horizon texture class column name
hzTopographyCodeToLineType Convert Horizon Boundary Topography to Line Type
hzTopographyCodeToOffset Convert Horizon Boundary Topography to Vertical Offset
hzTransitionProbabilities Horizon Transition Probabilities

-- I --

idname Get profile ID column name
idname-method Get profile ID column name
invertLabelColor Make High Contrast Label Colors

-- J --

jacobs2000 Soil Morphologic Data from Jacobs et al. 2002.

-- L --

L1_profiles Create Representative Soil Profiles via L1 Estimator
length Get the number of profiles in a SoilProfileCollection
length-method Get the number of profiles in a SoilProfileCollection
lunique Eliminate duplicate instances of profile IDs in a list of SoilProfileCollections

-- M --

max Get the maximum bottom depth in a SoilProfileCollection
max-method Get the maximum bottom depth in a SoilProfileCollection
maxDepthOf Get top or bottom depths of horizons matching a regular expression pattern
metadata Retrieve metadata from SoilProfileCollection
metadata-method Retrieve metadata from SoilProfileCollection
metadata<- Retrieve metadata from SoilProfileCollection
metadata<--method Retrieve metadata from SoilProfileCollection
min Get the minimum bottom depth in a SoilProfileCollection
min-method Get the minimum bottom depth in a SoilProfileCollection
minDepthOf Get top or bottom depths of horizons matching a regular expression pattern
missingDataGrid Missing Data Grid
mixMunsell Mix Munsell Colors via Spectral Library
mollic.thickness.requirement Calculate the minimum thickness requirement for Mollic epipedon
mostLikelyHzSequence Horizon Transition Probabilities
munsell Munsell to sRGB Lookup Table for Common Soil Colors
munsell.spectra Spectral Library of Munsell Colors
munsell.spectra.wide Spectral Library of Munsell Colors
munsell2rgb Convert Munsell Color Notation to other Color Space Coordinates (sRGB and CIELAB)
munsell2spc Merge Munsell Hue, Value, Chroma converted to sRGB & CIELAB into a SoilProfileCollection
munsell2spc-method Merge Munsell Hue, Value, Chroma converted to sRGB & CIELAB into a SoilProfileCollection
mutate Transform a SPC with expressions based on site or horizon level attributes
mutate-method Transform a SPC with expressions based on site or horizon level attributes
mutate_profile Transform a SPC (by profile) with a set of expressions
mutate_profile-method Transform a SPC (by profile) with a set of expressions

-- N --

names Get names of columns in site and horizons table
names-method Get names of columns in site and horizons table
nrow Get the number of horizons in a SoilProfileCollection
nrow-method Get the number of horizons in a SoilProfileCollection

-- O --

overlapMetrics Find and Quantify Overlap within a 1D Sequence

-- P --

panel.depth_function Lattice Panel Function for Soil Profiles
parseMunsell Parse Munsell Color Notation
pbindlist Combine a list of SoilProfileCollection objects
pc Numerical Soil Profile Comparison
pc.SPC Numerical Soil Profile Comparison
permute_profile Perturb soil horizon depths using boundary distinctness
perturb Perturb soil horizon depths using boundary distinctness
plot Create Soil Profile Sketches
plot,SoilProfileCollection,ANY-method,plot.SoilProfileCollection Create Soil Profile Sketches
plot-method Create Soil Profile Sketches
plotColorMixture Visualize Spectral Mixing of Munsell Colors
plotColorQuantiles Visualize Color Quantiles
plotMultipleSPC Plot Multiple 'SoilProfileCollection' Objects
plotSPC Create Soil Profile Sketches
plot_distance_graph Between Individual Distance Plot
pms.munsell.lut Pantone Colors / Munsell Lookup Table
prepanel.depth_function Lattice Panel Function for Soil Profiles
previewColors Preview Colors
profileApply Iterate over profiles in a SoilProfileCollection
profileApply-method Iterate over profiles in a SoilProfileCollection
profileGroupLabels Soil Profile Group Labels
profile_compare Numerical Soil Profile Comparison
profile_compare-method Numerical Soil Profile Comparison
profile_id Set profile IDs
profile_id-method Set profile IDs
profile_id<- Set profile IDs
profile_id<--method Set profile IDs
proj4string-method Set PROJ4 string for the SoilProfileCollection
proj4string<--method Set PROJ4 string for the SoilProfileCollection

-- R --

random_profile Random Profile
rebuildSPC Rebuild a SoilProfileCollection object
reorderHorizons Re-order corrupted horizon data
reorderHorizons-method Re-order corrupted horizon data
repairMissingHzDepths Repair Problematic Lower Horizon Depths
replaceHorizons<- Replace data in the horizon slot
replaceHorizons<--method Replace data in the horizon slot
resample.twotheta Resample an XRD Pattern
restrictions Retrieve restriction data from SoilProfileCollection
restrictions-method Retrieve restriction data from SoilProfileCollection
restrictions<- Add data to the restrictions slot
restrictions<--method Add data to the restrictions slot
rgb2munsell sRGB to Munsell Color Conversion
ROSETTA.centroids Average Hydraulic Parameters from the ROSETTA Model by USDA Soil Texture Class
rowley2019 Soil Morphologic, Geochemical, and Mineralogy Data from Rowley et al. 2019.
rruff.sample Sample XRD Patterns

