Joss-reviews: [REVIEW]: passt: An R implementation of the Probability Associator Time (PASS-T) model

[whedon]

Submitting author: @johannes-titz (Johannes Titz)
Repository: https://github.com/johannes-titz/passt
Version: v0.1.1
Editor: @oliviaguest
Reviewer: @nicksexton, @russellpierce
Archive: 10.5281/zenodo.3638130

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/17dd34a44194e85822195179079e606c"><img src="https://joss.theoj.org/papers/17dd34a44194e85822195179079e606c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/17dd34a44194e85822195179079e606c/status.svg)](https://joss.theoj.org/papers/17dd34a44194e85822195179079e606c)

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) by leaving comments 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

@nicksexton & @russellpierce, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @oliviaguest know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @nicksexton

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@johannes-titz) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @russellpierce

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@johannes-titz) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @nicksexton, @russellpierce it looks like you're currently assigned to review this paper :tada:.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Attempting to check references...

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[oliviaguest]

Hi both :wave: — @nicksexton, @russellpierce, this is where the review is carried out. Feel free to also open issues in the repo of the code itself if more appropriate.

[oliviaguest]

@nicksexton and @russellpierce let me know if anything is not clear and on a possible ETA? Thanks! :smile:

[russellpierce]

fyi I'm probably not going to be able to pick this up until Tuesday next week (at the earliest) - sorry!

[nicksexton]

Hey, sorry to be slow to reply.

I'm also aiming to get this done by Tuesday next week.

On Mon, 25 Nov 2019, 09:14 Olivia Guest, [e-mail] wrote:

@nicksexton https://github.com/nicksexton and @russellpierce
https://github.com/russellpierce let me know if anything is not clear
and on a possible ETA? Thanks! 😄

—
You are receiving this because you were mentioned.
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.

[oliviaguest]

@whedon remind @nicksexton in two days

[whedon]

Reminder set for @nicksexton in two days

[oliviaguest]

@whedon remind @russellpierce in two days

[whedon]

Reminder set for @russellpierce in two days

[oliviaguest]

OK, both — I set a reminder for you on Tuesday. This should not take long and I'd like to get the ball rolling. 😄

[whedon]

:wave: @nicksexton, please update us on how your review is going.

[whedon]

:wave: @russellpierce, please update us on how your review is going.

[johannes-titz]

Just for your information: I had to submit a patch to CRAN because the behavior of the class function has changed in the development version of R. So version 0.1.1 of my package is out now. If you happen to work with the development version or run tests on it, version 0.1.0 will throw an error. In the current version of R (3.6.1) passt v.0.1.0 still works fine. But note that version 3.6.2 is already in prerelease state and the final release is scheduled for 2019-12-12. If you cannot get the review done until then, I suggest that you review version 0.1.1. Not sure how this is best handled. If you want to install from CRAN, you will also get version 0.1.1 by default from now on. Basically, this is unavoidable since without the patch the package would be taken down from CRAN. @oliviaguest is it possible to change the version when the submission is still under review? I think in this specific case this would make sense.

[oliviaguest]

Do you want me to change the version to 0.1.1?

[johannes-titz]

If this is possible and does not create any problems, yes, please. Thank you!

[oliviaguest]

@whedon set v0.1.1 as version

[whedon]

OK. v0.1.1 is the version.

[oliviaguest]

Hi :wave: @nicksexton and @russellpierce — it's a been a few weeks since you said you'd take a look here. Would it be possible to give me a realistic ETA? Thanks!

[nicksexton]

Hi @oliviaguest @johannes-titz I'm happy to say I'm satisfied this meets JOSS guidelines. @johannes-titz Nice work on this, I have to say that while the instructions on how to use the package are good, it's not that easy to understand the cognitive detail of the model. I would be happier to see a more complete description of the cognitive model - ie. more formal than the instructions on how to use the package to run a simulation and get results, and higher level than just diving straight into the source code. However I assume these details are in the papers that are under review and I think is outside the scope of the JOSS review, so I'm happy to accept this.

[oliviaguest]

@nicksexton thank you — hopefully the authors can link to their papers from their code repo (and vice versa).

[johannes-titz]

Thank you for the feedback! In the papers that are under review the cognitive model is explained "verbally" and formally in detail. As soon as the papers are published, I will update the references (add a doi). For now, I do not want to upload a preprint version of the submitted papers since I stated that the material has not been disseminated before. The submitted papers already link to the code repository.

[oliviaguest]

@johannes-titz FWIW and perhaps for future reference, you can check out what policy the journal you have submitted to has w.r.t. preprints: http://sherpa.ac.uk/romeo/index.php

[russellpierce]

I'm clearly being unacceptably late here. Further I know it'll be at least two weeks before I can pick this back up. I'm sorry for holding up the works. At this late date it might be better to select an alternative reviewer. I'm sorry.

[oliviaguest]

Thank you for being clear and honest, @russellpierce... OK, lemme tag @labarba for advice since I am not sure on the exact policy here.

