Debugging the R output of RCaller

RCaller 2.0 has been submitted to Google Code before two or three days. Many RCaller users are testing it and except a Windows installation it seems not to be so problematic.

RCaller 2.0 receives the R outputs as XML files. If the user does not know the returned variable names or if there was a problem with the results some debugging stuff is needed.

Now the function 'getXMLFileAsString()' is implemented in RCaller, by using it, the converted R output can be investigated.

Suppose that we want to run some R code from Java and we want to have a look at the returned XML content. Have a look at these codes:



package test;

import rcaller.RCaller;

/**
 *
 * @author Mehmet Hakan Satman
 */

public class Test4 {
   
    public static void main (String[] args){
        new Test4();
    }
   
    public Test4(){
        try{
            /*
             * Creating an instance of RCaller
             */
            RCaller caller = new RCaller();
           
            /*
             * Defining the Rscript executable
             */
            caller.setRscriptExecutable("/usr/bin/Rscript");
           
            /*
             * Some R Stuff
             */
            caller.addRCode("set.seed(123)");
            caller.addRCode("x<-rnorm(10)");
            caller.addRCode("y<-rnorm(10)");
            caller.addRCode("ols<-lm(y~x)");
           
            /*
             * We want to handle the object 'ols'
             */
            caller.runAndReturnResult("ols");
           
            /*
             * Getting R results as XML
             * for debugging issues.
             */
            System.out.println(caller.getParser().getXMLFileAsString());
        }catch(Exception e){
            System.out.println(e.toString());
        }
    }
}


Because of the "set.seed()"  function of R, this code should produce the same results for all machines. The XML output is


<br /> <?xml version="1.0"?><root><variable name="coefficients" type="numeric"> <value>0.161707725055171</value> <value>0.628661050292344</value></variable><variable name="residuals" type="numeric"> <value>1.41472328100909</value> <value>0.342809724294407</value> <value>-0.740835480333516</value> <value>-0.0953508885174487</value> <value>-0.798827023185445</value> <value>0.547010855774239</value> <value>0.0463826870201345</value> <value>-1.33303015725294</value> <value>0.97144581177619</value> <value>-0.35432881058471</value></variable><variable name="effects" type="numeric"> <value>-0.659720566222913</value> <value>1.79882064905227</value> <value>-1.07914227425757</value> <value>-0.435098740016046</value> <value>-1.13851795731882</value> <value>0.208855465545432</value> <value>-0.292987123779934</value> <value>-1.67407127096485</value> <value>0.630964590291693</value> <value>-0.694576481494576</value></variable><variable name="rank" type="numeric"> <value>2</value></variable><variable name="fitted_values" type="numeric"> <value>-0.190641483569624</value> <value>0.0170041027629571</value> <value>1.14160693092757</value> <value>0.206033604462568</value> <value>0.24298588843137</value> <value>1.23990228102884</value> <value>0.451467791209105</value> <value>-0.633586999376702</value> <value>-0.270089910212505</value> <value>-0.118462597143224</value></variable><variable name="assign" type="numeric"> <value>0</value> <value>1</value></variable><variable name="df_residual" type="numeric"> <value>8</value></variable><variable name="call" type="character"> <value>lm, y ~ x</value> </variable><variable name="terms" type="character"> <value>~, y, x</value> </variable></root><br />



This structure of this XML file is simple and one can see that each single variable is encapsulated within a "" and a "" tag.

Another way of handling the variable names is to use "ROutputParser.getNames()". This function simply returns an ArrayList which includes the variable names returned by R.