Question

Currently, I’m copying one instance at a time from one dataset to the other. Is there a way to do this so that string mappings remain intact? The mergeInstances works horizontally, is there an equivalent vertical merge?

This is one step of a loop I use to read datasets of the same structure from multiple arff files into one large dataset. There has got to be a simpler way.

Instances iNew = new ConverterUtils.DataSource(name).getDataSet();
for (int i = 0; i < iNew.numInstances(); i++) {
    Instance nInst = iNew.instance(i);
    inst.add(nInst);
}

Answer 1

Why not make a new ARFF file which has the data from both of the originals? A simple

cat 1.arff > tmp.arff
tail -n+20 2.arff >> tmp.arff

where 20 is replaced by however many lines long your arff header is. This would then produce a new arff file with all of the desired instances, and you could read this new file with your existing code:

Instances iNew = new ConverterUtils.DataSource(name).getDataSet();

You could also invoke weka on the command line using this documentation: http://old.nabble.com/how-to-merge-two-data-file-a.arff-and-b.arff-into-one-data-list–td22890856.html

java weka.core.Instances append filename1 filename2 > output-file 

However, there is no function in the documentation http://weka.sourceforge.net/doc.dev/weka/core/Instances.html#main%28java.lang.String which will allow you to append multiple arff files natively within your java code. As of Weka 3.7.6, the code that appends two arff files is this:

     // read two files, append them and print result to stdout
  else if ((args.length == 3) && (args[0].toLowerCase().equals("append"))) {
DataSource source1 = new DataSource(args[1]);
DataSource source2 = new DataSource(args[2]);
String msg = source1.getStructure().equalHeadersMsg(source2.getStructure());
if (msg != null)
  throw new Exception("The two datasets have different headers:\n" + msg);
Instances structure = source1.getStructure();
System.out.println(source1.getStructure());
while (source1.hasMoreElements(structure))
  System.out.println(source1.nextElement(structure));
structure = source2.getStructure();
while (source2.hasMoreElements(structure))
  System.out.println(source2.nextElement(structure));
  }

Thus it looks like Weka itself simply iterates through all of the instances in a data set and prints them, the same process your code uses.