[labarba]

This is up to you to handle as you see fit, @oliviaguest. You can ask the author if they are open to waiting another two weeks, or you can look for a replacement reviewer. (If you do the latter, you run @whedon add @user as reviewer then manually edit the checklist in the header comment to this thread.)

[oliviaguest]

Thanks, OK.

1. I propose we wait to see what @russellpierce means by two weeks: please elaborate if you meant that literally. And..

2. we wait to how @johannes-titz feels about having to wait probably another 3-4 weeks (assuming 2 weeks is a rough estimate but not too far off) before getting something back from @russellpierce. Are you OK with this set-up and if not can you propose another reviewer, perhaps?

[russellpierce]

@oliviaguest If @johannes-titz is okay with a 3-4 week window, then I can recommit to that timeframe.

[johannes-titz]

@oliviaguest @russellpierce I can wait another 3-4 weeks. Thanks for the update.

@oliviaguest Thanks a lot for the website to check the preprint policy of journals. I am still a bit hesitant as I might submit to other journals (with other policies) if the papers are rejected (which is always a risk). If you feel an explanation of the cognitive model is needed, I will add one in the documentation on github.

[oliviaguest]

@whedon remind @russellpierce in two weeks

[whedon]

Reminder set for @russellpierce in two weeks

[whedon]

:wave: @russellpierce, please update us on how your review is going.

[oliviaguest]

@whedon remind @russellpierce in one weeks

[whedon]

Reminder set for @russellpierce in one weeks

[oliviaguest]

Hi @russellpierce, as promised I am bothering two weeks later and set up a reminder for in a week too. Let us know how this going and what ETA is realistic. Thank you! :smile:

[russellpierce]

Thank you very much for the ping. I've been able to do a first pass review the software; I want to kick the functionality tires a bit more and dig into the software paper. But, there is progress at least. I have one more hour on my schedule for tomorrow after which I'll wrap things up one way or another. So far, very good!

[oliviaguest]

@russellpierce Great!

[whedon]

:wave: @russellpierce, please update us on how your review is going.

[oliviaguest]

@russellpierce hopefully you almost done now! :smile:

[russellpierce]

Done now; I don't have anything at add to what the other reviewer said (sharing in their sentiment wishing for more context but understanding the nature of publication frustrations).

[oliviaguest]

@russellpierce what about:

Functionality: Have the functional claims of the software been confirmed?

[russellpierce]

Yes, sorry I just missed the check mark

[oliviaguest]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[oliviaguest]

@whedon check references

[oliviaguest]

@russellpierce thank you so much!

@johannes-titz please check and let me know if the PDF looks OK.

[johannes-titz]

@oliviaguest Thank you! There is a minor problem: one url does not resolve. I just fixed this and released version 0.1.2. The only change is the url in the bib file and the link in readme.md (see here: https://github.com/johannes-titz/passt/compare/v0.1.1...v0.1.2). Sorry for that. I believe the url resolved when I submitted. The updated link is now a persistent identifier (URN, comparable to doi).

[oliviaguest]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[oliviaguest]

@whedon check references

[oliviaguest]

@johannes-titz let me know if this looks better.

[johannes-titz]

@oliviaguest yes, perfect!

[oliviaguest]

@whedon accept

[whedon]

No archive DOI set. Exiting...

[oliviaguest]

@johannes-titz can you post it on Zenodo (anywhere with a DOI for software) if not yet and then post the DOI? :smiley_cat:

[johannes-titz]

@oliviaguest Zenodo doi: 10.5281/zenodo.3638130

[oliviaguest]

@whedon set 10.5281/zenodo.3638130 as archive

[whedon]

OK. 10.5281/zenodo.3638130 is the archive.

[oliviaguest]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[oliviaguest]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #1900 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/bibtex_parser.rb:45:in block in generate_citations': undefined methodkey' for # (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.0.1/lib/bibtex/bibliography.rb:149:in each' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.0.1/lib/bibtex/bibliography.rb:149:ineach'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/bibtex_parser.rb:41:in generate_citations' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/compilers.rb:245:incrossref_from_markdown'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/compilers.rb:21:in generate_crossref' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/lib/whedon/processor.rb:95:incompile'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:79:in compile' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun'
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:indispatch'
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-9847f98e9ec6/bin/whedon:116:in 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

'

[johannes-titz]

@oliviaguest The bib file is auto-generated by zotero. It has a @preamble that is a command. If this causes problems, I can remove it.

[oliviaguest]

@johannes-titz feel free to try and we can try the above again! :smile:

[oliviaguest]

@openjournals/joss-eics please accept this after also please advising on the error above.

[johannes-titz]

@oliviaguest Just removed the preamble. Can you try it again?

