bayonet

Installing from source

Requires: gradle, git, eclipse

• Clone the repository
• Type gradle eclipse from the root of the repository
• From eclipse:
  • Import in File menu
  • Import existing projects into workspace
  • Select the root
  • Deselect Copy projects into workspace to avoid having duplicates
• You can call bayonet.Main from the command line via ./bayonet
  • Move the executable bayonet to a PATH folder (or add this folder to PATH) to have access from anywhere
  • Changes done via eclipse will be reflected right away

Coda utils

Coda is a format used by WinBugs and JAGS to store MCMC samples. codaToCSV() converts to a simpler format, with each variable in a separate, self-explanatory csv file.

@org.junit.Test
public void testParseWrite() throws java.io.IOException {
    java.io.File originalCodaIndex = new java.io.File("src/test/resources/CODAindex.txt");
    java.io.File originalCoda = new java.io.File("src/test/resources/CODAchain1.txt");
    java.io.File dest = com.google.common.io.Files.createTempDir();
    bayonet.coda.CodaParser.codaToCSV(originalCodaIndex ,originalCoda ,dest);
    java.io.File newCodaIndex = briefj.BriefIO.createTempFile();
    java.io.File newCoda = briefj.BriefIO.createTempFile();
    bayonet.coda.CodaParser.CSVToCoda(newCodaIndex ,newCoda ,dest);
    java.io.File finalDest = com.google.common.io.Files.createTempDir();
    bayonet.coda.CodaParser.codaToCSV(newCodaIndex ,newCoda ,finalDest);
    org.junit.Assert.assertTrue(((briefj.BriefIO.ls(finalDest ,"csv").size()) == (briefj.BriefIO.ls(dest ,"csv").size())));
    org.junit.Assert.assertTrue(!(briefj.BriefIO.ls(finalDest ,"csv").isEmpty()));
    for (java.io.File f : briefj.BriefIO.ls(finalDest ,"csv")) {
        java.io.File f2 = new java.io.File(dest , f.getName());
        org.junit.Assert.assertTrue(((("Files do not match: " + f) + " vs ") + f2) ,com.google.common.io.Files.equal(f ,f2));
    }
}

Bugs wrapper

This module makes it easier to call JAGS.