Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[PRE REVIEW]: sleev: An R Package for Semiparametric Likelihood Estimation with Errors in Variables #7297

Closed
editorialbot opened this issue Sep 27, 2024 · 43 comments
Closed

[PRE REVIEW]: sleev: An R Package for Semiparametric Likelihood Estimation with Errors in Variables #7297

editorialbot opened this issue Sep 27, 2024 · 43 comments
Assignees
@aalfons @jbytecode @alemermartinez
Labels
C++ pre-review R TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning

Comments

@editorialbot
Copy link
Collaborator

editorialbot commented Sep 27, 2024 •
edited
Loading

Submitting author: @JiangmeiRubyXiong (Jiangmei Xiong)
Repository: https://github.com/dragontaoran/sleev
Branch with paper.md (empty if default branch):
Version: v1.0.3
Editor: @jbytecode
Reviewers: @alemermartinez, @aalfons
Managing EiC: Chris Vernon

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2dc012ed16ca93ac2f265dc6725f1466"><img src="https://joss.theoj.org/papers/2dc012ed16ca93ac2f265dc6725f1466/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2dc012ed16ca93ac2f265dc6725f1466/status.svg)](https://joss.theoj.org/papers/2dc012ed16ca93ac2f265dc6725f1466)

Author instructions

Thanks for submitting your paper to JOSS @JiangmeiRubyXiong. Currently, there isn't a JOSS editor assigned to your paper.

@JiangmeiRubyXiong if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands
@editorialbot editorialbot added pre-review Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels Sep 27, 2024
@editorialbot
Copy link
Collaborator Author

Hello human, 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:

@editorialbot commands

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

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1577.3 files/s, 254582.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               30            524           1164           2131
C++                              5            252            360           1379
Markdown                         2             80              0            369
TeX                              1              0              0             65
C/C++ Header                     1             19             67             22
YAML                             1              1              4             19
-------------------------------------------------------------------------------
SUM:                            40            876           1595           3985
-------------------------------------------------------------------------------

Commit count by author:

   112	Joey Sherrill
    26	Sarah Lotspeich
     6	JiangmeiRubyXiong
     5	Sarah
     3	Ran Tao
     3	Sarah Lotspeich (She/Her)
     2	Ruby XIONG
     2	dragontaoran
     1	Shawn Garbett

@editorialbot
Copy link
Collaborator Author

Paper file info:

📄 Wordcount for paper.md is 2157

✅ The paper includes a Statement of need section

@editorialbot
Copy link
Collaborator Author

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

@editorialbot
Copy link
Collaborator Author 

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: An empirical study for impacts of measurement erro...
- No DOI given, and none found for title: Efficient odds ratio estimation under two-phase sa...
- No DOI given, and none found for title: Spline functions: basic theory
- No DOI given, and none found for title: On profile likelihood

❌ MISSING DOIs

- 10.1002/sim.8799 may be a valid DOI for title: Efficient semiparametric inference for two-phase s...
- 10.1080/01621459.2017.1295864 may be a valid DOI for title: Efficient semiparametric inference under two-phase...
- 10.1214/20-aoas1343 may be a valid DOI for title: Accounting for dependent errors in predictors and ...

❌ INVALID DOIs

- None

@editorialbot
Copy link
Collaborator Author

⚠️ An error happened when generating the pdf. Author (Jiangmei Xiong) is missing affiliation.

@JiangmeiRubyXiong
Copy link

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@editorialbot
Copy link
Collaborator Author

Five most similar historical JOSS papers:

enetLTS: Robust and Sparse Methods for High Dimensional Linear, Binary, and Multinomial Regression
Submitting author: @fskurnaz
Handling editor: @fabian-s (Active)
Reviewers: @mcavs, @marastadler
Similarity score: 0.6579

robustHD: An R package for robust regression with high-dimensional data
Submitting author: @aalfons
Handling editor: @mikldk (Retired)
Reviewers: @valentint, @msalibian
Similarity score: 0.6548

RBF: An R package to compute a robust backfitting estimator for additive models
Submitting author: @alemermartinez
Handling editor: @mikldk (Retired)
Reviewers: @mcavs, @mmrabe
Similarity score: 0.6487

serp: An R package for smoothing in ordinal regression
Submitting author: @ejikeugba
Handling editor: @Bisaloo (Retired)
Reviewers: @bernardsilenou, @wesleyburr
Similarity score: 0.6439

cvCovEst: Cross-validated covariance matrix estimator selection and evaluation in R
Submitting author: @PhilBoileau
Handling editor: @fboehm (Active)
Reviewers: @Marie-PerrotDockes, @yunanwu123
Similarity score: 0.6391

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

@JiangmeiRubyXiong
Copy link

⚠️ An error happened when generating the pdf. Author (Jiangmei Xiong) is missing affiliation.

Affiliation updated and issue resolved.

@JiangmeiRubyXiong
Copy link 

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: An empirical study for impacts of measurement erro...
- No DOI given, and none found for title: Efficient odds ratio estimation under two-phase sa...
- No DOI given, and none found for title: Spline functions: basic theory
- No DOI given, and none found for title: On profile likelihood

❌ MISSING DOIs

- 10.1002/sim.8799 may be a valid DOI for title: Efficient semiparametric inference for two-phase s...
- 10.1080/01621459.2017.1295864 may be a valid DOI for title: Efficient semiparametric inference under two-phase...
- 10.1214/20-aoas1343 may be a valid DOI for title: Accounting for dependent errors in predictors and ...