[oliviaguest]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[oliviaguest]

@johannes-titz FWIW I think you can play with @whedon too with respect to making PDFs. But maybe I'm mistaken. :blush:

[oliviaguest]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1268

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1268, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[whedon]

Reference check summary:

OK DOIs

- 10.1038/nn.3648 is OK
- 10.1037/gpr0000143 is OK
- 10.1207/S15327906MBR3803_02 is OK
- 10.1111/j.1467-9280.1991.tb00174.x is OK
- 10.1037/a0032921 is OK
- 10.1037/met0000195 is OK
- 10.3389/fpsyg.2012.00196 is OK
- 10.1146/annurev.neuro.28.061604.135709 is OK
- 10.1348/000712608X377117 is OK
- 10.18637/jss.v067.i01 is OK
- 10.1016/j.paid.2004.06.017 is OK
- 10.1111/j.1365-2869.2007.00572.x is OK
- 10.1093/pan/mpr057 is OK
- 10.1177/0146167299025004006 is OK
- 10.1177/001872088602800203 is OK
- 10.1037/0033-2909.106.2.265 is OK
- 10.1111/j.1469-8986.2008.00654.x is OK
- 10.1177/0959354315617253 is OK
- 10.1098/rstb.2009.0028 is OK
- 10.1037/h0031337 is OK
- 10.1177/1745691617706516 is OK
- 10.1038/nrn1764 is OK
- 10.1016/j.neuropsychologia.2009.05.024 is OK
- 10.1177/2515245919847196 is OK
- 10.1016/j.cognition.2007.03.004 is OK
- 10.1111/j.1551-6709.2010.01094.x is OK
- 10.1037/0033-2909.132.3.354 is OK
- 10.1016/S0140-6736(17)32802-7 is OK
- 10.1037/h0047773 is OK
- 10.1037/h0025052 is OK
- 10.1037/a0025897 is OK
- 10.3758/s13428-014-0458-y is OK
- 10.1126/science.7256273 is OK
- 10.1037/met0000079 is OK
- 10.1016/j.actpsy.2005.06.003 is OK
- 10.1037/0033-295X.106.1.180 is OK
- 10.1016/S0022-0965(02)00180-7 is OK
- 10.1016/j.tics.2016.03.014 is OK
- 10.1037/0033-295X.95.1.91 is OK
- 10.1098/rstb.2009.0026 is OK
- 10.18637/jss.v040.i08 is OK
- 10.1007/978-1-4614-6868-4 is OK
- 10.7287/peerj.preprints.3188v1 is OK
- 10.1136/bmj.316.7129.469 is OK
- 10.1111/j.1467-9450.2009.00773.x is OK
- 10.1186/1471-2202-15-S1-P159 is OK
- 10.1155/S0161171290001107 is OK
- 10.1177/0963721410386677 is OK
- 10.1016/j.paid.2014.10.051 is OK
- 10.6084/m9.figshare.7291172 is OK
- 10.6084/m9.figshare.7294670 is OK
- 10.6084/m9.figshare.7294673 is OK
- 10.1063/1.2915126 is OK
- 10.1207/s15328031us0301_1 is OK
- 10.1016/j.neuroscience.2010.07.052 is OK
- 10.1016/j.socec.2004.09.033 is OK
- 10.3758/s13428-016-0789-y is OK
- 10.1162/00335530360698496 is OK
- 10.1080/0305498930190401 is OK
- 10.1037/h0038479 is OK
- 10.1002/sim.4780130514 is OK
- 10.1080/10503309712331331843 is OK
- 10.1037/gpr0000051 is OK
- 10.1037/0278-7393.15.3.371 is OK
- 10.3366/cor.2015.0068 is OK
- 10.1016/j.tics.2005.11.006 is OK
- 10.3758/APP.72.3.561 is OK
- 10.1109/MIE.2014.2361237 is OK
- 10.1111/j.2044-8295.1973.tb01383.x is OK
- 10.1037/0003-066X.39.12.1372 is OK
- 10.3758/s13428-017-0935-1 is OK
- 10.3389/fpsyg.2013.00246 is OK
- 10.2307/2265754 is OK
- 10.3389/fpsyt.2018.00517 is OK
- 10.1037/h0027133 is OK
- 10.1037/h0028865 is OK
- 10.1016/S0022-5371(73)80013-1 is OK
- 10.3758/BF03208903 is OK
- 10.1016/S0079-7421(08)60464-8 is OK
- 10.3758/BF03202365 is OK
- 10.1037/0033-295X.95.4.528 is OK
- 10.1037//0278-7393.27.6.1347 is OK
- 10.3758/BF03196863 is OK
- 10.1177/1745691611406924 is OK
- 10.3758/s13423-015-0890-8 is OK
- 10.4324/9781315650982 is OK
- 10.1016/0028-3932(77)90069-0 is OK
- 10.2307/1942661 is OK
- 10.1016/S0079-7421(08)60358-8 is OK
- 10.3758/BF03208849 is OK
- 10.1037/0278-7393.18.2.368 is OK
- 10.1037/h0078820 is OK
- 10.1016/j.neuropsychologia.2012.08.001 is OK
- 10.1111/j.1467-9280.1993.tb00589.x is OK
- 10.1007/BF00412045 is OK
- 10.1037/1082-989X.8.3.305 is OK
- 10.1037/1082-989X.11.4.363 is OK
- 10.1037/met0000127 is OK
- 10.1007/s12671-017-0700-7 is OK
