I'm trying to perform parameter resampling using Latin Hypercube sampling in HYPHY, and had a couple of questions:

1) Is it possible to perform LHS from the command line in HYPHY?

2) After resampling, it looks like some of my LHS samples have a likelihood value of -infinity.  I thought that the re-samples are chosen with probability somehow proportional to their likelihood, so that impossible parameter combinations would be excluded?  Any idea why some of the re-samples might have a likelihood value of -infinity?   (I chose M << N, so there should have been plenty of initial samples to choose from.

3)Is it correct to turn LHS samples into confidence bounds by taking the interval containing 95% of the resampled parameter estimates?

Thanks!!

Hi rss,

1). Yes, you can perform such an analysis. Assuming you have a NEXUS file containing the HyPhy block.
[To export such a file assuming you have a likelihood function lfID (or any other name defined), just use
[code]
Export (lfNEXUS, lfID);
fprintf (file_to_save_to, CLEAR_FILE, lfNEXUS);
[/code]
]

To do so call

$HYPHYMP -p nexus_with_lf_data

Using the '-p' flag will prompt HyPhy to offer you a list of post-processing options, including LHC

2). This is definitely NOT normal (could be a bug, or something wonky with the likelihood function). -Infinity basically means that the likelihood of your data is exactly 0, which should not happen.
Can you send me an example?

3). That is the idea, yes.

Sergei