R Integration API

The R integration module provides functions for calling R scripts and functions from Python and for transferring data between Python and R.

Overview

The R integration module includes the following key functionalities:

• run_r_script: Run an R script from Python
• initialize_r: Initialize the R environment
• r_to_pandas: Convert R objects to pandas DataFrames
• pandas_to_r: Convert pandas DataFrames to R objects
• run_r_function: Call R functions from Python

Function Reference

def run_r_script(script_path, args=None, return_output=False):
    """
    Run an R script from Python.

    Parameters
    ----------
    script_path : str
        Path to the R script
    args : list, optional
        Command line arguments to pass to the R script
    return_output : bool, optional
        Whether to return the script's output

    Returns
    -------
    str or None
        Output of the R script if return_output is True
    """
    pass

def initialize_r(packages=None):
    """
    Initialize the R environment.

    Parameters
    ----------
    packages : list, optional
        List of R packages to load

    Returns
    -------
    bool
        Whether initialization was successful
    """
    pass

def r_to_pandas(r_object):
    """
    Convert R objects to pandas DataFrames.

    Parameters
    ----------
    r_object : rpy2.robjects.vectors.DataFrame or str
        R DataFrame object or name of R object

    Returns
    -------
    pandas.DataFrame
        Pandas DataFrame
    """
    pass

def pandas_to_r(df, r_variable_name=None):
    """
    Convert pandas DataFrames to R objects.

    Parameters
    ----------
    df : pandas.DataFrame
        Pandas DataFrame to convert
    r_variable_name : str, optional
        Name to assign to the R object

    Returns
    -------
    rpy2.robjects.vectors.DataFrame
        R DataFrame object
    """
    pass

def run_r_function(function_name, *args, **kwargs):
    """
    Call R functions from Python.

    Parameters
    ----------
    function_name : str
        Name of the R function to call
    *args : tuple
        Positional arguments to pass to the R function
    **kwargs : dict
        Keyword arguments to pass to the R function

    Returns
    -------
    object
        Result of the R function call
    """
    pass

Dependency Handling

The R integration module has several optional dependencies:

Dependency	Required For	Fallback Behavior
rpy2	Direct R integration	Fallback to subprocess R script execution
pandas	Data manipulation	Required dependency
numpy	Matrix operations	Required dependency
R	R script execution	Required for any R functionality

When rpy2 is missing, SMINT will still allow you to run R scripts through subprocess calls, but the direct function calling and data transfer capabilities will be limited.