Algorithms for Quantitative Pedology
Accumulate horizon depths, and reflect reversed depths, relative to ne...
Algorithms for Quantitative Pedology
Return upper boundary of argillic horizon
Coerce SoilProfileCollection with as()
Initialize a SoilProfileCollection from data.frame
Return a vector of contributing fractions over a depth interval
Flag perfectly overlapping horizons within a SoilProfileCollection
Get aqp_df_class entry from metadata or return a safe value.
Add Depth Brackets
Annotate Diagnostic Features
Symbolize Volume Fraction within a Soil Profile Collection Plot
Summarize Soil Colors
Probabilistic Estimation of Soil Depth within Groups
Calculate Relative Positions from Transect Data
Allocate soil properties within various classification systems.
Barron & Torrent (1986) Redness Index in LAB color space
Bootstrap Soil Texture Data
Multinominal Brier Score
Buntley-Westin (1965) Index
Check a SoilProfileCollection object for errors in horizon depths.
Test for a valid SoilProfileCollection
Get top or bottom depths of horizons matching a regular expression pat...
Convert colors into Munsell Notation
Collapse Horizons within Profiles Based on Pattern Matching
Visualize soil colors in Munsell notation according to within-group fr...
Metrics of Contrast Suitable for Comparing Soil Colors
Color Contrast Plot
Soil Color Range via Quantiles
Combine SoilProfileCollection objects
Compare Site Level Attributes of a SoilProfileCollection
Return a list representation of site and horizon level data
Confusion Index
Color Contrast Chart
Store groupings within a profile collection.
Soil Color Contrast
Apply rock fragment or salt correction to available water content
Determines threshold (minimum) clay content for argillic upper bound
Create a (redundant) horizon-level attribute from a site-level attribu...
Get depth units from metadata
Get or Set Diagnostic Horizon data in a SoilProfileCollection
Efficient Slicing of SoilProfileCollection Objects
Set data in column of horizon or site data in a SoilProfileCollection
Get data from column of horizon or site data in a SoilProfileCollectio...
Add or change column of horizon or site data in a SoilProfileCollectio...
Get column of horizon or site data in a SoilProfileCollection
Duplicate Profiles of a SoilProfileCollection
Label placement based on a simulation of electrostatic forces
Identify "equivalent" (whole number value/chroma) Munsell chips
Estimate available water capacity for fine-earth fraction
Estimate boundaries of the U.S Soil Taxonomy Particle Size Control Sec...
Estimate dry soil colors from moist soil colors and vice versa.
Estimate Soil Depth
Evaluate Generalized Horizon Labels
Evaluate Missing Data within a SoilProfileCollection
Visual Explanation for plotSPC
Find and Fill Horizon Gaps
Fix Overlap within a Sequence
Coarse Fragment Class Labels and Diameter
Sieve the Coarse Fraction of Soil
Generalize Horizon Names
Convert cross-tabulation to adjacency matrix.
Generate Labels for Slabs
Compute Pair-wise Distances of Soil Properties over Depth
Determine ML Horizon Boundaries
Estimate upper and lower boundary of argillic diagnostic subsurface ho...
Find all intervals that are potentially part of a Cambic horizon
Get Approximate Munsell Chip
Get IDs of Deepest Horizons by Profile
Hurst (1977) Redness Index
Generate Soil Depth Class Matrix
Determine thickness of horizons (continuous from surface) matching a p...
Get or Set Generalized Horizon Label (GHL) Column Name
Subset soil horizon data using a depth or depth interval
Subset an SPC by applying glom to each profile
Subset SPC with pattern-matching for text-based attributes
Grouped Soil Profile Plot
Guess Appropriate Ordering for Generalized Horizon Labels
Guess Horizon Slot Column Names
Harden (1982) Melanization
Harden (1982) Rubification
Harmonize a property by profile-level denormalization for convenient v...
Find horizons with colors darker than a Munsell hue, value, chroma thr...
Dissolving horizon boundaries by grouping variables
Horizon Color Indices
Set horizon depth column names
Set horizon column names
Retrieve horizon data from SoilProfileCollection
Munsell Hue Reference and Position Searching
Visual Description of Munsell Hue Ordering
Intersecting horizon boundaries by horizon depths
Find lagged horizon values
Segmenting of Soil Horizon Data by Depth Interval
Allocate Particle Size Class for the Control Section.
Subset SoilProfileCollection Objects or Horizons via `checkHzDepthLo...
