Bootstrapping for PDM

Use MATLAB pogram LambdaMarkovEstimation.m to estimate lambda. Do this in three steps.
  1. Transform the trajectory file you get from JAMBE from string code to integer code. This assumes that you keep the trajectory originally generated by JAMBE in file resultsAllTopos.bak .
    java PruneInputConvertStringToInteger >! resultsAllToposInt.out
  2. Next, in MATLAB, load the new file:
    MATLAB> load resultsAllToposInt.out
  3. Finally, still in MATLAB, give the following command:
    MATLAB> lambda=LambdaMarkovEstimation(resultsAllToposInt)
Next, create the file bootstrap.in, which contains two lines: the number of bootstrap replications (integer), and lambda (float).

Example:

100
0.64

Here, 100 bootstrap replications are carried out with a value of lambda=0.64.

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