Daisy chaining code needs to be refined

[AugustT]

@FrancescaMancini has been exploring this

[AugustT]

@FrancescaMancini Would you be able to put a bullet pointed list here of the issues you have been having that we can pick up in the future?

[FrancescaMancini]

• rslurm code to create job scripts was not optimal for daisy chaining; this is now partially fixed, but requires changing the submit.sh template and so it does not fit well with the pipeline for the runs that do not require daisy chaining
• The first chain is run with sparta, which saves an object out, a sparta object containing all the elements expected (BUGoutput, model etc.); all other chains are run by the function daisy, which saves an object also called out, but this object is a list containing the JAGS object out so basically we end up with out$out. This created problems when the second chain was being updated (because you cannot recompile a list). I made a temporary fix, with a series of if statements but it would be better if the object out saved by daisy was the same as that saved by sparta.

[AugustT]

Thanks. To the first point, I think you can supply the template as a character variable rather than a path. If so, the first point could be addressed by creating a function that returns your new template and passing that to the relevant argument.