If you post sample data and code you are using, we might be able to help.
> you will need to know what the correlation is for reference 1 to reference 2 and
> test 1 to test 2 which can not be obtained from your 2x2 trial.
In simulation studies, the parameters for the simulation have to come from somewhere. In clinical trials, they sometimes come from a small pilot study that estimates the parameters. Another option is to use parameters from other similar studies. A third option is to use an expert's opinion as the best guess.
You can also choose a discrete set of parameter values and run a family of simulations. For example, you can choose R1 = {0.2, 0.4, 0.6} as possible values for the correlation of "reference 1 to reference 2" and R2 = {0.0, 0.1, 0.2} as possible values for the correlation of "test1 to test 2". You can then run the 3x3=9 simulation studies. If you have some way to compare the simulation studies to reality, you might be able to decide which one matches reality the best.
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