Learn R Programming

⚠️There's a newer version (2.2) of this package.Take me there.

aqp (version 1.32)

Algorithms for Quantitative Pedology

Description

The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks . These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb . Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.

Copy Link

Version

Install

install.packages('aqp')

Monthly Downloads

2,013

Version

1.32

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/ncss-tech/aqp

Maintainer

Dylan Beaudette

Last Published

September 29th, 2021

Functions in aqp (1.32)

SoilTextureLevels

Ranking Systems for USDS Soil Texture Classes

Create Soil Profile Sketches

addDiagnosticBracket

Annotate Diagnostic Features

Create Representative Soil Profiles via L1 Estimator

SoilProfileCollection

An S4 object representation of a group of soil profiles.

accumulateDepths

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

HzDepthLogicSubset

Subset SoilProfileCollection Objects or Horizons via checkHzDepthLogic

Add Depth Brackets

Convert Pantone PMS codes to Munsell notation

ROSETTA.centroids

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

Visualize soil colors in Munsell notation according to within-group frequency.

buntley.westin.index

Buntley-Westin (1965) Index

Multinominal Brier Score

Allocate soil properties within various classification systems.

Algorithms for Quantitative Pedology

Test for a valid SoilProfileCollection

barron.torrent.redness.LAB

Barron & Torrent (1986) Redness Index in LAB color space

Apply rock fragment or salt correction to available water content

Coerce SoilProfileCollection with as()

bootstrapSoilTexture

Bootstrap Soil Texture Data

aqp_df_class,SoilProfileCollection-method

Get aqp_df_class entry from metadata or return a safe value.

Metrics of Contrast Suitable for Comparing Soil Colors

Soil Color Range via Quantiles

Summarize Soil Colors

diagnostic_hz<-

Add data to the diagnostic slot

Color Contrast Chart

addVolumeFraction

Symbolize Volume Fraction on a Soil Profile Collection Plot

Confusion Index

depths<-,SoilProfileCollection-method

Initialize a SoilProfileCollection from a data.frame object

aggregateSoilDepth

Probabalistic Estimation of Soil Depth within Groups

colorContrastPlot

Color Contrast Plot

Soil Color Contrast

Calculate Relative Positions from Transect Data

evalMissingData

Evaluate Missing Data

equivalentMunsellChips

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

Set data in column of horizon or site data in a SoilProfileCollection

coordinates,SoilProfileCollection-method

Get coordinates from spatial slot

Get data from column of horizon or site data in a SoilProfileCollection

equivalent_munsell

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

checkHzDepthLogic

Check a SoilProfileCollection object for errors in horizon depths.

Soil Data from the Central Sierra Nevada Region of California

Get column of horizon or site data in a SoilProfileCollection

Get top or bottom depths of horizons matching a regular expression pattern

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

Visual Explanation for plotSPC

crit.clay.argillic

Determines threshold (minimum) clay content for argillic upper bound

get.increase.matrix

compute pair-wise distances to determine where an attribute increases within a vertical distance specified

.makeEquivalentMunsellLUT

.makeEquivalentMunsellLUT

Make a data.frame from non-standard expressions evaluated in a data environment

Generalize Horizon Names

diagnostic_hz,SoilProfileCollection-method

Retrieve diagnostic data from SoilProfileCollection

Find and Fill Horizon Gaps

Duplicte Profiles of a SoilProfileCollection

Efficient Slicing of SoilProfileCollection Objects

Estimate available water capacity for fine-earth fraction

horizonDepths<-

Set horizon depth column names

Example Objective Function for Full-Pattern Matching

getArgillicBounds

Estimate upper and lower boundary of argillic diagnostic subsurface horizon

get.increase.depths

Return the horizon top depths from a call to get.increase.matrix()

getCambicBounds

Find all intervals that are potentially part of a Cambic horizon

Determine ML Horizon Boundaries

Subset SPC with pattern-matching for text-based attributes

c,SoilProfileCollection-method

Combine SoilProfileCollection objects

Return a list representation of site and horizon level data

argillic.clay.increase.depth

Return upper boundary of argillic horizon

depth_units,SoilProfileCollection-method

Get depth units from metadata

Return a vector of contributing fractions over a depth interval

Find Overlap within a Sequence

Fix Overlap within a Sequence via Simulated Annealing

estimateSoilDepth

Estimate Soil Depth

Evaluate Generalized Horizon Labels

Set horizon column names

Estimate boundaries of the particle size control section (U.S Soil Taxonomy; 12th edition)

invertLabelColor

Make High Contrast Label Colors

Mix Munsell Colors via Spectral Library

idname,SoilProfileCollection-method

Get profile ID column name

missingDataGrid

Missing Data Grid

(EXPERIMENTAL) Store groupings within a profile collection.

guessHzAttrName

Guess Horizon Slot Column Names

harden.melanization

Harden (1982) Melanization

hzDistinctnessCodeToOffset

Convert Horizon Boundary Distinctness to Vertical Offset

Soil Morphologic Data from Jacobs et al. 2002.

