Package index • aqp

All functions

GHL(<SoilProfileCollection>) `GHL<-`(<SoilProfileCollection>): Get or Set Generalized Horizon Label (GHL) Column Name

HzDepthLogicSubset(): Subset SoilProfileCollection Objects or Horizons via checkHzDepthLogic

L1_profiles(): Create Representative Soil Profiles via L1 Estimator

NCSP(): Numerical Classification of Soil Profiles

ROSETTA.centroids: Average Hydraulic Parameters from the ROSETTA Model by USDA Soil Texture Class

SANN_1D(): Fix Overlap within a Sequence via Simulated Annealing

SPC.with.overlap: Example SoilProfileCollection with Overlapping Horizons

SoilProfileCollection(): An S4 object representation of a group of soil profiles.

prj(<SoilProfileCollection>) `prj<-`(<SoilProfileCollection>) proj4string(<SoilProfileCollection>) `proj4string<-`(<SoilProfileCollection>): Get or Set Coordinate Reference System for SoilProfileCollection

plotSPC() plot(<SoilProfileCollection>): Create Soil Profile Sketches

SoilTextureLevels(): Ranking Systems for USDA Soil Texture Classes

accumulateDepths(): Accumulate horizon depths, and reflect reversed depths, relative to new datum

addBracket(): Add Depth Brackets

addDiagnosticBracket(): Annotate Diagnostic Features

addVolumeFraction(): Symbolize Volume Fraction within a Soil Profile Collection Plot

aggregateColor(): Summarize Soil Colors

aggregateColorPlot(): Plot aggregate soil color data

aggregateSoilDepth(): Probabilistic Estimation of Soil Depth within Groups

alignTransect(): Calculate Relative Positions from Transect Data

allocate(): Allocate soil properties within various classification systems.

aqp-package aqp aqp.env: Algorithms for Quantitative Pedology

aqp_df_class(<SoilProfileCollection>) `aqp_df_class<-`(<SoilProfileCollection>): Get aqp_df_class entry from metadata or return a safe value.

argillic.clay.increase.depth(): Return upper boundary of argillic horizon

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

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

as.data.frame(<SoilProfileCollection>): Coerce SoilProfileCollection with as()

col2Munsell(): Convert colors into Munsell Notation

collapseHz(): Collapse Horizons within Profiles Based on Pattern Matching

colorChart(): Visualize soil colors in Munsell notation according to within-group frequency.

colorContrast(): Metrics of Contrast Suitable for Comparing Soil Colors

colorContrastPlot(): Color Contrast Plot

colorQuantiles(): Soil Color Range via Quantiles

c(<SoilProfileCollection>) combine(<SoilProfileCollection>) combine(<list>): Combine SoilProfileCollection objects

compareSites(): Compare Site Level Attributes of a SoilProfileCollection

compositeSPC(): Return a list representation of site and horizon level data

confusionIndex(): Confusion Index

contrastChart(): Color Contrast Chart

contrastClass(): Soil Color Contrast

correctAWC(): Apply rock fragment or salt correction to available water content

crit.clay.argillic(): Determines threshold (minimum) clay content for argillic upper bound

denormalize(): Create a (redundant) horizon-level attribute from a site-level attribute

depthOf() maxDepthOf() minDepthOf(): Get top or bottom depths of horizons matching a regular expression pattern

depthWeights(): Return a vector of contributing fractions over a depth interval

depth_units(<SoilProfileCollection>) `depth_units<-`(<SoilProfileCollection>): Get depth units from metadata

depths(<SoilProfileCollection>) `depths<-`(<SoilProfileCollection>) `depths<-`(<data.frame>): Initialize a SoilProfileCollection from data.frame

diagnostic_hz(<SoilProfileCollection>) `diagnostic_hz<-`(<SoilProfileCollection>): Get or Set Diagnostic Horizon data in a SoilProfileCollection

dice(<SoilProfileCollection>): Efficient Slicing of SoilProfileCollection Objects

