Compute Soil Quality Index with property selection

This enhanced workflow function allows explicit property selection and integrates with scoring constructor functions. It validates property selection, subsets the data, and orchestrates the complete SQI calculation pipeline.

Usage

compute_sqi_properties(
  data,
  properties = NULL,
  id_column = NULL,
  pairwise_matrix = NULL,
  scoring_rules = NULL,
  var_threshold = 0.05,
  loading_threshold = 0.5,
  ...
)

Arguments

data

Data frame containing soil property data with samples in rows and properties in columns.

properties

Optional character vector of property names to include in the analysis. If NULL, all numeric columns are used automatically.

id_column

Optional character string specifying the name of the ID column to preserve in the output. If NULL, no ID column is preserved.

pairwise_matrix

Optional pairwise comparison matrix (as matrix or data frame). If NULL, equal weights are used for all indicators.

scoring_rules

Optional named list of scoring_rule objects created with constructor functions (higher_better, lower_better, optimum_range, threshold_scoring). If NULL, all indicators use higher-is-better scoring.

var_threshold

Numeric value for PCA variance threshold (default 0.05).

loading_threshold

Numeric value for PCA loading threshold (default 0.5).

...

Additional arguments (currently unused).

Value

An object of class "sqi_result" containing:

mds

Character vector of selected MDS indicators

weights

Named numeric vector of AHP weights

CR

Consistency Ratio from AHP

results

Data frame with original data, scored indicators, and SQI

pca

PCA object from stats::prcomp

loadings

Matrix of variable loadings

var_exp

Numeric vector of variance explained by each PC

Details

The function performs the following steps:

1. Validate that all specified properties exist in data

2. Subset data to selected properties plus ID column

3. Convert scoring_rule objects to directions list

4. Call compute_sqi_df() to perform the analysis

If properties is NULL, the function automatically detects and uses all numeric columns in the data.

See also

compute_sqi, compute_sqi_df, higher_better, lower_better, optimum_range, threshold_scoring, standard_scoring_rules

Examples

# Create example data
soil_data <- data.frame(
  SampleID = paste0("S", 1:20),
  Sand = rnorm(20, 45, 10),
  Silt = rnorm(20, 30, 5),
  Clay = rnorm(20, 25, 5),
  pH = rnorm(20, 6.5, 0.5),
  OM = rnorm(20, 3, 0.5),
  BD = rnorm(20, 1.4, 0.1)
)

# Select specific properties
result <- compute_sqi_properties(
  data = soil_data,
  properties = c("pH", "OM", "BD"),
  id_column = "SampleID"
)

# With custom scoring rules
rules <- list(
  pH = optimum_range(optimal = 7, tolerance = 1.5),
  OM = higher_better(),
  BD = lower_better()
)
result <- compute_sqi_properties(
  data = soil_data,
  properties = c("pH", "OM", "BD"),
  id_column = "SampleID",
  scoring_rules = rules
)

# Use standard scoring rules for available properties
result <- compute_sqi_properties(
  data = soil_data,
  properties = c("pH", "OM"),
  id_column = "SampleID",
  scoring_rules = standard_scoring_rules(c("pH", "OM"))
)