Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
There is an example call of jphyloref with dummy data in the README. However, a couple more examples would be great. This could also be used to demonstrate the kind of problems that are detected by jphyloref, i.e. reasons why a phyloreference can not be resolved in the reference phylogeny. The examples need not be real world (in size) but small trees with a hand full of taxa that illustrate what jphyloref does help a lot.
One of the JOSS review checklist (https://github.com/openjournals/joss-reviews/issues/3374) items about documentation is:
There is an example call of
jphylorefwith dummy data in theREADME. However, a couple more examples would be great. This could also be used to demonstrate the kind of problems that are detected byjphyloref, i.e. reasons why a phyloreference can not be resolved in the reference phylogeny. The examples need not be real world (in size) but small trees with a hand full of taxa that illustrate whatjphylorefdoes help a lot.