Package index • soilquality

Main SQI Computation

Core functions for computing Soil Quality Index with different workflows

compute_sqi(): Compute Soil Quality Index from CSV file
compute_sqi_df(): Compute Soil Quality Index from data frame
compute_sqi_properties(): Compute Soil Quality Index with property selection

Data Handling

Functions for importing and preprocessing soil data

read_soil_csv(): Read Soil Data from CSV File
standardize_numeric(): Standardize Numeric Columns
to_numeric(): Convert Values to Numeric

MDS Selection

Selecting a Minimum Data Set, by variance (PCA) or by centrality (correlation network)

pca_select_mds(): Select Minimum Data Set (MDS) Using PCA
pca_adequacy(): Test whether data is adequate for PCA
na_select_mds(): Select a Minimum Data Set by correlation-network analysis
mds_consensus(): Take the consensus of two Minimum Data Set selection routes

Functional Grouping

Selecting one indicator per soil function (EMDS) rather than across the whole pool

soil_function_groups: Soil indicators grouped by ecosystem function
assign_function_groups(): Map property names onto soil function groups

AHP Weighting

Analytic Hierarchy Process for expert-based indicator weighting

ahp_weights(): Calculate AHP weights from pairwise comparison matrix
create_ahp_matrix(): Create AHP pairwise comparison matrix interactively
ratio_to_saaty(): Convert importance ratios to Saaty pairwise comparison matrix

Scoring Functions

Functions for transforming soil properties into quality scores

score_indicators(): Score multiple indicators using specified scoring functions
score_higher_better(): Score indicator with higher-is-better normalization
score_lower_better(): Score indicator with lower-is-better normalization
score_optimum(): Score indicator with optimum range
score_threshold(): Score indicator with threshold-based piecewise interpolation
score_sigmoid(): Score indicator with a non-linear (sigmoidal) curve

Scoring Constructors

Object-oriented constructors for scoring rules

higher_better(): Create a higher-is-better scoring rule
lower_better(): Create a lower-is-better scoring rule
optimum_range(): Create an optimum range scoring rule
threshold_scoring(): Create a threshold-based scoring rule
sigmoid_scoring(): Create a non-linear (sigmoidal) scoring rule
reference_scoring(): Create a reference-soil scoring rule

Reference-Soil Standardisation

Scoring against an undisturbed reference soil, the documented escape from index incomparability

standardize_to_reference(): Standardise an indicator against a non-degraded reference soil
sensitivity_resistance(): Classify indicators as sensitive or resistant to degradation
adjust_inherent(): Adjust indicators for inherent soil properties

Aggregation

Combining scored indicators into a single index

sqi_area(): Aggregate indicator scores by the area of a radar diagram

Validation

Assessing whether an index actually discriminates, and whether a conclusion survives a change of recipe

sqi_validate(): Validate a Soil Quality Index
sqi_stability(): Test whether a conclusion survives a change of index recipe
check_circularity(): Detect circularity between an index and its predictors

Property Sets and Standard Rules

Pre-defined property collections and automatic scoring rules

soil_property_sets: Pre-defined soil property sets
standard_scoring_rules(): Generate standard scoring rules for soil properties

Visualization

Functions for plotting and visualizing SQI results

plot(<sqi_result>): Plot SQI Results
plot_sqi_report(): Create Multi-Panel SQI Report
plot_sqi_validation(): Plot the distribution of an index across decision categories

Interactive Tools

Shiny-based interactive applications

run_sqi_app(): Launch Interactive Soil Quality Index Calculator

Example Data

Three datasets, for three different jobs. soil_data for scoring, weighting and aggregation; soil_structured for anything reading the structure between indicators; soil_inherent for design factors and nesting.

soil_data: Soil Data from Ucayali, Peru
soil_structured: Simulated Soil Data with Realistic Covariance Structure
soil_inherent: Simulated Soil Data with Inherent Factors and a Nested Design

Print Methods

S3 print methods for custom objects

print(<ahp_matrix>): Print method for ahp_matrix objects
print(<scoring_rule>): Print method for scoring_rule objects
print(<sqi_validation>): Print method for sqi_validation objects
print(<sqi_stability>): Print method for sqi_stability objects
print(<pca_adequacy>): Print method for pca_adequacy objects
print(<sqi_circularity>): Print method for sqi_circularity objects
print(<inherent_adjustment>): Print method for inherent_adjustment objects