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update tutorial to use MCMC2NS utility
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rbouckaert committed Mar 24, 2019
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Expand Up @@ -4,7 +4,7 @@ level: Intermediate
title: Model selection
subtitle: Model selection with nested sampling
beastversion: 2.5.2
nsversion: 1.0.3
nsversion: 1.0.4

Expand Down Expand Up @@ -137,6 +137,24 @@ To use nested sampling, first have to install the NS (version {{ page.nsversion

## Setting up the nested sampling analyses

You can convert an MCMC analysis to an NS analysis using the `MCMC2NS` tool that comes with the NS package.

> * launch the applauncher via the `File > Launch apps` menu in BEAUti
> * in the dialog that pops up, select the `MCMC to NS converter` app, and click `Launch`
> * select the XML file with strict clock analysis, set `HBVStrict-NS.xml` as output file in the same directory.
> * change settings as in the figure below
> * click `OK`, and the file with the nested sampling analysis will be created
> * repeat the process for the relaxed clock analysis
<a name="fig:priors"></a>
<img style="width:80.0%;" src="figures/MCMC2NS.png" alt="">
<figcaption>Figure 4: converting an MCMC analysis to an NS analysis using the applauncher</figcaption>

Alternatively, you can do this in a text editor as follows:

> * copy the file `HBVStrict.xml` to `HBVStric-NS.xml` and
> * copy `HBVUCLN.xml` to `HBVUCLN-NS.xml`
> * start a text editor and in both copied files, change
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Binary file added figures/MCMC2NS.png
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