All functions

accumulateDepths()

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

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.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

Coerce SoilProfileCollection with as()

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

compositeSPC()

Return a list representation of site and horizon level data

confusionIndex()

Confusion Index

contrastChart()

Color Contrast Chart

contrastClass()

Soil Color Contrast

coordinates(<SoilProfileCollection>) `coordinates<-`(<SoilProfileCollection>)

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

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<-`(<SoilProfileCollection>) `depths<-`(<data.frame>)

Initialize a SoilProfileCollection from a data.frame object

depthWeights()

Return a vector of contributing fractions over a depth interval

depth_units(<SoilProfileCollection>) `depth_units<-`(<SoilProfileCollection>)

Get depth units from metadata

`diagnostic_hz<-`()

Add data to the diagnostic slot

diagnostic_hz(<SoilProfileCollection>)

Retrieve diagnostic data from SoilProfileCollection

dice()

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

.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

.makeEquivalentMunsellLUT()

.makeEquivalentMunsellLUT

.parseGrouped_formula()

.parseHSD_formula

`[[<-`(<SoilProfileCollection>,<ANY>,<ANY>)

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

`[[`(<SoilProfileCollection>,<ANY>,<ANY>)

Get column of horizon or site data in a SoilProfileCollection

duplicate()

Duplicte Profiles of a SoilProfileCollection

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 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.noise()

Example Objective Function for Full-Pattern Matching

fillHzGaps()

Find and Fill Horizon Gaps

findOverlap()

Find Overlap within a Sequence

fixOverlap()

Fix Overlap within a Sequence via Simulated Annealing

generalize.hz()

Generalize Horizon Names

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

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()

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

glom(<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

groupedProfilePlot()

Grouped Soil Profile Plot

groupSPC()

(EXPERIMENTAL) Store groupings within a profile collection.

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<-`() horizonDepths(<SoilProfileCollection>)

Set horizon depth column names

`horizonNames<-`() horizonNames(<SoilProfileCollection>)

Set horizon column names

horizons(<SoilProfileCollection>) `horizons<-`()

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

HzDepthLogicSubset()

Subset SoilProfileCollection Objects or Horizons via checkHzDepthLogic

hzDepthTests()

Tests of horizon depth logic

hzDesgn(<SoilProfileCollection>)

Get horizon designation column name

hzdesgnname(<SoilProfileCollection>) `hzdesgnname<-`(<SoilProfileCollection>)

Get or Set Horizon Designation Column Name

hzDistinctnessCodeToOffset()

Convert Horizon Boundary Distinctness to Vertical Offset

`hzID<-`(<SoilProfileCollection>) hzID(<SoilProfileCollection>)

Set horizon IDs

`hzidname<-`() hzidname(<SoilProfileCollection>)

Set horizon ID column name

hztexclname(<SoilProfileCollection>) `hztexclname<-`(<SoilProfileCollection>)

Get or 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

idname(<SoilProfileCollection>)

Get profile ID column name

invertLabelColor()

Make High Contrast Label Colors

jacobs2000

Soil Morphologic Data from Jacobs et al. 2002.

L1_profiles()

Create Representative Soil Profiles via L1 Estimator

length(<SoilProfileCollection>)

Get the number of profiles in a SoilProfileCollection

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()

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

overlapMetrics()

Find and Quantify Overlap within a 1D Sequence

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

perturb()

Perturb soil horizon depths using boundary distinctness

plotColorMixture()

Visualize Spectral Mixing of Munsell Colors

plotColorQuantiles()

Visualize Color Quantiles

plotMultipleSPC()

Plot Multiple SoilProfileCollection Objects

plot_distance_graph()

Between Individual Distance Plot

pms.munsell.lut

Pantone Colors / Munsell Lookup Table

PMS2Munsell()

Convert Pantone PMS codes to Munsell notation

previewColors()

Preview Colors

profileApply(<SoilProfileCollection>)

Iterate over profiles in a SoilProfileCollection

profileGroupLabels()

Soil Profile Group Labels

`profile_id<-`() profile_id(<SoilProfileCollection>)

Set profile IDs

`proj4string<-`(<SoilProfileCollection>,<ANY>)

Set PROJ4 string for the SoilProfileCollection

proj4string(<SoilProfileCollection>)

Set PROJ4 string for the SoilProfileCollection

random_profile()

Random Profile

rebuildSPC()

Rebuild a SoilProfileCollection object

reorderHorizons(<SoilProfileCollection>)

Re-order corrupted horizon data

repairMissingHzDepths()

Repair Problematic Lower Horizon Depths

`replaceHorizons<-`()

Replace data in the horizon slot

resample.twotheta()

Resample an XRD Pattern

`restrictions<-`()

Add data to the restrictions slot

restrictions(<SoilProfileCollection>)

Retrieve restriction data from SoilProfileCollection

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

segment()

Segmenting of Soil Horizon Data by Depth Interval

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<-`() siteNames(<SoilProfileCollection>)

Set site column names

slab(<SoilProfileCollection>)

Slab-Wise Aggregation 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.

plotSPC() plot()

Create Soil Profile Sketches

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(<SoilProfileCollection>)

Missing-data-safe, SPC-wide wrapper around mpspline2::mpspline "continuous" 1cm output

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()

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

texcl_to_ssc() ssc_to_texcl() texmod_to_fragvoltot() texture_to_taxpartsize()

Textural conversions

textureTriangleSummary()

Soil Texture Low-RV-High as Defined by Quantiles

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

trunc(<SoilProfileCollection>)

Truncate a SoilProfileCollection to specified top and bottom depth

unique(<SoilProfileCollection>)

Uniqueness within a SoilProfileCollection via MD5 Hash

unroll()

Unroll Genetic Horizons

us.state.soils

US State Soils

validSpatialData(<SoilProfileCollection>)

Get names of columns in site table

xtableTauW()

Format a LaTeX table with results