I think that this ms is "in between" an Application ms and a full Research ms.
While the idea can be generally applied to phylogenetic inference,
your piroutte R package is associated with BEAST2.
I would suggest either writing it as a short Applications ms (3000 words)
if you stick with the latter (and leave some programming details to
Supplementary Information or vignette in R or github); OR expanding it to a
full Research ms but being more general and thorough with exploring the
interpretations and limitations of the approach (see reviewer 1 comments).
We agree. We chose to shorten the main section of the manuscript to fit the
Applications section. At the same time, the reviewers requested more detail,
so we add this, but moved it to the supplementary information.
[ ] Shorten to Application
[ ] Use only one example
[ ] Move empiricists' guidelines, 'step by step and long explanation',
to Appendix
richelbilderbeek
commented
4 years ago
We agree. We chose to shorten the main section of the manuscript to fit the Applications section. At the same time, the reviewers requested more detail, so we add this, but moved it to the supplementary information.