- 10.3389/fpsyg.2013.00513 is OK
- 10.1111/j.1469-8986.2010.01069.x is OK
- 10.1002/sim.4780071009 is OK
- 10.1016/0160-5402(86)90002-1 is OK
- 10.1021/jm500317a is OK
- 10.3389/fpsyg.2018.00460 is OK
- 10.1016/j.paid.2016.07.010 is OK
- 10.1177/1745691611427305 is OK
- 10.1016/j.neubiorev.2016.03.003 is OK
- 10.1002/ejsp.2023 is OK
- 10.1177/1745691614528520 is OK
- 10.1186/1471-2202-11-5 is OK
- 10.1080/09541440802453006 is OK
- 10.1016/j.aap.2012.12.028 is OK
- 10.1037/0033-295X.111.4.835 is OK
- 10.1002/0471214426.pas0401 is OK
- 10.1016/j.jmp.2011.05.004 is OK
- 10.5281/zenodo.1308157 is OK
- 10.1016/j.evolhumbehav.2014.03.002 is OK
- 10.1002/sim.698 is OK
- 10.1037/h0056029 is OK
- 10.3758/BF03201006 is OK
- 10.1146/annurev.psych.59.103006.093735 is OK
- 10.1002/per.2180 is OK
- 10.1037//0033-295X.102.3.419 is OK
- 10.1177/1745691616662243 is OK
- 10.1037/0097-7403.9.3.320 is OK
- 10.1348/000712603767876262 is OK
- 10.1177/0959354300105004 is OK
- 10.1348/000711007X243582 is OK
- 10.1103/PhysRev.2.109 is OK
- 10.1068/p160005 is OK
- 10.3758/BF03328900 is OK
- 10.1371/journal.pone.0146721 is OK
- 10.1016/0022-1031(92)90055-O is OK
- 10.1037/0033-295X.89.6.609 is OK
- 10.1038/s41562-018-0522-1 is OK
- 10.1167/13.2.11 is OK
- 10.1111/j.2041-210x.2012.00261.x is OK
- 10.1098/rsif.2017.0213 is OK
- 10.1037/0278-7393.14.4.676 is OK
- 10.1037/h0082899 is OK
- 10.1037/0033-295X.110.4.611 is OK
- 10.1002/hipo.20855 is OK
- 10.1016/0883-0355(89)90027-X is OK
- 10.1126/science.aac4716 is OK
- 10.1111/j.1551-6709.2011.01214.x is OK
- 10.1093/oxfordhb/9780199842193.013.8 is OK
- 10.1037/1076-898X.14.2.101 is OK
- 10.1063/1.2743125 is OK
- 10.1016/j.aap.2014.06.019 is OK
- 10.1037/0033-295X.91.3.281 is OK
- 10.3758/s13428-011-0172-y is OK
- 10.3758/BF03200459 is OK
- 10.1037/a0036576 is OK
- 10.1016/0361-9230(94)90175-9 is OK
- 10.1152/jn.00673.2003 is OK
- 10.1037//0033-295X.107.2.358 is OK
- 10.1016/j.actpsy.2006.03.008 is OK
- 10.1037//0033-2909.86.5.1165 is OK
- 10.1037/0022-0663.74.2.166 is OK
- 10.1016/S0364-0213(85)80010-0 is OK
- 10.1348/000711007X255327 is OK
- 10.1016/j.jrp.2013.05.009 is OK
- 10.1037/met0000061 is OK
- 10.1016/j.jrp.2018.02.010 is OK
- 10.1016/0191-8869(95)00216-2 is OK
- 10.1016/j.psychsport.2015.11.005 is OK
- 10.1027/0044-3409.217.1.1 is OK
- 10.1037/a0028168 is OK
- 10.1126/science.2392679 is OK
- 10.1037/h0032076 is OK
- 10.1007/s11336-04-1221-6 is OK
- 10.1146/annurev.ps.41.020190.000245 is OK
- 10.1007/s12124-015-9339-x is OK
- 10.3758/PBR.17.4.499 is OK
- 10.1016/j.actpsy.2017.03.008 is OK
- 10.3758/s13423-018-1451-8 is OK
- 10.1037/h0029096 is OK
- 10.1016/B0-08-043076-7/00553-2 is OK
- 10.1037/pspp0000187 is OK
- 10.1016/j.jclinepi.2005.01.006 is OK
- 10.3758/s13428-017-0954-y is OK
- 10.1186/1756-6606-3-15 is OK
- 10.18637/jss.v048.i09 is OK
- 10.1016/0010-0285(73)90033-9 is OK
- 10.1037/h0030544 is OK
- 10.1037/h0032785 is OK
- 10.1007/BF02294384 is OK
- 10.1037/1082-989X.10.4.428 is OK
- 10.1016/j.jbusres.2017.12.043 is OK
- 10.18637/jss.v036.i03 is OK
- 10.1016/j.tics.2003.09.002 is OK
- 10.1037/h0026871 is OK
- 10.2307/2289844 is OK
- 10.1037/h0037205 is OK
- 10.1198/tas.2011.11077 is OK
- 10.18637/jss.v021.i12 is OK
- 10.32614/RJ-2011-002 is OK
- 10.18637/jss.v059.i10 is OK
- 10.1037/0278-7393.12.3.387 is OK
- 10.1088/1742-6596/588/1/012034 is OK
- 10.1371/journal.pone.0126974 is OK
- 10.1016/j.cortex.2014.10.015 is OK
- 10.1214/aoms/1177732676 is OK
- 10.1006/jmla.2002.2864 is OK
- 10.1097/WNN.0b013e31815f237c is OK
- 10.1037/h0025848 is OK
- 10.1111/1467-8721.ep11512604 is OK
- 10.1080/17470218.2014.975730 is OK
- 10.1080/13506285.2011.598482 is OK
- 10.1370/afm.197 is OK
- 10.1370/afm.197 is OK

