/**
* returns a single Double result. Assumes that the R code uses the variable "results" for storing
* the results of the process.
*
* @param template
* @return
*/
protected Double getSingleResult(String template) {
code.clear();
code.addRCode(template);
String call = "results";
caller.setRCode(code);
caller.runAndReturnResultOnline(call);
String[] res = caller.getParser().getAsStringArray(call);
// the codestore is always updated at the end of the operation
addToCodestore(code, call);
return convertStringToNumber(res[0]);
}
protected void installPackageIfNotInstalled(String packageName) {
code.clear();
code.addRCode(
"if(!('"
+ packageName
+ "' %in% installed.packages()[,\"Package\"])){install.packages('"
+ packageName
+ "')}");
caller.setRCode(code);
String call = "library('" + packageName + "')";
caller.runAndReturnResultOnline("library('" + packageName + "')");
// the codestore is always updated at the end of the operation
addToCodestore(code, call);
}
@Test
public void testStack2() {
double[][] data =
new double[][] {
{197.136, 124.32, 63.492, 59.052},
{124.32, 78.4, 40.04, 37.24},
{63.492, 40.04, 20.449, 19.019},
{59.052, 37.24, 19.019, 17.689}
};
RCaller caller = new RCaller();
Globals.detect_current_rscript();
caller.setRscriptExecutable(Globals.Rscript_current);
RCode code = new RCode();
code.addDoubleMatrix("mydata", data);
code.addRCode("result <- chisq.test(mydata)");
code.addRCode("mylist <- list(pval = result$p.value, df=result$parameter)");
caller.setRCode(code);
caller.runAndReturnResult("mylist");
double pvalue = caller.getParser().getAsDoubleArray("pval")[0];
double df = caller.getParser().getAsDoubleArray("df")[0];
System.out.println("Pvalue is : " + pvalue);
System.out.println("Df is : " + df);
caller.deleteTempFiles();
}
@Test
public void testStack1() {
RCaller caller = new RCaller();
RCode code = new RCode();
Globals.detect_current_rscript();
caller.setRscriptExecutable(Globals.Rscript_current);
caller.cleanRCode();
String x =
"is.installed <- function(mypkg){ \n"
+ "is.element(mypkg, installed.packages()[,1])\n"
+ "}\n"
+ "result <- is.installed(\"bbmle\")\n";
StringBuffer s = new StringBuffer(x);
code.setCode(s);
System.out.println(x);
caller.setRCode(code);
// caller.redirectROutputToConsole();
// caller.runOnly();
caller.runAndReturnResult("result");
boolean result = caller.getParser().getAsLogicalArray("result")[0];
Assert.assertFalse(result);
caller.deleteTempFiles();
}
protected void clearAndSetCode(String somecode) {
code.clear();
code.addRCode(somecode);
caller.setRCode(code);
}
protected void initialize() {
code.clear();
caller.cleanRCode();
caller.setRExecutable(this.rPath + "R.exe");
caller.setRscriptExecutable(this.rPath + "Rscript.exe");
}