[REVIEW]: konfound: An R Sensitivity Analysis Package to Quantify the Robustness of Causal #5779
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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks. For a list of things I can do to help you, just type: For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type: |
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👋🏼 @jrosen48 @fartist @wjakethompson this is the review thread for the paper. All of our communications will happen here from now on. As a reviewer, the first step is to create a checklist for your review by entering
as the top of a new comment in this thread. These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines. The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention We aim for reviews to be completed within about 2-4 weeks (@fartist, please let us know how much additional time you think you'll need). Please feel free to ping me (@fabian-s) if you have any questions/concerns. |
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@jrosen48 : to speed up the review process it would be good to start working on konfound-project/konfound#50 while we wait for reviews by @fartist and @wjakethompson |
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Hi @fartist, @wjakethompson -- |
Review checklist for @wjakethompsonConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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This was referenced Sep 19, 2023
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I have completed my review, with a few outstanding issues:
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I will get reviews in by this month – sorry for the delay.
From: Fabian Scheipl ***@***.***>
Date: Wednesday, September 20, 2023 at 3:52 AM
To: openjournals/joss-reviews ***@***.***>
Cc: Feeeeeeeeeeng ***@***.***>, Mention ***@***.***>
Subject: Re: [openjournals/joss-reviews] [REVIEW]: konfound: An R Sensitivity Analysis Package to Quantify the Robustness of Causal (Issue #5779)
@jrosen48<https://github.com/jrosen48> : to speed up the review process it would be good to start working on these while we wait for the missing review by @fartist<https://github.com/fartist>. please let us know your timeframe for doing so.
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hi @fartist, we are still waiting for your review of this JOSS submission. |
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Hi I am in the middle of reviewing it – two more weeks to finish. Hope it is okay, sorry for the delay.
Best,
From: Fabian Scheipl ***@***.***>
Date: Monday, October 23, 2023 at 6:48 AM
To: openjournals/joss-reviews ***@***.***>
Cc: Feeeeeeeeeeng ***@***.***>, Mention ***@***.***>
Subject: Re: [openjournals/joss-reviews] [REVIEW]: konfound: An R Sensitivity Analysis Package to Quantify the Robustness of Causal (Issue #5779)
hi @fartist<https://github.com/fartist>, we are still waiting for your review of this JOSS submission.
It's been a month since your last post to this thread, please let us know how much more time you will need.
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Reply to this email directly, view it on GitHub<#5779 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADMVHB3QYYLCWJEZFVBWLS3YAZDQ7AVCNFSM6AAAAAA35EWJ4WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONZUHEZDMOBVGU>.
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@fartist sure, it can't be helped if it takes this long. to speed things up at least a little bit:
no need to hold back your feedback until you are all done. |
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@jrosen48: to speed up the review process it would be good to start working on the issues me and https://github.com/wjakethompson have opened in your repo while we wait for the missing review by @fartist |
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Thank you. We will do that. I'm sorry, I am returning from parental leave and am catching up. This is a priority for the next two weeks. |
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@fartist two more weeks have now passed, can we please have your review? |
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Apologies for the delay. In brief, I lost access to 2FA and GitHub because my cellphone was stolen in an accident. I have been trying to recover my account but have not been able to fix it. Currently, I can only respond to your email and not access the thread. I have read the paper, examined, and tested the package, and everything seems good to me. I just have a few minor comments on the draft.
Line 149, SE should have a hat and standard error should be standard error estimate.
Number of digits should be consistent throughout the text: e.g., .568 in line 173 vs. .52 in line 109.
APA style were not followed at multiple places e.g., line 108, line 134.
Best.
From: Fabian Scheipl ***@***.***>
Date: Monday, November 6, 2023 at 5:42 AM
To: openjournals/joss-reviews ***@***.***>
Cc: Feeeeeeeeeeng ***@***.***>, Mention ***@***.***>
Subject: Re: [openjournals/joss-reviews] [REVIEW]: konfound: An R Sensitivity Analysis Package to Quantify the Robustness of Causal (Issue #5779)
@fartist<https://github.com/fartist> two more weeks have now passed, can we please have your review?
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Reply to this email directly, view it on GitHub<#5779 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADMVHBY4JJDXUMBR3Q53IOLYDC5KLAVCNFSM6AAAAAA35EWJ4WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOJUGUZTMMRTGE>.
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@jrosen48 please adress those points in addition to the ones pointed out by the other reviewer and me. |
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@editorialbot set 10.5281/zenodo.10708094 as archive |
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Done! archive is now 10.5281/zenodo.10708094 |
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@editorialbot recommend-accept |
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👋 @openjournals/sbcs-eics, this paper is ready to be accepted and published. Check final proof 👉📄 Download article If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5052, then you can now move forward with accepting the submission by compiling again with the command |
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Noticed a small typo I corrected - changed |
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@editorialbot generate pdf |
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@fabian-s just thought to confirm - there is nothing I must do at this stage; is that correct? |
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@jrosen48 you're good -- I think @openjournals/sbcs-eics are just busy but they should get to this soon. |
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@editorialbot recommend-accept |
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👋 @openjournals/sbcs-eics, this paper is ready to be accepted and published. Check final proof 👉📄 Download article If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5083, then you can now move forward with accepting the submission by compiling again with the command |
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@editorialbot accept |
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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘 |
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Huge thanks to the editor: @fabian-s and the reviewers: @fartist, @wjakethompson! ✨ JOSS appreciates your work and effort. ✨ Also, big congratulations to the @jrosen48! 🥳 🍾 |
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Thank you very kindly!
…--
Joshua M. Rosenberg, Ph.D.
Associate Professor, STEM Education
Coordinator, Educational Data Science Graduate Certificate Program
Faculty Fellow, College of Emerging and Collaborative Studies
The University of Tennessee, Knoxville
https://joshuamrosenberg.com<https://joshuamrosenberg.com/>
PI, CAREER: Project CREDIBLE<https://www.projectcredible.com/> (NSF Grant No. 2239152)
NASEM Committee Member, Developing Competencies for the Future of Data and Computing: The Role of K-12<https://www.nationalacademies.org/our-work/developing-competencies-for-the-future-of-data-and-computing-the-role-of-k-12>
Associate Editor, Journal of Statistics and Data Science Education<https://www.tandfonline.com/journals/ujse21>
From: The Open Journals editorial robot ***@***.***>
Date: Saturday, March 9, 2024 at 9:08 AM
To: openjournals/joss-reviews ***@***.***>
Cc: Rosenberg, Joshua ***@***.***>, Mention ***@***.***>
Subject: Re: [openjournals/joss-reviews] [REVIEW]: konfound: An R Sensitivity Analysis Package to Quantify the Robustness of Causal (Issue #5779)
🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉
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qinyun-lin
added a commit
to konfound-project/konfound
that referenced
this issue
Mar 19, 2024
](https://doi.org/10.21105/joss.05779){kind=link}
* add missing dois
* Update README.md to include coding team meeting note link
* fix typo in title
* Update README.md
* change default to control group throughout
* fixed formatting issues with output
* Update helper_output_dataframe.R
The default assignment of function parameters retains the value "=", and when assigning values to the columns of the dplyr::tibble I chose to replace the assignment "=" with the value "<-", (this change can be retained or not).
* Update nonlinear_auxiliary.R
The main change comes from the assignment of variables with T changed to "TRUE", not all = changed to <-, the main principle is: function parameter assignment with "=", variable assignment for "<-". "
In addition, for the definition of the matrix "byrow = TRUE" this way usually use "=", instead of the assignment symbol <-. This is a way of passing a function parameter without using the assignment "<-" symbol.
* Update helper_plot_threshold.R
change“ est_eff = est_eff,
beta_threshold = beta_threshold”
to
est_eff <- est_eff,
beta_threshold <- beta_threshold
* Update test_cop.R
Maintain "=" for function parameter assignments and "<-" for variable assignments.
* Update test_pse.R
Maintain "=" for function parameter assignments and "<-" for variable assignments.
* Update test_sensitivity_ln.R
T to TRUE;F to FALSE
* Update tkonfound.R
T to TRUE
* Update tkonfound_fig.R
T to TRUE; F to FALSE
* update nrow issue
* add CONTRIBUTING and update README; also change email for JR
* add CONTRIBUTING and update README; also change email for S narvaiz
* fix the bug pkonfound error #64
* fix bug error with thresh_plot output #63
* Update links in DESCRIPTION
* remove rounding in itcv calculation
* work on tests
* move
* minor edits to tests
* to close #65 and to close #70
* add tests
* update docs
* update docs
* update README
* add check badges
* setting covr up again
* undo lme4 edits
trying another approach
* Revert "undo lme4 edits"
This reverts commit 2810fd0.