MISSING DOIs

- https://doi.org/10.5962/bhl.title.7309 may be missing for title: Design for a Brain: The Origin of Adaptive Behavior
- https://doi.org/10.1007/978-3-642-14749-4_15 may be missing for title: Implicit Spatial Length Modulates Time Estimates, but Not Vice Versa
- https://doi.org/10.3758/bf03205526 may be missing for title: Attentional Resources in Timing: Interference Effects in Concurrent Temporal and Nontemporal Working Memory Tasks.
- https://doi.org/10.1016/c2013-0-10517-x may be missing for title: Statistical Power Analysis for the Behavioral Sciences
- https://doi.org/10.1198/tech.2008.s540 may be missing for title: Pharmaceutical Statistics Using SAS: A Practical Guide
- https://doi.org/10.1081/qen-120038013 may be missing for title: Qualitative Ordinal Scales: The Concept of Ordinal Range
- https://doi.org/10.1007/978-3-540-73339-3_27 may be missing for title: GNU General Public License
- https://doi.org/10.1037/0033-295x.91.1.1 may be missing for title: A Retrieval Model for Both Recognition and Recall
- https://doi.org/10.3758/bf03212913 may be missing for title: What Causes the Spacing Effect? Some Effects of Repetition, Duration, and Spacing on Memory for Pictures.
- https://doi.org/10.1017/cbo9781139173865.013 may be missing for title: The Contemporary Theory of Metaphor
- https://doi.org/10.4324/9781315807614 may be missing for title: An Introduction to the Logic of Psychological Measurement
- https://doi.org/10.1037/h0027470 may be missing for title: Recognition Memory for a Rapid Sequence of Pictures
- https://doi.org/10.1037/1082-989x.1.2.199 may be missing for title: Measurement Error in Psychological Research: Lessons From 26 Research Scenarios
- https://doi.org/10.1093/acprof:oso/9780198508632.003.0001 may be missing for title: Frequency Processing and Cognition: Introduction and Overview
- https://doi.org/10.1093/acprof:oso/9780198508632.003.0009 may be missing for title: Associative Learning and Frequency Judgments: The PASS Model
- https://doi.org/10.1016/0004-3702(84)90029-8 may be missing for title: The Sciences of the Artificial
- https://doi.org/10.1093/acprof:oso/9780198508632.003.0002 may be missing for title: Frequency Processing: A Twenty-Five Year Perspective
- https://doi.org/10.1111/j.1365-2044.1976.tb11887.x may be missing for title: Lord of the Flies

INVALID DOIs

- None

[oliviaguest]

@johannes-titz check those missing DOIs and then try to regenerate PDF, please? :thinking:

[johannes-titz]

@oliviaguest Sorry for the mess. My bib-file contains all papers I use. whedon checks them all, although only a small subset is used in the actual paper. The pdf looks fine to me. There are some references that do not have doi. I can also clean up the bib file.

[oliviaguest]

@johannes-titz ah, that's probably fine then. I'll let @openjournals/joss-eics take it from here. :tada:

[whedon]

Reference check summary:

