Open trvrb opened 7 months ago
@trvrb Thanks for these suggestions!
I've gone ahead and addressed 1-8 and have updated the main branch accordingly. I'll start working on #9 but it might take a bit of time. Given the time crunch to return to the editor sooner rather than later, I think the best course might be to do it while the editor revises the updated submission. Unless you think it's something that needs to be done before resubmitting?
A few points that could use cleanup / could be better organized:
/data
expecting to find sequence FASTAs, but instead only find ancillary data. Looking more it's clear that core sequence data is indta/alignments/
andmascot_glm/alignments/
. Rename/data
to something more descriptive of move it to live in the appropriate analysis subdirectory..DS_Store
cruft. This should be listed in your.gitignore
file. I see it is. Perhaps these snuck in before you added to.gitignore
. You should just manually delete all these.DS_Store
files from the repo now..Rhistory
files. Add.Rhistory
to.gitignore
..ipynb_checkpoints/
directories.sequence_information.zip
is a complete duplicate ofsequence_information/
. Just delete the.zip
file. Also renamesequence_information/
tosequence_acknowledgments
. I expected "sequence information" to mean metadata.out/
could be named something more informative. I can't tell what in here./dta
and/mascot-glm
. Again see https://github.com/blab/dengue-antigenic-dynamics/tree/master/titer_model or https://github.com/blab/global-migration/tree/master/geo for decent examples..ipynb
for each figure ala https://github.com/blab/adaptive-evolution/blob/master/adaptive-evolution-analysis/Figure1.ipynb