Ranking Systems for USDA Taxonomic Particle-Size and Substitute Classe...
Tests of horizon depth logic
Get horizon designation column name
Get or Set Horizon Designation Column Name
Convert Horizon Boundary Distinctness to Vertical Offset
Set horizon IDs
Set horizon ID column name
Get horizon-level metadata
Lattice Panel Function for Soil Profiles
Get or Set Horizon Metadata Column Name
Horizons Above or Below
Get or Set Horizon Texture Class Column Name
Convert Horizon Boundary Topography to Line Type
Simulate Soil Colors
Convert Horizon Boundary Topography to Vertical Offset
Horizon Transition Probabilities
Get profile ID column name
Initialize Spatial Data in a SoilProfileCollection
Make High Contrast Label Colors
Check for "empty" profiles in a SoilProfileCollection
Create Representative Soil Profiles via L1 Estimator
Get the number of profiles in a SoilProfileCollection
Eliminate duplicate instances of profile IDs in a list of SoilProfileC...
Get the maximum bottom depth in a SoilProfileCollection
Retrieve metadata from SoilProfileCollection
Get the minimum bottom depth in a SoilProfileCollection
Missing Data Grid
Mix Munsell Colors via Spectral Library
Matrix/data.frame-like access to profiles and horizons in a SoilProfil...
Calculate the minimum thickness requirement for Mollic epipedon
Convert Munsell Color Notation to other Color Space Coordinates (sRGB ...
Merge Munsell Hue, Value, Chroma converted to sRGB & CIELAB into a Soi...
Transform a SPC (by profile) with a set of expressions
Get names of columns in site and horizons table
Numerical Classification of Soil Profiles
Get the number of horizons in a SoilProfileCollection
Find Overlap within a Sequence
Parse Munsell Color Notation
Combine a list of SoilProfileCollection objects
Perturb soil horizon depths using boundary distinctness
Between Individual Distance Plot
Visualize Spectral Mixing of Munsell Colors
Visualize Color Quantiles
Plot Multiple SoilProfileCollection Objects
Preview Colors
Deprecated: Numerical Soil Profile Comparison
Set profile IDs
Iterate over profiles in a SoilProfileCollection
Soil Profile Group Labels
Soil Profile Information Index
Quickly Assemble a SoilProfileCollection
Random Profile
Convert pH to/from Reaction Classes
Rebuild a SoilProfileCollection object
Select a subset of columns from a SoilProfileCollection
Re-order corrupted horizon data
Repair Problematic Lower Horizon Depths
Replace Data in Horizon Slot
Get or Set Restriction data in a SoilProfileCollection
sRGB to Munsell Color Conversion
Fix Overlap within a Sequence via Simulated Annealing
Shannon Entropy
SoilProfileCollection show method
DEPRECATED Simulate Soil Profiles
Retrieve site data from SoilProfileCollection
Set site column names
Slab-Wise Aggregation of SoilProfileCollection Objects
Slicing of SoilProfileCollection Objects
Tukey's HSD Over Slices
Soil Profile Color Signatures
Soil Color Palette
An S4 object representation of a group of soil profiles.
Get or Set Coordinate Reference System for SoilProfileCollection
Create Soil Profile Sketches
Soil Texture Color Palettes
Ranking Systems for USDA Soil Texture Classes
Quickly assess relative state of site and horizon slots
SoilProfileCollection wrapper for mpspline2::mpspline()
Convert reflectance spectra to closest Munsell chip
Split a SoilProfileCollection object into a list of SoilProfileCollect...
Split a SoilProfileCollection into a list based on types of horizon ...
Subset SPC based on result of performing function on each profile
Subset a SoilProfileCollection with logical expressions
Subset the horizons in a SoilProfileCollection using logical criteria
DEPRECATED use subset
Perform summaries on groups (from group_by) and create new site or h...
Compute weighted naive and tau statistics for a cross-classificati...
Textural conversions
Soil Texture Low-RV-High as Defined by Quantiles
Calculate Thickness of Horizons Matching Logical Criteria
Thompson-Bell (1996) Index
Transform a SPC with expressions based on site or horizon level attrib...
Uniqueness within a SoilProfileCollection via MD5 Hash
Unroll Genetic Horizons
Check for valid spatial reference of profiles
Inflate / Deflate Horizon Thickness
Format a LaTeX table with results
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 <doi:10.1016/j.cageo.2012.10.020>. 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 <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. 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.
Useful links