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Simulate by site (Read 2110 times)

wayne

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Simulate by site
Nov 15^th, 2007 at 7:37am

Hi Sergei, I've been struggling to simulate data by site. I need to use the SimulateData function since I want to simulate from a predefined root state. Since SimulateData does not have the option to export a matrix of rates for each site, I thought I could do this manually by applying SimulateData on a site-by-site basis, choosing the rate category from a predefined distribution. I'm having some trouble with this though. Is there any reason why you think this wouldn't work? Alternatively, is there another method to extract the site category data when using SimulateData, as is possible with SimulateDataSet. thanks ./

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Simulate by site Reply #1 - Nov 15^th, 2007 at 11:54am Dear Wayne, When you call, Code: DataSet id = Simulate (....); HyPhy will spawn a matrix [b]id.rates[b] and stick site-specific rates (a column of values per site, if you have one category var, it'll be just a number) used for data generation into that mattrix. HTH, Sergei
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wayne Global Moderator Offline I love YaBB 1G - SP1! Posts: 57 San Diego, CA Gender:	Re: Simulate by site Reply #2 - Nov 19^th, 2007 at 5:45am thanks, this has made my task substantially easier. cheers ./w
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Simulate by site Reply #3 - Nov 19^th, 2007 at 12:10pm Dear Wayne, Excellent. I forgot to mention that the question you asked about support for ancestral states at internal nodes ages ago needs a new modification to a core C++ function - it can't be done with existing code:( Cheers, Sergei
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