archeozoo_r_analysis.py¶

Overview¶

This file contains 15 documented elements.

Classes¶

ArcheozooRAnalysis¶

R-based analysis functions for archeozoology data.

Provides methods for: - Database connection (PostgreSQL/SQLite) - Semivariogram calculation and visualization - Automated kriging with automap - Statistical plots (histograms, boxplots, coplots) - Correlation matrices - HTML report generation

Methods¶

init(self)¶

Initialize the analysis class with R session manager.

is_r_available(self)¶

Check if R is available for analysis.

connect_to_database(self, db_type, host, port, database, user, password)¶

Establish R connection to the database.

Args: db_type: Database type ('postgres' or 'sqlite') host: Database host (for PostgreSQL) port: Database port (for PostgreSQL) database: Database name or path user: Database user (for PostgreSQL) password: Database password (for PostgreSQL)

Returns: True if connection successful, False otherwise.

load_data(self, site_filter)¶

Load archeozoology data from the database into R.

Args: site_filter: Optional site name to filter data.

Returns: True if data loaded successfully, False otherwise.

calculate_semivariogram(self, variables, model, psill, range_val, nugget, output_path)¶

Calculate and plot semivariogram for selected variables.

Args: variables: List of variable names to analyze model: Variogram model type ('Sph', 'Exp', 'Gau', 'Mat') psill: Sill parameter range_val: Range parameter nugget: Nugget parameter output_path: Path to save the output plot

Returns: Path to the generated plot, or None if failed.

run_automap_kriging(self, variable, model, output_path, fix_nugget, fix_range, fix_psill)¶

Run automated kriging using the automap package.

Args: variable: Variable name to krige model: Variogram model type output_path: Path to save outputs fix_nugget: Fixed nugget value (optional) fix_range: Fixed range value (optional) fix_psill: Fixed psill value (optional)

Returns: Tuple of (plot_path, raster_path) or (None, None) if failed.

generate_histogram(self, variable, output_path, title)¶

Generate histogram for a variable.

Args: variable: Variable name to plot output_path: Path to save the plot title: Optional plot title

Returns: Path to the generated plot, or None if failed.

generate_boxplot(self, variable, output_path)¶

Generate boxplot for a variable with statistical details.

Args: variable: Variable name to plot output_path: Path to save the plot

Returns: Path to the generated plot, or None if failed.

generate_coplot(self, variable, output_path)¶

Generate conditional scatter plot (coplot) for spatial distribution.

Args: variable: Variable name for conditioning output_path: Path to save the plot

Returns: Path to the generated plot, or None if failed.

generate_correlation_matrix(self, variables, output_path)¶

Generate correlation matrix plot for multiple variables.

Args: variables: List of variable names to correlate output_path: Path to save the plot

Returns: Path to the generated plot, or None if failed.

generate_html_report(self, variables, output_path, title)¶

Generate HTML report with statistics and plots.

Args: variables: List of variables to include in report output_path: Path to save the report title: Report title

Returns: Path to the generated report, or None if failed.

close_connection(self)¶

Close the database connection in R.

get_available_variables(self)¶

Get list of numeric variables available in the loaded data.

Returns: List of numeric column names.