OK DOIs

- 10.1038/nn.3648 is OK
- 10.1037/gpr0000143 is OK
- 10.1207/S15327906MBR3803_02 is OK
- 10.1111/j.1467-9280.1991.tb00174.x is OK
- 10.1037/a0032921 is OK
- 10.1037/met0000195 is OK
- 10.3389/fpsyg.2012.00196 is OK
- 10.1146/annurev.neuro.28.061604.135709 is OK
- 10.1348/000712608X377117 is OK
- 10.18637/jss.v067.i01 is OK
- 10.1016/j.paid.2004.06.017 is OK
- 10.1111/j.1365-2869.2007.00572.x is OK
- 10.1093/pan/mpr057 is OK
- 10.1177/0146167299025004006 is OK
- 10.1177/001872088602800203 is OK
- 10.1037/0033-2909.106.2.265 is OK
- 10.1111/j.1469-8986.2008.00654.x is OK
- 10.1177/0959354315617253 is OK
- 10.1098/rstb.2009.0028 is OK
- 10.1037/h0031337 is OK
- 10.1177/1745691617706516 is OK
- 10.1038/nrn1764 is OK
- 10.1016/j.neuropsychologia.2009.05.024 is OK
- 10.1177/2515245919847196 is OK
- 10.1016/j.cognition.2007.03.004 is OK
- 10.1111/j.1551-6709.2010.01094.x is OK
- 10.1037/0033-2909.132.3.354 is OK
- 10.1016/S0140-6736(17)32802-7 is OK
- 10.1037/h0047773 is OK
- 10.1037/h0025052 is OK
- 10.1037/a0025897 is OK
- 10.3758/s13428-014-0458-y is OK
- 10.1126/science.7256273 is OK
- 10.1037/met0000079 is OK
- 10.1016/j.actpsy.2005.06.003 is OK
- 10.1037/0033-295X.106.1.180 is OK
- 10.1016/S0022-0965(02)00180-7 is OK
- 10.1016/j.tics.2016.03.014 is OK
- 10.1037/0033-295X.95.1.91 is OK
- 10.1098/rstb.2009.0026 is OK
- 10.18637/jss.v040.i08 is OK
- 10.1007/978-1-4614-6868-4 is OK
- 10.7287/peerj.preprints.3188v1 is OK
- 10.1136/bmj.316.7129.469 is OK
- 10.1111/j.1467-9450.2009.00773.x is OK
- 10.1186/1471-2202-15-S1-P159 is OK
- 10.1155/S0161171290001107 is OK
- 10.1177/0963721410386677 is OK
- 10.1016/j.paid.2014.10.051 is OK
- 10.6084/m9.figshare.7291172 is OK
- 10.6084/m9.figshare.7294670 is OK
- 10.6084/m9.figshare.7294673 is OK
- 10.1063/1.2915126 is OK
- 10.1207/s15328031us0301_1 is OK
- 10.1016/j.neuroscience.2010.07.052 is OK
- 10.1016/j.socec.2004.09.033 is OK
- 10.3758/s13428-016-0789-y is OK
- 10.1162/00335530360698496 is OK
- 10.1080/0305498930190401 is OK
- 10.1037/h0038479 is OK
- 10.1002/sim.4780130514 is OK
- 10.1080/10503309712331331843 is OK
- 10.1037/gpr0000051 is OK
- 10.1037/0278-7393.15.3.371 is OK
- 10.3366/cor.2015.0068 is OK
- 10.1016/j.tics.2005.11.006 is OK
- 10.3758/APP.72.3.561 is OK
- 10.1109/MIE.2014.2361237 is OK
- 10.1111/j.2044-8295.1973.tb01383.x is OK
- 10.1037/0003-066X.39.12.1372 is OK
- 10.3758/s13428-017-0935-1 is OK
- 10.3389/fpsyg.2013.00246 is OK
- 10.2307/2265754 is OK
- 10.3389/fpsyt.2018.00517 is OK
- 10.1037/h0027133 is OK
- 10.1037/h0028865 is OK
- 10.1016/S0022-5371(73)80013-1 is OK
- 10.3758/BF03208903 is OK
- 10.1016/S0079-7421(08)60464-8 is OK
- 10.3758/BF03202365 is OK
- 10.1037/0033-295X.95.4.528 is OK
- 10.1037//0278-7393.27.6.1347 is OK
- 10.3758/BF03196863 is OK
- 10.1177/1745691611406924 is OK
- 10.3758/s13423-015-0890-8 is OK
- 10.4324/9781315650982 is OK
- 10.1016/0028-3932(77)90069-0 is OK
- 10.2307/1942661 is OK
- 10.1016/S0079-7421(08)60358-8 is OK
- 10.3758/BF03208849 is OK
- 10.1037/0278-7393.18.2.368 is OK
- 10.1037/h0078820 is OK
- 10.1016/j.neuropsychologia.2012.08.001 is OK
- 10.1111/j.1467-9280.1993.tb00589.x is OK
- 10.1007/BF00412045 is OK
- 10.1037/1082-989X.8.3.305 is OK
- 10.1037/1082-989X.11.4.363 is OK
- 10.1037/met0000127 is OK
- 10.1007/s12671-017-0700-7 is OK
- 10.3389/fpsyg.2013.00513 is OK
- 10.1111/j.1469-8986.2010.01069.x is OK
- 10.1002/sim.4780071009 is OK
- 10.1016/0160-5402(86)90002-1 is OK
- 10.1021/jm500317a is OK
- 10.3389/fpsyg.2018.00460 is OK