`$<-`(<SoilProfileCollection>): Set data in column of horizon or site data in a SoilProfileCollection

`$`(<SoilProfileCollection>): Get data from column of horizon or site data in a SoilProfileCollection

`[[<-`(<SoilProfileCollection>): Add or change column of horizon or site data in a SoilProfileCollection

`[[`(<SoilProfileCollection>): Get column of horizon or site data in a SoilProfileCollection

duplicate(): Duplicate Profiles of a SoilProfileCollection

electroStatics_1D(): Label placement based on a simulation of electrostatic forces

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

equivalent_munsell: Indices of "equivalent" Munsell chips in the munsell data set

estimateAWC(): Estimate available water capacity for fine-earth fraction

estimatePSCS(): Estimate boundaries of the U.S Soil Taxonomy Particle Size Control Section

estimateSoilColor(): Estimate dry soil colors from moist soil colors and vice versa.

estimateSoilDepth(): Estimate Soil Depth

evalGenHZ(): Evaluate Generalized Horizon Labels

evalMissingData(): Evaluate Missing Data within a SoilProfileCollection

explainPlotSPC(): Visual Explanation for plotSPC

fillHzGaps(): Find and Fill Horizon Gaps

fixOverlap(): Fix Overlap within a Sequence

flagOverlappingHz(): Flag perfectly overlapping horizons within a SoilProfileCollection

fragmentClasses(): Coarse Fragment Class Labels and Diameter

fragmentSieve(): Sieve the Coarse Fraction of Soil

genSlabLabels(): Generate Labels for Slabs

generalize.hz() generalizeHz(<character>) generalizeHz(<SoilProfileCollection>): Generalize Horizon Names

genhzTableToAdjMat(): Convert cross-tabulation to adjacency matrix.

get.increase.matrix() get.increase.depths(): Compute Pair-wise Distances of Soil Properties over Depth

get.ml.hz(): Determine ML Horizon Boundaries

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

getSoilDepthClass(): Generate Soil Depth Class Matrix

getSurfaceHorizonDepth() getMineralSoilSurfaceDepth() getPlowLayerDepth(): Determine thickness of horizons (continuous from surface) matching a pattern

glom(<SoilProfileCollection>) trunc(<SoilProfileCollection>): Subset soil horizon data using a depth or depth interval

glomApply(): Subset an SPC by applying glom to each profile

grepSPC(): Subset SPC with pattern-matching for text-based attributes

groupSPC(): Store groupings within a profile collection.

groupedProfilePlot(): Grouped Soil Profile Plot

guessGenHzLevels(): Guess Appropriate Ordering for Generalized Horizon Labels

guessHzAttrName() guessHzDesgnName() guessHzTexClName(): Guess Horizon Slot Column Names

harden.melanization(): Harden (1982) Melanization

harden.rubification(): Harden (1982) Rubification

harmonize(<SoilProfileCollection>): 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<-`(<SoilProfileCollection>) horizonDepths(<SoilProfileCollection>): Set horizon depth column names

`horizonNames<-`(<SoilProfileCollection>) horizonNames(<SoilProfileCollection>): Set horizon column names

horizons(<SoilProfileCollection>) `horizons<-`(<SoilProfileCollection>): Retrieve horizon data from SoilProfileCollection

huePosition(): Munsell Hue Reference and Position Searching

huePositionCircle(): Visual Description of Munsell Hue Ordering

hurst.redness(): Hurst (1977) Redness Index

hzDepthTests(): Tests of horizon depth logic

hzDesgn(<SoilProfileCollection>): Get horizon designation column name

hzDistinctnessCodeToOffset(): Convert Horizon Boundary Distinctness to Vertical Offset