* update Matrix depends
* update lme4 version
* update README
* edit description
* update tests and docs
* update testing with Qinyun
* get rid of test_all = TRUE
* remove test_all = TRUE
* remove test_all = TRUE
* patch to konfound to address test_all = TRUE error
* add pkgdown action
* address warnings in tests that were due to an unititialized column
* iterate version
* fix minor discrepancy with package name
* continue to update tests, remove unused code
* further enhancing tests
* add badges and update README
* address error in vignette
* remove mention of functionality to call multiple forms of output at once
* address error in mkonfound
* remove calling of multiple forms of output
* remove commented out code
* address NOTES in R CMD CHECK
* add a few more tests
* address note about class(flag_cov)
* work on documentation to address imports issue
* edits to JOSS paper in response to feedback from @fartist and @wjakethompson
* simplify the function test_sensitivity_ln
now almost all calculations are moved to subfunctions in nonlinear_auxiliary
* minor edits to DESCRIPTION, removing aes_string and data_frame to address warnings, and moving print output out of test_sensitivity_ln
* Update helper_output_print.R
round up 'r_con' for ITCV
* Update helper_output_print.R
* Update cop_pse_auxiliary.R（F - FALSE） (#78)
* Update cop_pse_auxiliary.R
* Update cop_pse_auxiliary.R
* Update concord1.R
* Update cop_pse_auxiliary.R
* Update helper_output_print.R
* Update helper_output_dataframe.R
* Update helper_plot_correlation.R
* Update helper_plot_threshold.R
* Update konfound-glm-dichotomous.R
* Update konfound-glm.R
* Update konfound-lm.R
* Update konfound-lmer.R
* Update konfound.R
* Update mkonfound-data.R
* Update mkonfound.R
* Update core-sensitivity-mkonfound.R
* Update pkonfound.R
* Update test_cop.R
* Update test_cop.R
* Update test_pse.R
* Update test_sensitivity.R
* Update test_sensitivity_ln.R
* Update tkonfound.R
* Update tkonfound_fig.R
* Update zzz.R
* Update helper_output_table.R
* Update nonlinear_auxiliary.R
* Update test_cop.R
* Update test_pse.R
* Update test_sensitivity_ln.R
* Update test_pse.R
* Update test_cop.R
* Update cop_pse_auxiliary.R
* Update concord1.R
* Update cop_pse_auxiliary.R
* Update core-sensitivity-mkonfound.R
* Update konfound-glm.R
* Update konfound-lmer.R
* Update mkonfound.R
* Update nonlinear_auxiliary.R
* Update zzz.R
* Update DESCRIPTION
* addressing namespace issue - trying to rewrite the NAMESPACE and docs
* delete dup doc file
* remove glue and lifecycle
* make edits to remove import lavaan and import ggplot2
* remove summary function
* remove summary function to simplify codebase and address remaining NAMESPACE issue
* Update paper.md
* Update paper.bib
* Update paper.bib
* Update paper.bib
* Update paper.bib
* Update paper.bib
* edits to paper.bib to address APA issues
* edits to the paper and .bib to related to issues 3 and 5 in #80
* minor edits to .bib
* Update CONTRIBUTING.md
* a few more edits to address formatting issues with the paper
* a few more minor edits to the paper after viewing the rendered PDF
* update README to link to CONTRIBUTING.md and minor edits to paper.md based on Ken's feedback
* Update helper_output_print.R
* Update CONTRIBUTING.md
* edits to paper.bib and paper.md in response to request from @fabian-s: openjournals/joss-reviews#5779 (comment)
* minor edit to .bib
* additional edits to .bib
* fix bug when single predictor and test_all == T
* minor copy edits to paper
* Update helper_output_print.R
* a few more edits in response to Ken's feedback
* Update test_sensitivity_ln.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* remove mice and tibble as they are not used
* Revert "remove mice and tibble as they are not used"
This reverts commit 16cad9f.
* updates to links
* add Wei to DESCRIPTION, remove unused license
* edit license
* rename license
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update konfound-lm.R
* Update konfound-lm.R
* Update konfound-lm.R
* Update konfound-lm.R
* Update konfound-lm.R
* Update helper_output_print.R
* edits in response to @fabian-s feedback on the paper
* Update helper_output_print.R
* Update helper_output_print.R
* Update helper_output_print.R
* Update test_sensitivity_ln.R
* Update test_sensitivity_ln.R
* Update test_sensitivity_ln.R
* Update test_sensitivity_ln.R
* super small edit to the paper - changing &beta so it appears correctly as β
* fix the bug when est_eff_start = 0 and needtworows
fix the bug when est_eff_start = 0 and needtworows
* update URL in README
* update urls
* CRAN submission
* Update CONTRIBUTING.md
* Update konfound.R
revised warning message for non-linear model in konfound
* update testing
no errors now in devtools::check()
* Revert "Merge branch 'master' into newitcv_output"
This reverts commit fc199f7, reversing
changes made to 04fbc43.
---------
Co-authored-by: jrosen48 <[email protected]>
Co-authored-by: Bret Staudt Willet <[email protected]>
Co-authored-by: wwang93 <[email protected]>
Co-authored-by: Joshua Rosenberg <[email protected]>
Co-authored-by: olivroy <[email protected]>
Co-authored-by: Jihoon_Choi <[email protected]>
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Submitting author: @jrosen48 (Joshua Rosenberg)
Repository: https://github.com/konfound-project/konfound
Branch with paper.md (empty if default branch):
Version: 0.4.0
Editor: @fabian-s
Reviewers: @fartist, @wjakethompson
Archive: 10.5281/zenodo.10708094
Status
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