- 10.1016/j.paid.2016.07.010 is OK
- 10.1177/1745691611427305 is OK
- 10.1016/j.neubiorev.2016.03.003 is OK
- 10.1002/ejsp.2023 is OK
- 10.1177/1745691614528520 is OK
- 10.1186/1471-2202-11-5 is OK
- 10.1080/09541440802453006 is OK
- 10.1016/j.aap.2012.12.028 is OK
- 10.1037/0033-295X.111.4.835 is OK
- 10.1002/0471214426.pas0401 is OK
- 10.1016/j.jmp.2011.05.004 is OK
- 10.5281/zenodo.1308157 is OK
- 10.1016/j.evolhumbehav.2014.03.002 is OK
- 10.1002/sim.698 is OK
- 10.1037/h0056029 is OK
- 10.3758/BF03201006 is OK
- 10.1146/annurev.psych.59.103006.093735 is OK
- 10.1002/per.2180 is OK
- 10.1037//0033-295X.102.3.419 is OK
- 10.1177/1745691616662243 is OK
- 10.1037/0097-7403.9.3.320 is OK
- 10.1348/000712603767876262 is OK
- 10.1177/0959354300105004 is OK
- 10.1348/000711007X243582 is OK
- 10.1103/PhysRev.2.109 is OK
- 10.1068/p160005 is OK
- 10.3758/BF03328900 is OK
- 10.1371/journal.pone.0146721 is OK
- 10.1016/0022-1031(92)90055-O is OK
- 10.1037/0033-295X.89.6.609 is OK
- 10.1038/s41562-018-0522-1 is OK
- 10.1167/13.2.11 is OK
- 10.1111/j.2041-210x.2012.00261.x is OK
- 10.1098/rsif.2017.0213 is OK
- 10.1037/0278-7393.14.4.676 is OK
- 10.1037/h0082899 is OK
- 10.1037/0033-295X.110.4.611 is OK
- 10.1002/hipo.20855 is OK
- 10.1016/0883-0355(89)90027-X is OK
- 10.1126/science.aac4716 is OK
- 10.1111/j.1551-6709.2011.01214.x is OK
- 10.1093/oxfordhb/9780199842193.013.8 is OK
- 10.1037/1076-898X.14.2.101 is OK
- 10.1063/1.2743125 is OK
- 10.1016/j.aap.2014.06.019 is OK
- 10.1037/0033-295X.91.3.281 is OK
- 10.3758/s13428-011-0172-y is OK
- 10.3758/BF03200459 is OK
- 10.1037/a0036576 is OK
- 10.1016/0361-9230(94)90175-9 is OK
- 10.1152/jn.00673.2003 is OK
- 10.1037//0033-295X.107.2.358 is OK
- 10.1016/j.actpsy.2006.03.008 is OK
- 10.1037//0033-2909.86.5.1165 is OK
- 10.1037/0022-0663.74.2.166 is OK
- 10.1016/S0364-0213(85)80010-0 is OK
- 10.1348/000711007X255327 is OK
- 10.1016/j.jrp.2013.05.009 is OK
- 10.1037/met0000061 is OK
- 10.1016/j.jrp.2018.02.010 is OK
- 10.1016/0191-8869(95)00216-2 is OK
- 10.1016/j.psychsport.2015.11.005 is OK
- 10.1027/0044-3409.217.1.1 is OK
- 10.1037/a0028168 is OK
- 10.1126/science.2392679 is OK
- 10.1037/h0032076 is OK
- 10.1007/s11336-04-1221-6 is OK
- 10.1146/annurev.ps.41.020190.000245 is OK
- 10.1007/s12124-015-9339-x is OK
- 10.3758/PBR.17.4.499 is OK
- 10.1016/j.actpsy.2017.03.008 is OK
- 10.3758/s13423-018-1451-8 is OK
- 10.1037/h0029096 is OK
- 10.1016/B0-08-043076-7/00553-2 is OK
- 10.1037/pspp0000187 is OK
- 10.1016/j.jclinepi.2005.01.006 is OK
- 10.3758/s13428-017-0954-y is OK
- 10.1186/1756-6606-3-15 is OK
- 10.18637/jss.v048.i09 is OK
- 10.1016/0010-0285(73)90033-9 is OK
- 10.1037/h0030544 is OK
- 10.1037/h0032785 is OK
- 10.1007/BF02294384 is OK
- 10.1037/1082-989X.10.4.428 is OK
- 10.1016/j.jbusres.2017.12.043 is OK
- 10.18637/jss.v036.i03 is OK
- 10.1016/j.tics.2003.09.002 is OK
- 10.1037/h0026871 is OK
- 10.2307/2289844 is OK
- 10.1037/h0037205 is OK
- 10.1198/tas.2011.11077 is OK
- 10.18637/jss.v021.i12 is OK
- 10.32614/RJ-2011-002 is OK
- 10.18637/jss.v059.i10 is OK
- 10.1037/0278-7393.12.3.387 is OK
- 10.1088/1742-6596/588/1/012034 is OK
- 10.1371/journal.pone.0126974 is OK
- 10.1016/j.cortex.2014.10.015 is OK
- 10.1214/aoms/1177732676 is OK
- 10.1006/jmla.2002.2864 is OK
- 10.1097/WNN.0b013e31815f237c is OK
- 10.1037/h0025848 is OK
- 10.1111/1467-8721.ep11512604 is OK
- 10.1080/17470218.2014.975730 is OK
- 10.1080/13506285.2011.598482 is OK
- 10.1370/afm.197 is OK
- 10.1370/afm.197 is OK

