/**
 * Stats.java                                         
 *
 * --Copyright notice-- 
 *
 * Author: Andy Evans. 
 * http://www.geog.leeds.ac.uk/people/a.evans/
 * This code relies on the GPL2-protected library rJava
 * http://www.rforge.net/rJava/ 
 * This code also relies on the GPL2-protected software R
 * http://www.r-project.org/
 * This code is also licensed under GPL2 which can be found at 
 * the Open Source Initiative website at... 
 * http://cran.r-project.org/web/licenses/GPL-2
 *
 * --End of Copyright notice-- 
 *
**/
import java.awt.*;
import java.awt.event.*;

import org.rosuda.JRI.REXP;
import org.rosuda.JRI.Rengine;

/**
 * This class shows how to connect to R and send commands without callback using rJava.
 * The associated practical and data files can be found at 
 * <A href="http://www.geog.leeds.ac.uk/courses/postgrad/geog5790/lecture7/practical/index.html">http://www.geog.leeds.ac.uk/courses/postgrad/geog5790/lecture7/practical/index.html</A>
 * @author <A href="http://www.geog.leeds.ac.uk/people/a.evans/">Andy Evans</A>
 * @version 1.0
**/
public class Stats {

	/**
	 * Opens a link to a datafile, reads in some data, plots it, generates a linear regression.
	 * Note that this class is purposely broken - see practical.
	**/
	public Stats(String[] args) {
	
		// Rengine run like this opens up a GUI-less version of R. 
		// For options to open a java-based GUI and interact with it, see the 
		// Examples that come with rJava in rJava\jri\examples\
		Rengine re=new Rengine(args, false, null);
		
		// Recommended, though not needed as such.
		if (!Rengine.versionCheck()) {System.exit(0);}
		
		// This just reports whether R was running and we connected to it, or whether we started it.
		if (re.isStandAlone()) System.out.println("R initialised by java");
		
		// We're going to use R to read the file but we'll get all the data back out from it 
		// into java, including the predicted points from our linear regression.
		
		// Original data.
		double[] x1 = null;
		double[] y1 = null;
		// Prediction data.
		double[] x2 = null;
		double[] y2 = null;
		
		
		try {
			// The easiest way to deal with R is to use the Rengine eval method. This takes in standard R commands as Strings.
			// Note in the file string that the original text, which needed escaping, is now within a larger String, meaning all the 
			// escape characters need escaping themselves. Easier to use forward-slashes, but I've used back-slashes here to show the point.
			REXP a = re.eval("data1 <- read.csv(\"M:\\\\yourDirectory\\\\data.tab\", header = TRUE)");
			
			// The eval method returns a very useful object of REXP class. This can be converted to 
			// various things to extract data. Here were just convert it to a String, more than anything so you can see it working.
			System.out.println("1: " + a.toString());
			
			a = re.eval("attach(data1)");
			
			// The problem with toString is that it can give you a whole complicated object.
			// The nice thing about the following command is that, while it doesn't have any output in R, in 
			// rJava it sets up the REXP with a copy of the data asked for. 
			a = re.eval("data1$Age");
			
			// We can then use the following method to get the data as a double array.
			x1 = a.asDoubleArray();
			for (int i = 0; i < x1.length; i++) System.out.println(x1[i]); 

			a = re.eval("data1$Desperation");
			y1 = a.asDoubleArray();
			for (int i = 0; i < y1.length; i++) System.out.println(y1[i]); 
			
			// That's got our two original data sets out. Now we plot that data.
			// Note that this opens up the R plot window. This will hang until the 
			// application is terminated, which you can do on the Eclipse output window by 
			// pushing the square red icon. This causes some issues, as we'll see.
			a = re.eval("plot(Age, Desperation, main=\"Age vs. Desperation\")");

			// Do the regression.
			a = re.eval("lineeq <- lm(Desperation ~ Age, data=data1)");
			a = re.eval("x <- seq(min(Age), max(Age), by=10.0)");
			
			// Get the novel x-axis data.
			x2 = a.asDoubleArray();
			for (int i = 0; i < x2.length; i++) System.out.println(x2[i]);
			
			a = re.eval("newData <- data.frame(Age = x)");
			a = re.eval("predictions <- predict(lineeq, newdata = newData)");

			// Get the predicted y-axis data.
			y2 = a.asDoubleArray();
			for (int i = 0; i < y2.length; i++) System.out.println(y2[i]); 

			// Add to the plot. Or so we'd think. 
			a = re.eval("lines(Age, predictions)");
			a = re.eval("title(main=\"Autos\", col.main=\"red\", font.main=4)");

			// Clean up.
			a = re.eval("detach(data1)");
			a = re.eval("rm (data1, lineeq, newData, predictions, x)");

		} catch(Exception e) {
			System.out.println(e.getMessage());
		}

		
	}

	/**
	 * Runs the whole shebang.
	**/
	public static void main(String[] args) {
		
		new Stats(args);

	}

}