Closed whedon closed 5 years ago
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Attempting PDF compilation. Reticulating splines etc...
@stablemarkets, we are starting review in this issue tracker. To expedite the review process do you mind going through above list of check boxes and make sure they can be ticked (you can't tick them). Also check the PDF output carefully. Ping us here when you are done.
Hi @pjotrp. Thank you for working on this.
I've provided responses to several items in the check list below:
ChiRP
, R automatically checks for these dependencies and installs if necessarytestthat()
R package is used for automated testing. This is integrated with Travis CI so that tests are run upon every commit. Coveralls is used to track the coverage of these automated tests. Coverage is currently 92%.Thank you. @agisga feel free to start review. Guide lines are at the top of this page.
Hi!
I have reviewed this submission. Generally it is pretty good. My review is given below.
Summary:
This submission is an R package that implements several Bayesian models from the family of Chinese Restaurant Process (CRP) mixtures. The methods implemented in ChiRP can be used for regression, binary classification, clustering, and related inference tasks. These are very common data analysis tasks, which one commonly encounters in many scientific disciplines. However, the author seems to be motivated specifically by biomedical applications. The advantages of the ChiRP models against alternative methods, include their nonparametric nature, the ability to return interval estimates, and to obtain posterior distributions for predictions as well as for cluster assignments on training and test data. In particular, unlike many other clustering algorithms, here the number of clusters is not specified a priori, and is determined automatically from the data (although an initial number of clusters needs to be given to kick off the MCMC sampler). The package website including model description and examples is really informative and great (in addition, the R Shiny tutorial based on Dirichlet Processes is just awesome). The R code is well-documented, and includes automated tests too. Code quality seems to be good (based on a very quick look through each of the source code files). I'm not an expert on the methodology but, running and tweaking the provided examples, the package code seems to be doing what it's supposed to do. Some minor issues are listed below.
Potential Issues:
testthat
when running the automated tests. Not really an issue, but it probably would be better to not have any warning. (test_ndp.r:23: warning: Test Init K Errors
, test_pdp.r:25: warning: Test Init K Errors
, and test_zdp.r:28: warning: Test Init K Errors
)../R/helper_funtions_pdp.R
~~> might want to change to ./R/helper_functions_pdp.R
("functions" spelled with a "c")None of these are serious issues.
Thank you @agisga! @stablemarkets if you can address these points quickly we can publish!
Hi @pjotrp and @agisga. Thank you for your thorough review! Thanks especially for reviewing the companion web site - extremely helpful.
The package repository has been updated with edits that address your feedback (see below for details). I think the paper.md file will need to be recompiled for the edits to be visible?
I added DOIs to all but two references in paper.bib. I could not find DOIs for two of the papers. One is an ArXiv paper (currently unpublished) so I think it has no DOI yet. For both papers, URLs are provided. Hope this is okay.
Thanks! I've added an acknowledgements sections to the paper mentioning these individuals.
I've added two citations to seminal CRP papers - Ferguson 1973, Blackwell 1973 - to the first paragraph when introducing CRPs.
Contribution instructions have been added to both the ChiRP repository and the companion site. Users can contribute by proposing modifications to the base code or by adding usage examples to the companion site.
testthat warnings: Thanks for catching this! I looked into it. The warning is triggered when someone specifies and init_k
with a length greater than 1. In error_checks()
, I run a single check that returns an error if init_k
is not numeric, or if init_k
is not a scalar (e.g. length 2), or if init_k<0
. If init_k
is of length 2, an error is indeed returned so the test is passed. However, evaluating init_k<0
, yields a length 2 logical vector while the other two conditions in the check yield length 1 logicals. So it shoots a warning saying it will only use the first element of init_k<0
to evaluate the entire check. I fixed this by doing a nested check: first making sure init_k
is numeric and length 1. Then, if that is passed, check to make sure if init_k>0
. If it's not, throw an error message at the user. This passes the automated test without shooting an additional warning since init_k<0
is evaluated only when we are sure init_k
is a scalar.
I'm not sure but the ARCHIVE link is probably not working since I haven't archived the paper yet. According to review process it seems like we only archive after the review process is completed?
Thanks for catching these typos: I've renamed helper/functions_pdp.r, fixed the notation rendering on the site, as well as spell-checked each of the three pages on the companion site.
Excellent. @agisga can you run through those points and confirm you are happy?
@pjotrp
Everything looks good to me!