MISSING DOIs

- https://doi.org/10.5962/bhl.title.7309 may be missing for title: Design for a Brain: The Origin of Adaptive Behavior
- https://doi.org/10.1007/978-3-642-14749-4_15 may be missing for title: Implicit Spatial Length Modulates Time Estimates, but Not Vice Versa
- https://doi.org/10.3758/bf03205526 may be missing for title: Attentional Resources in Timing: Interference Effects in Concurrent Temporal and Nontemporal Working Memory Tasks.
- https://doi.org/10.1016/c2013-0-10517-x may be missing for title: Statistical Power Analysis for the Behavioral Sciences
- https://doi.org/10.1198/tech.2008.s540 may be missing for title: Pharmaceutical Statistics Using SAS: A Practical Guide
- https://doi.org/10.1081/qen-120038013 may be missing for title: Qualitative Ordinal Scales: The Concept of Ordinal Range
- https://doi.org/10.1007/978-3-540-73339-3_27 may be missing for title: GNU General Public License
- https://doi.org/10.1037/0033-295x.91.1.1 may be missing for title: A Retrieval Model for Both Recognition and Recall
- https://doi.org/10.3758/bf03212913 may be missing for title: What Causes the Spacing Effect? Some Effects of Repetition, Duration, and Spacing on Memory for Pictures.
- https://doi.org/10.1017/cbo9781139173865.013 may be missing for title: The Contemporary Theory of Metaphor
- https://doi.org/10.4324/9781315807614 may be missing for title: An Introduction to the Logic of Psychological Measurement
- https://doi.org/10.1037/h0027470 may be missing for title: Recognition Memory for a Rapid Sequence of Pictures
- https://doi.org/10.1037/1082-989x.1.2.199 may be missing for title: Measurement Error in Psychological Research: Lessons From 26 Research Scenarios
- https://doi.org/10.1093/acprof:oso/9780198508632.003.0001 may be missing for title: Frequency Processing and Cognition: Introduction and Overview
- https://doi.org/10.1093/acprof:oso/9780198508632.003.0009 may be missing for title: Associative Learning and Frequency Judgments: The PASS Model
- https://doi.org/10.1016/0004-3702(84)90029-8 may be missing for title: The Sciences of the Artificial
- https://doi.org/10.1093/acprof:oso/9780198508632.003.0002 may be missing for title: Frequency Processing: A Twenty-Five Year Perspective
- https://doi.org/10.1111/j.1365-2044.1976.tb11887.x may be missing for title: Lord of the Flies

INVALID DOIs

- None

[johannes-titz]

@oliviaguest Actually, there seem to be dois I was not aware of (e.g. for book chapters). If it is okay, I will sort this out. Sorry, again!

[johannes-titz]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[whedon]

Reference check summary:

OK DOIs

- 10.3758/BF03212913 is OK
- 10.1371/journal.pone.0126974 is OK
- 10.1037/h0028865 is OK
- 10.1037/h0025052 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1093/acprof:oso/9780198508632.003.0009 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1093/acprof:oso/9780198508632.003.0001 is INVALID because of 'https://doi.org/' prefix

[whedon]

Reference check summary:

OK DOIs

- 10.3758/BF03212913 is OK
- 10.1371/journal.pone.0126974 is OK
- 10.1037/h0028865 is OK
- 10.1037/h0025052 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1093/acprof:oso/9780198508632.003.0009 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1093/acprof:oso/9780198508632.003.0001 is INVALID because of 'https://doi.org/' prefix

[johannes-titz]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[oliviaguest]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1093/acprof:oso/9780198508632.003.0009 is OK
- 10.3758/BF03212913 is OK
- 10.1371/journal.pone.0126974 is OK
- 10.4324/9781410601247 is OK
- 10.1037/h0028865 is OK
- 10.1037/h0025052 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1269

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1269, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[oliviaguest]

OK @openjournals/joss-eics I think we're finally good to go. :balloon:

[oliviaguest]

@johannes-titz is the final proof good? :smile:

[johannes-titz]

@oliviaguest yes, it looks good. Thanks for your patience! :smile:

[kthyng]

Looks good to me!

[kthyng]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1270
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01900
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[kthyng]

Congratulations to @johannes-titz on your new publication! Thanks to @oliviaguest for editing and @nicksexton and @russellpierce for reviewing, for your time and expertise.

[whedon]

: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](https://joss.theoj.org/papers/10.21105/joss.01900/status.svg)](https://doi.org/10.21105/joss.01900)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01900">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01900/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01900/status.svg
   :target: https://doi.org/10.21105/joss.01900

This is how it will look in your documentation:

We need your help!

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:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[oliviaguest]

@nicksexton, @russellpierce, @johannes-titz Thank you all so much! Have a lovely rest of week and congratulations to Johannes! :clap: :blush:

[johannes-titz]

@kthyng Thank you very much for the last steps!

@oliviaguest Thank you so much for the professional editing! Specifically for the link to the sherpa/romeo database and the communication with me and the reviewers---very polite, but also clear and motivating.

@nicksexton, @russellpierce Thank you very much for the reviews! I really appreciate your time and effort.