-- S --

segment Segmenting of Soil Horizon Data by Depth Interval
shannonEntropy Shannon Entropy
show SoilProfileCollection show method
show-method SoilProfileCollection show method
sierraTransect Soil Physical and Chemical Data Related to Studies in the Sierra Nevada Mountains, CA, USA.
sim DEPRECATED Simulate Soil Profiles
site Retrieve site data from SoilProfileCollection
site-method Retrieve site data from SoilProfileCollection
site<- Retrieve site data from SoilProfileCollection
site<--method Retrieve site data from SoilProfileCollection
siteNames Set site column names
siteNames-method Set site column names
siteNames<- Set site column names
siteNames<--method Set site column names
slab Slab-Wise Aggregation of SoilProfileCollection Objects
slab-method Slab-Wise Aggregation of SoilProfileCollection Objects
slab-methods 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-methods Slicing of SoilProfileCollection Objects
slice.fast Slicing of SoilProfileCollection Objects
slicedHSD Tukey's HSD Over Slices
soilColorSignature Soil Profile Color Signatures
soilPalette Soil Color Palette
SoilProfileCollection An S4 object representation of a group of soil profiles.
SoilProfileCollection-class An S4 object representation of a group of soil profiles.
soiltexture Lookup tables for sand, silt, clay, texture class, and textural modifiers.
SoilTextureLevels Ranking Systems for USDS Soil Texture Classes
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
spc2mpspline Missing-data-safe, SPC-wide wrapper around mpspline2::mpspline "continuous" 1cm output
spc2mpspline-method Missing-data-safe, SPC-wide wrapper around mpspline2::mpspline "continuous" 1cm output
spc_in_sync Quickly assess relative state of site and horizon slots
spc_in_sync-method Quickly assess relative state of site and horizon slots
split-method Split a SoilProfileCollection object into a list of SoilProfileCollection objects.
splitLogicErrors Split a SoilProfileCollection into a list based on types of horizon logic errors
ssc_to_texcl Textural conversions
subApply Subset SPC based on result of performing function on each profile
subApply-method Subset SPC based on result of performing function on each profile
subset Subset a SoilProfileCollection with logical expressions
subset-method Subset a SoilProfileCollection with logical expressions
subsetProfiles DEPRECATED use subset
subsetProfiles-method DEPRECATED use subset
summarize Perform summaries on groups (from 'group_by') and create new site or horizon level attributes
summarizeSPC Perform summaries on groups (from 'group_by') and create new site or horizon level attributes
summarizeSPC,SoilProfileCollection-method, Perform summaries on groups (from 'group_by') and create new site or horizon level attributes
summaryTauW Compute weighted naive and _tau_ statistics for a cross-classification matrix

-- T --

tauW Compute weighted naive and _tau_ statistics for a cross-classification matrix
texcl_to_ssc Textural conversions
texmod_to_fragvoltot Textural conversions
textureTriangleSummary Soil Texture Low-RV-High as Defined by Quantiles
texture_to_taxpartsize Textural conversions
thompson.bell.darkness Thompson-Bell (1996) Index
transform-method Transform a SPC with expressions based on site or horizon level attributes
trunc Truncate a SoilProfileCollection to specified top and bottom depth
trunc-method Truncate a SoilProfileCollection to specified top and bottom depth

-- U --

unique Get the indexes of unique profiles in a SoilProfileCollection
unique-method Get the indexes of unique profiles in a SoilProfileCollection
unroll Unroll Genetic Horizons
us.state.soils US State Soils

-- V --

validSpatialData Get names of columns in site table
validSpatialData-method Get names of columns in site table

-- X --

xtableTauW Format a LaTeX table with results

-- misc --

$ Get data from column of horizon or site data in a SoilProfileCollection
$-method Get data from column of horizon or site data in a SoilProfileCollection
$<- Set data in column of horizon or site data in a SoilProfileCollection
$<--method Set data in column of horizon or site data in a SoilProfileCollection
.as.data.frame.aqp Wrapper method for data.frame subclass conversion
.data_dots Make a data.frame from non-standard expressions evaluated in a data environment
.HSD .HSD
.lpp Random Profile
.makeEquivalentMunsellLUT .makeEquivalentMunsellLUT
.parseGrouped_formula .parseHSD_formula
[-method Matrix/data.frame-like access to profiles and horizons in a SoilProfileCollection
[[ Get column of horizon or site data in a SoilProfileCollection
[[,SoilProfileCollection,ANY-method, Get column of horizon or site data in a SoilProfileCollection
[[-method Get column of horizon or site data in a SoilProfileCollection
[[<- Add or change column of horizon or site data in a SoilProfileCollection
[[<--method Add or change column of horizon or site data in a SoilProfileCollection