`hzID<-`(<SoilProfileCollection>) hzID(<SoilProfileCollection>): Set horizon IDs

hzMetadata(<SoilProfileCollection>): Get horizon-level metadata

hzAbove() hzBelow() hzOffset(): Horizons Above or Below

hzTopographyCodeToLineType(): Convert Horizon Boundary Topography to Line Type

hzTopographyCodeToOffset(): Convert Horizon Boundary Topography to Vertical Offset

hzTransitionProbabilities() mostLikelyHzSequence(): Horizon Transition Probabilities

hz_dissolve() dissolve_hz(): Dissolving horizon boundaries by grouping variables

hz_intersect(): Intersecting horizon boundaries by horizon depths

hz_lag(): Find lagged horizon values

hz_segment() segment(): Segmenting of Soil Horizon Data by Depth Interval

hz_to_taxpartsize(): Allocate Particle Size Class for the Control Section.

hzdesgnname(<SoilProfileCollection>) `hzdesgnname<-`(<SoilProfileCollection>): Get or Set Horizon Designation Column Name

`hzidname<-`(<SoilProfileCollection>) hzidname(<SoilProfileCollection>): Set horizon ID column name

hzmetaname(<SoilProfileCollection>) `hzmetaname<-`(<SoilProfileCollection>): Get or Set Horizon Metadata Column Name

hztexclname(<SoilProfileCollection>) `hztexclname<-`(<SoilProfileCollection>): Get or Set Horizon Texture Class Column Name

idname(<SoilProfileCollection>): Get profile ID column name

`initSpatial<-`(<SoilProfileCollection>,<ANY>,<ANY>) `initSpatial<-`(<SoilProfileCollection>,<ANY>,<character>) getSpatial(<SoilProfileCollection>) coordinates(<SoilProfileCollection>) `coordinates<-`(<SoilProfileCollection>,<ANY>) `coordinates<-`(<SoilProfileCollection>,<character>): Initialize Spatial Data in a SoilProfileCollection

invertLabelColor(): Make High Contrast Label Colors

isEmpty(<SoilProfileCollection>): Check for "empty" profiles in a SoilProfileCollection

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

length(<SoilProfileCollection>): Get the number of profiles in a SoilProfileCollection

lookup_taxpartsize(): Ranking Systems for USDA Taxonomic Particle-Size and Substitute Classes of Mineral Soils

lunique(): Eliminate duplicate instances of profile IDs in a list of SoilProfileCollections

max(<SoilProfileCollection>): Get the maximum bottom depth in a SoilProfileCollection

metadata(<SoilProfileCollection>) `metadata<-`(<SoilProfileCollection>): Retrieve metadata from SoilProfileCollection

min(<SoilProfileCollection>): Get the minimum bottom depth in a SoilProfileCollection

missingDataGrid(): Missing Data Grid

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

munsell2rgb(): Convert Munsell Color Notation to other Color Space Coordinates (sRGB and CIELAB)

munsell2spc(<SoilProfileCollection>): Merge Munsell Hue, Value, Chroma converted to sRGB & CIELAB into a SoilProfileCollection

munsellHuePosition: Munsell Hue Position Reference

mutate_profile() mutate_profile_raw(): Transform a SPC (by profile) with a set of expressions

names(<SoilProfileCollection>): Get names of columns in site and horizons table

nrow(<SoilProfileCollection>): Get the number of horizons in a SoilProfileCollection

osd: Example Output from soilDB::fetchOSD()

findOverlap() overlapMetrics(): Find Overlap within a Sequence

panel.depth_function() prepanel.depth_function(): Lattice Panel Function for Soil Profiles

parseMunsell(): Parse Munsell Color Notation

pbindlist(): Combine a list of SoilProfileCollection objects

perturb(): Perturb soil horizon depths using boundary distinctness

plotColorMixture(): Visualize Spectral Mixing of Munsell Colors

plotColorQuantiles(): Visualize Color Quantiles

plotMultipleSPC(): Plot Multiple SoilProfileCollection Objects

plotProfileDendrogram(): Plot soil profiles below a dendrogram

plot_distance_graph(): Between Individual Distance Plot

previewColors(): Preview Colors

profileApply(<SoilProfileCollection>): Iterate over profiles in a SoilProfileCollection

profileGroupLabels(): Soil Profile Group Labels

profileInformationIndex(): Soil Profile Information Index

`profile_id<-`(<SoilProfileCollection>) profile_id(<SoilProfileCollection>): Set profile IDs