length,SoilProfileCollection-method

Get the number of profiles in a SoilProfileCollection

hzID<-,SoilProfileCollection-method

Set horizon IDs

Subset an SPC by applying glom to each profile

glom,SoilProfileCollection-method

Subset soil horizon data using a depth or depth interval

Find horizons with colors darker than a Munsell hue, value, chroma threshold

horizons,SoilProfileCollection-method

Retrieve horizon data from SoilProfileCollection

horizonColorIndices

Horizon Color Indices

hzTransitionProbabilities

Horizon Transition Probabilities

Transform a SPC (by profile) with a set of expressions

Munsell Hue Reference and Position Searching

getClosestMunsellChip

Get Approximate Munsell Chip

.parseGrouped_formula

.parseHSD_formula

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

munsell.spectra

Spectral Library of Munsell Colors

.as.data.frame.aqp

Wrapper method for data.frame subclass conversion

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

getSoilDepthClass

Generate Soil Depth Class Matrix

min,SoilProfileCollection-method

Get the minimum bottom depth in a SoilProfileCollection

metadata,SoilProfileCollection-method

Retrieve metadata from SoilProfileCollection

Tests of horizon depth logic

harden.rubification

Harden (1982) Rubification

getLastHorizonID

Get IDs of Deepest Horizons by Profile

harmonize,SoilProfileCollection-method

Harmonize a property by profile-level denormalization for convenient visualization or analysis of ranges

Get or Set Horizon Designation Column Name

mollic.thickness.requirement

Calculate the minimum thickness requirement for Mollic epipedon

Find and Quantify Overlap within a 1D Sequence

Munsell to sRGB Lookup Table for Common Soil Colors

nrow,SoilProfileCollection-method

Get the number of horizons in a SoilProfileCollection

names,SoilProfileCollection-method

Get names of columns in site and horizons table

getSurfaceHorizonDepth

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

Iterate over profiles in a SoilProfileCollection

groupedProfilePlot

Grouped Soil Profile Plot

profileGroupLabels

Soil Profile Group Labels

Set horizon ID column name

hzDesgn,SoilProfileCollection-method

Get horizon designation column name

Add data to the restrictions slot

restrictions,SoilProfileCollection-method

Retrieve restriction data from SoilProfileCollection

Set profile IDs

DEPRECATED Simulate Soil Profiles

Tukey's HSD Over Slices

guessGenHzLevels

Guess Appropriate Ordering for Generalized Horizon Labels

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

Get or Set Horizon Texture Class Column Name

Combine a list of SoilProfileCollection objects

Numerical Soil Profile Comparison

soilColorSignature

Soil Profile Color Signatures

plot_distance_graph

Between Individual Distance Plot

thompson.bell.darkness

Thompson-Bell (1996) Index

Unroll Genetic Horizons

textureTriangleSummary

Soil Texture Low-RV-High as Defined by Quantiles

huePositionCircle

Visual Description of Munsell Hue Ordering

Hurst (1977) Redness Index

munsell2spc,SoilProfileCollection-method

Merge Munsell Hue, Value, Chroma converted to sRGB & CIELAB into a SoilProfileCollection

munsellHuePosition

Munsell Hue Position Reference

hzTopographyCodeToLineType

Convert Horizon Boundary Topography to Line Type

proj4string<-,SoilProfileCollection,ANY-method

Set PROJ4 string for the SoilProfileCollection

sRGB to Munsell Color Conversion

proj4string,SoilProfileCollection-method

Set PROJ4 string for the SoilProfileCollection

pms.munsell.lut

Pantone Colors / Munsell Lookup Table

Soil Color Palette

reorderHorizons

Re-order corrupted horizon data

repairMissingHzDepths

Repair Problematic Lower Horizon Depths

hzTopographyCodeToOffset

Convert Horizon Boundary Topography to Vertical Offset

Eliminate duplicate instances of profile IDs in a list of SoilProfileCollections

max,SoilProfileCollection-method

Get the maximum bottom depth in a SoilProfileCollection

Perturb soil horizon depths using boundary distinctness

Sample XRD Patterns

Segmenting of Soil Horizon Data by Depth Interval

subset,SoilProfileCollection-method

Subset a SoilProfileCollection with logical expressions

Soil Chemical Data from Serpentinitic Soils of California

Sample Soil Database #5

Parse Munsell Color Notation

site,SoilProfileCollection-method

Retrieve site data from SoilProfileCollection

Munsell Colors of Common Soil Minerals

panel.depth_function

Lattice Panel Function for Soil Profiles

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

Set site column names

plotColorMixture

Visualize Spectral Mixing of Munsell Colors

replaceHorizons<-

Replace data in the horizon slot

Shannon Entropy

resample.twotheta

Resample an XRD Pattern

Slab-Wise Aggregation of SoilProfileCollection Objects

Soil Physical and Chemical Data from Manganiferous Soils

SoilProfileCollection show method

Slicing of SoilProfileCollection Objects

split,SoilProfileCollection-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

Honcut Creek Soil Profile Data

subsetHz,SoilProfileCollection-method

Subset the horizons in a SoilProfileCollection using logical criteria

spectral.reference

Standard Illuminants and Observers

trunc,SoilProfileCollection-method

Truncate a SoilProfileCollection to specified top and bottom depth

Soil Profile Data Example 3

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

Textural conversions

spc2mpspline,SoilProfileCollection-method

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

Subset SPC based on result of performing function on each profile

traditionalColorNames

Traditional Soil Color Names

transform,SoilProfileCollection-method

Transform a SPC with expressions based on site or horizon level attributes

plotColorQuantiles

Visualize Color Quantiles

Rebuild a SoilProfileCollection object

plotMultipleSPC

Plot Multiple SoilProfileCollection Objects

Simulate Soil Colors

[,SoilProfileCollection-method

Matrix/data.frame-like access to profiles and horizons in a SoilProfileCollection

Quickly assess relative state of site and horizon slots

Convert reflectance spectra to closest Munsell chip

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

DEPRECATED use subset

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

validSpatialData,SoilProfileCollection-method

Get names of columns in site table

Format a LaTeX table with results

Soil Profile Data Example 1

unique,SoilProfileCollection-method

Uniqueness within a SoilProfileCollection via MD5 Hash