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should I add density plots of the priors in tree_priors?

How to collect a bunch of rates from different patients perhaps and estimate using an HPM.

Needs an introduction and explanation how this flows from the Rates and Dates tutorial.

Port a workshop practical? This can build on the continuous trait tutorial but for the specific case where the traits are coordinates.

Extract from SISMID rabies example.

The Mac app packaging script will use the JRE that is installed as a browser plugin, so the JRE should be OK (as downloaded from java.com). Will test on a clean OS X install.

The Linux install instruction currently suggest installing the JDK as well as the JRE - is this necessary? Does OpenJDK work OK with BEAST (older versions did not)?

This is not so bad for the GH pages version but when developing locally it is painful. Currently, called _beast_xml_reference.md which seems to prevent it being compiled (and seen). Need a solution like caching or similar.

A few conventions to follow when creating content:

Internal Links:

These go in square brackets i.e., [beauti] will link to a page called BEAUti.html (case is ignored and the .html should be omitted for simplicity). To create a link with more readable text:
[BEAUti application](beauti).

Images:

Use the 'image.html' include like this:

{% include image.html file="image1.png" %}

This will link to images in the root level /images folder.

Use the prefix attribute to link elsewhere (still assumes an 'images' folder):

{% include image.html prefix="tutorials/tutorial1/" file="image1.png" %}

This will link to '/tutorials/tutorial1/images/image1.png'

The size of the image can be controlled with the 'width' setting:

{% include image.html width="50%" prefix="tutorials/tutorial1/" file="image1.png" %}

Specify width as a percentage of the page width so that it will scale on smaller devices like phones.

A caption can also be included:

{% include image.html caption="This is a nice image" width="50%" prefix="tutorials/tutorial1/" file="image1.png" %}

Port: http://web.archive.org/web/20170709212717/http://beast.bio.ed.ac.uk/Substitution-model-code

http://beast.community/model_selection_1

Currently has a section on HME, sHME and AICM. This should probably be removed and replaced with a note saying these are not recommended and have be deprecated in Tracer. Perhaps with a link to an explanation?

Mac OS doesn't have Java installed by default. A page about installing a suitable JVM would be useful especially to have a M1/M2 and BEAGLE 4 compatible version.

Analysis isn't important, just the steps.

Perhaps this could be two pages - a list of the priors densities we have available, and a list of all the parameters that may appear in BEAUti and the priors we have chosen and why?

I see these as stand alone beginning to end tutorials that we do in workshops. They are longer and more complete. They will tend not to reference other pages but include other information as 'boxes' or similar. However, it would be good to modularize these to avoid duplication and divergence with the online tutorials. Perhaps they could be constructed using the 'include' Jekyll feature and shared with online tutorials.

The expectation is the workshop tutorials get converted to PDF for inclusion in workshop materials.

The current 'How to create taxon sets' tutorial has no explanation on the option to import taxon sets and the screenshot there doesn't even have the Import button.

Update for new online SPREAD?

https://beast.community/spread3

https://beast.community/about

• update funding, contributors and citation advice

Need an explanation of the difference between nu and mu (relative rate parameters) and the Dirichlet prior on nu.

Create a full set of tutorials in markdown with data downloads. Port from other sources.

A basic page exists but more detail about all the options would be useful

This could be the bat rabies host species one? Non-geographic.

Some from beast.bio.ed.ac.uk but probably needs refreshing

List of common error messages and how to solve them. Can be ported from beast.bio.ed.ac.uk but will need updating.

I am thinking about a tutorial that starts with a constant pop size model, then exponential, then skygrid. Showing how to set them up and visualize in Tracer. This is different from the reference guide on tree priors. Could be based on the Influenza 'Workshop tutorial'.

Port a workshop tutorial. This would build on the discrete trait tutorial but for when the trait is location. It would include using SpreaD3 for maps etc.

if you type stuff into the search box and press return nothing happens