quickSPC(): Quickly Assemble a SoilProfileCollection

random_profile(): Random Profile

ph_to_rxnclass() rxnclass_to_ph() ReactionClassLevels(): Convert pH to/from Reaction Classes

reactionclass: pH Reaction Classes

rebuildSPC(): Rebuild a SoilProfileCollection object

reduceSPC(): Select a subset of columns from a SoilProfileCollection

reorderHorizons(<SoilProfileCollection>): Re-order corrupted horizon data

repairMissingHzDepths(): Repair Problematic Lower Horizon Depths

`replaceHorizons<-`(<SoilProfileCollection>): Replace Data in Horizon Slot

restrictions(<SoilProfileCollection>) `restrictions<-`(<SoilProfileCollection>): Get or Set Restriction data in a SoilProfileCollection

rgb2munsell(): sRGB to Munsell Color Conversion

rowley2019: Soil Morphologic, Geochemical, and Mineralogy Data from Rowley et al. 2019.

rp(): Generate a SoilProfileCollection of random profiles

shannonEntropy(): Shannon Entropy

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

sim(): DEPRECATED Simulate Soil Profiles

simulateColor(): Simulate Soil Colors

`[`(<SoilProfileCollection>): Matrix/data.frame-like access to profiles and horizons in a SoilProfileCollection

site(<SoilProfileCollection>) `site<-`(): Retrieve site data from SoilProfileCollection

`siteNames<-`(<SoilProfileCollection>) siteNames(<SoilProfileCollection>): Set site column names

slab(<SoilProfileCollection>) slab_function(): Slab-Wise Aggregation of SoilProfileCollection Objects

slice.fast() slice(<SoilProfileCollection>) get.slice(): Slicing of SoilProfileCollection Objects

slicedHSD(): Tukey's HSD Over Slices

soilColorSignature(): Soil Profile Color Signatures

soilPalette(): Soil Color Palette

soilTextureColorPal(): Soil Texture Color Palettes

soil_minerals: Munsell Colors of Common Soil Minerals

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

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(<SoilProfileCollection>): SoilProfileCollection wrapper for mpspline2::mpspline()

spc_in_sync(): Quickly assess relative state of site and horizon slots

spec2Munsell(): Convert reflectance spectra to closest Munsell chip

spectral.reference: Standard Illuminants and Observers

split(<SoilProfileCollection>): Split a SoilProfileCollection object into a list of SoilProfileCollection objects.

splitLogicErrors(): Split a SoilProfileCollection into a list based on types of horizon logic errors

subApply(): Subset SPC based on result of performing function on each profile

subset(<SoilProfileCollection>): Subset a SoilProfileCollection with logical expressions

subsetHz(<SoilProfileCollection>): Subset the horizons in a SoilProfileCollection using logical criteria

subsetProfiles(<SoilProfileCollection>): DEPRECATED use subset

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

tauW() summaryTauW(): Compute weighted naive and tau statistics for a cross-classification matrix

texcl_to_ssc() ssc_to_texcl() texmod_to_fragvoltot() texture_to_taxpartsize() texture_to_texmod() fragvol_to_texmod(): Textural conversions

textureTriangleSummary(): Soil Texture Low-RV-High as Defined by Quantiles

thicknessOf(): Calculate Thickness of Horizons Matching Logical Criteria

thompson.bell.darkness(): Thompson-Bell (1996) Index

traditionalColorNames: Traditional Soil Color Names

transform(<SoilProfileCollection>): Transform a SPC with expressions based on site or horizon level attributes

unique(<SoilProfileCollection>): Uniqueness within a SoilProfileCollection via MD5 Hash

us.state.soils: US State Soils

validSpatialData(<SoilProfileCollection>): Check for valid spatial reference of profiles

warpHorizons(): Inflate / Deflate Horizon Thickness

wilson2022: Example Data from Wilson et al. 2022

xtableTauW(): Format a LaTeX table with results