I don't think there is a new article proof. So, can't check that. But I have looked at all new commits in the ChiRP repo, and also confirmed that the automated tests now run without warnings.
I don't know how strict JOSS is about having DOIs for every article reference, but in my opinion it's fine to have those two DOIs missing, especially because URLs are provided. Thus, I have checked the last checkbox. I leave the final decision up to you.
Thank you for the thorough review @agisga. @stablemarkets: to finalize your submission and accept your paper in JOSS, we need two things. First, can you confirm that all references in your bibliography have a DOI in the bibliography (if one exists).
Second, we need you to deposit a copy of your software repository (including any revisions made during the JOSS review process) with a data-archiving service.
To do so:
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@whedon set 10.5281/zenodo.2591600 as archive
OK. 10.5281/zenodo.2591600 is the archive.
@whedon accept
Attempting dry run of processing paper acceptance...
PDF failed to compile for issue #1287 with the following error:
/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/1287 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in
collect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/lib/whedon/processor.rb:57:in
find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/bin/whedon:73:in compile' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in
run'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in
dispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/bin/whedon:116:in
<top (required)>'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in
OK DOIs
- 10.1007/978-3-319-18968-0 is OK
- 10.1080/10618600.2000.10474879 is OK
- 10.1016/j.jmp.2011.08.004 is OK
- 10.2307/2334940 is OK
- 10.1080/10618600.2012.735624 is OK
- 10.1111/1467-9868.00265 is OK
- 10.1214/aos/1176342360 is OK
- 10.1214/aos/1176342372 is OK
MISSING DOIs
- https://doi.org/10.1145/1015330.1015439 may be missing for title: Dirichlet process mixtures of generalized linear models
- https://doi.org/10.2172/1212177 may be missing for title: A Bayesian Nonparametric Model for Zero-Inflated Outcomes: Prediction, Clustering, and Causal Estimation
INVALID DOIs
- None
@arfon can you check why the PDF is failing?
@whedon generate pdf
Attempting PDF compilation. Reticulating splines etc...
@whedon check references
Attempting to check references...
OK DOIs
- 10.1007/978-3-319-18968-0 is OK
- 10.1080/10618600.2000.10474879 is OK
- 10.1016/j.jmp.2011.08.004 is OK
- 10.2307/2334940 is OK
- 10.1080/10618600.2012.735624 is OK
- 10.1111/1467-9868.00265 is OK
- 10.1214/aos/1176342360 is OK
- 10.1214/aos/1176342372 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@whedon accept
Attempting dry run of processing paper acceptance...
OK DOIs
- 10.1007/978-3-319-18968-0 is OK
- 10.1080/10618600.2000.10474879 is OK
- 10.1016/j.jmp.2011.08.004 is OK
- 10.2307/2334940 is OK
- 10.1080/10618600.2012.735624 is OK
- 10.1111/1467-9868.00265 is OK
- 10.1214/aos/1176342360 is OK
- 10.1214/aos/1176342372 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/575
If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/575, then you can now move forward with accepting the submission by compiling again with the flag deposit=true
e.g.
@whedon accept deposit=true
ping eic @openjournals/joss-eics
@whedon accept deposit=true
Doing it live! Attempting automated processing of paper acceptance...
🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨
Here's what you must now do:
Party like you just published a paper! 🎉🌈🦄💃👻🤘
Any issues? notify your editorial technical team...
@agisga - many thanks for your review and to @pjotrp for editing this submission ✨
@stablemarkets - your paper is now accepted into JOSS :zap::rocket::boom:
:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:
If you would like to include a link to your paper from your README use the following code snippets:
Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01287/status.svg)](https://doi.org/10.21105/joss.01287)
HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01287">
<img src="http://joss.theoj.org/papers/10.21105/joss.01287/status.svg" alt="DOI badge" >
</a>
reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01287/status.svg
:target: https://doi.org/10.21105/joss.01287
This is how it will look in your documentation:
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Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
Submitting author: @stablemarkets (Arman Oganisian) Repository: https://github.com/stablemarkets/ChiRP Version: 1.0.0 Editor: @pjotrp Reviewer: @agisga Archive: 10.5281/zenodo.2591600
Status
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Reviewers and authors:
Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)
Reviewer instructions & questions
@agisga, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @pjotrp know.
✨ Please try and complete your review in the next two weeks ✨
Review checklist for @agisga
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?