Open ezraporter opened 1 month ago
Hi @ezraporter,
Thank you very much for your valuable suggestions. I have reviewed them one by one and made edits according to every bullet point you listed under "Installation," "Documentation," and "Manuscript." Could you please take a look at the repository again and let me know if you feel further changes are needed? Regarding the "Additional suggestions not impacting the review," I will make those changes in the next few weeks.
Thanks, Sidi
Thanks! I'll have a chance to review tomorrow and will report back!
Thanks for those updates! All looks good to me and I've noted it in the review issue 😊
@ezraporter Thank you!
Thanks for allowing me to review https://github.com/openjournals/joss-reviews/issues/6971! Below are some comments that address the unchecked boxes on my checklist.
Installation
README
should include a link out to where JAGS came be downloaded or instructions like these: https://gist.github.com/dennisprangle/e26923fae7477566510757ab3341f54c.Documentation
BJSM_binary()
saysn_MCMC_chain
defaults to 1 but it has no default.LPJSM_binary()
says...
are not currently used but they appear to be forwarded togeepack::geeglm()
Manuscript
Additional suggestions not impacting the review
BJSM_binary()
,group_seq()
, andBJSM_c()
. Harmonizing them might make for a cleaner user experience. For example, these sets of values all seem to contain similar information but have different names:treatment_stageI
/response_stageI
/treatment_stageII
/response_stageII
trt.1st
/resp.1st
/trt.2nd
/resp.2nd
trt1
/stage1outcome
/trt2
/stage2outcome
rjags::jags.model
. It would be helpful to note in the documentation where this is happening so the user can know where to get more information.BJSM_binary()
might be improved by grouping together common elements into a nested list. For example, there are many elements prefixed withci_
. Could those be better collected into aci
element where you could accessci$pi_A
andci$pi_B
. My general advice would be to look at where you have underscores and consider if that's better as a nested list.