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Compute Soil Quality Index from CSV file

Source: R/sqi_compute.R
compute_sqi.Rd

This is the main file-based workflow function that orchestrates the complete SQI calculation pipeline. It reads soil data from a CSV file, performs standardization, PCA-based MDS selection, AHP weighting, indicator scoring, and calculates the final Soil Quality Index.

Usage

compute_sqi(
  input_csv,
  id_column = NULL,
  pairwise_csv = NULL,
  output_csv = NULL,
  directions = NULL,
  var_threshold = 0.05,
  loading_threshold = 0.5,
  ...
)

Arguments

input_csv

Character string specifying the path to the input CSV file containing soil property data. The file should have samples in rows and properties in columns.

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_csv

Optional character string specifying the path to a CSV file containing the AHP pairwise comparison matrix. If NULL, equal weights are used for all indicators.

output_csv

Optional character string specifying the path where the results should be saved as a CSV file. If NULL, results are not saved.

directions

Optional named list specifying scoring functions for each indicator. 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 passed to other functions.

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. Read soil data from CSV file

  2. Standardize numeric columns (z-score)

  3. Perform PCA and select MDS indicators

  4. Calculate AHP weights (from pairwise matrix or equal weights)

  5. Score each MDS indicator

  6. Calculate weighted SQI as sum of (weight * score)

  7. Optionally save results to CSV

See also

compute_sqi_df, compute_sqi_properties

Examples

if (FALSE) { # \dontrun{
# Basic usage with CSV file
result <- compute_sqi(
  input_csv = "soil_data.csv",
  id_column = "SampleID"
)

# With AHP pairwise matrix
result <- compute_sqi(
  input_csv = "soil_data.csv",
  id_column = "SampleID",
  pairwise_csv = "pairwise_matrix.csv"
)

# With custom scoring directions
directions <- list(
  pH = list(type = "optimum", optimum = 7, tol = 1.5, penalty = "linear"),
  OM = list(type = "higher"),
  BD = list(type = "lower")
)
result <- compute_sqi(
  input_csv = "soil_data.csv",
  id_column = "SampleID",
  directions = directions,
  output_csv = "sqi_results.csv"
)
} # }