❌ INVALID DOIs

- None

DOIs are now added to the paper.bib

@crvernon
Copy link

crvernon commented Oct 1, 2024

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@editorialbot
Copy link
Collaborator Author

Five most similar historical JOSS papers:

enetLTS: Robust and Sparse Methods for High Dimensional Linear, Binary, and Multinomial Regression
Submitting author: @fskurnaz
Handling editor: @fabian-s (Active)
Reviewers: @mcavs, @marastadler
Similarity score: 0.6579

robustHD: An R package for robust regression with high-dimensional data
Submitting author: @aalfons
Handling editor: @mikldk (Retired)
Reviewers: @valentint, @msalibian
Similarity score: 0.6549

RBF: An R package to compute a robust backfitting estimator for additive models
Submitting author: @alemermartinez
Handling editor: @mikldk (Retired)
Reviewers: @mcavs, @mmrabe
Similarity score: 0.6487

serp: An R package for smoothing in ordinal regression
Submitting author: @ejikeugba
Handling editor: @Bisaloo (Retired)
Reviewers: @bernardsilenou, @wesleyburr
Similarity score: 0.6442

cvCovEst: Cross-validated covariance matrix estimator selection and evaluation in R
Submitting author: @PhilBoileau
Handling editor: @fboehm (Active)
Reviewers: @Marie-PerrotDockes, @yunanwu123
Similarity score: 0.6389

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

@crvernon
Copy link

crvernon commented Oct 1, 2024

@editorialbot invite @jbytecode as editor

👋 @jbytecode can you take on this submission as editor?

@editorialbot
Copy link
Collaborator Author

Invitation to edit this submission sent!

@jbytecode
Copy link

@editorialbot set me as editor

@crvernon - sure, gladly. thank you for inviting me!

@editorialbot
Copy link
Collaborator Author

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

@jbytecode
Copy link

@editorialbot assign me as editor

@editorialbot
Copy link
Collaborator Author

Assigned! @jbytecode is now the editor

@jbytecode
Copy link

jbytecode commented Oct 1, 2024 •
edited
Loading

@JiangmeiRubyXiong - Hi, thank you for submitting your manuscript and software to JOSS. I am the handling editor of this submission.

While I study your work and try to find a list of suitable reviewers, please take a look at the issue below:

In the manuscript the citations (@tao2021efficient; @lotspeich2022efficient) look a little bit awkward. Could you please read the documentations

and correct the citation style of your citations in your paper?

Thank you in advance.

@jbytecode
Copy link

@JiangmeiRubyXiong - The other missing thing in the manuscript is the DOIs handles of the authors. Please add the ORCIDs in the metadata of the manuscript markdown. When you are done with the task, please ping me. Thank you in advance.

@JiangmeiRubyXiong
Copy link

@jbytecode All citations and author DOIs are now updated! Please let me know if there is anything else I can help.

@jbytecode
Copy link

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@editorialbot
Copy link
Collaborator Author

Five most similar historical JOSS papers:

enetLTS: Robust and Sparse Methods for High Dimensional Linear, Binary, and Multinomial Regression
Submitting author: @fskurnaz
Handling editor: @fabian-s (Active)
Reviewers: @mcavs, @marastadler
Similarity score: 0.6694

RBF: An R package to compute a robust backfitting estimator for additive models
Submitting author: @alemermartinez
Handling editor: @mikldk (Retired)
Reviewers: @mcavs, @mmrabe
Similarity score: 0.6638

robustHD: An R package for robust regression with high-dimensional data
Submitting author: @aalfons
Handling editor: @mikldk (Retired)
Reviewers: @valentint, @msalibian
Similarity score: 0.6637

serp: An R package for smoothing in ordinal regression
Submitting author: @ejikeugba
Handling editor: @Bisaloo (Retired)
Reviewers: @bernardsilenou, @wesleyburr
Similarity score: 0.6549

wbacon: Weighted BACON algorithms for multivariate outlier nomination (detection) and robust linear regression
Submitting author: @tobiasschoch
Handling editor: @fboehm (Active)
Reviewers: @msalibian, @aalfons
Similarity score: 0.6519

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

@jbytecode
Copy link

👋👋👋 Dear @alemermartinez , @aalfons 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled:

sleev: An R Package for Semiparametric Likelihood Estimation with Errors in Variables

You can find more information at the top of this Github issue (#7297).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be about 25 check items for each single reviewer.

Thank you in advance!

@jbytecode
Copy link

👋👋👋 Dear @ejikeugba , @tobiasschoch 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled:

sleev: An R Package for Semiparametric Likelihood Estimation with Errors in Variables

You can find more information at the top of this Github issue (#7297).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be about 25 check items for each single reviewer.

Thank you in advance!

@alemermartinez
Copy link

alemermartinez commented Oct 3, 2024 via email

@jbytecode
Copy link

@editorialbot add @alemermartinez as reviewer

@editorialbot
Copy link
Collaborator Author

@alemermartinez added to the reviewers list!

@tobiasschoch
Copy link

tobiasschoch commented Oct 5, 2024 via email

@jbytecode
Copy link

👋👋👋 Dear @msalibian 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled:

sleev: An R Package for Semiparametric Likelihood Estimation with Errors in Variables

You can find more information at the top of this Github issue (#7297).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be about 25 check items for each single reviewer.

Thank you in advance!

@aalfons
Copy link

aalfons commented Oct 7, 2024

@jbytecode, sorry for the late response. By when would the review need to be done? I currently have a lot of other reviews on my plate, so I need the timeline to see if it is feasible for me. Thanks!

@jbytecode
Copy link

@aalfons - We generally ask our reviewers to finalize their reports within 4-6 weeks and I can give you extra time when it's required. Is this range suitable to you?

@aalfons
Copy link

aalfons commented Oct 7, 2024

@jbytecode, given my current workload, I expect that I'd need more like 8-10 weeks to get to it. If that is ok, then I can accept the invitation. If you want to keep looking a bit longer to see if you can find someone who can do it sooner, that is also fine by me.

@jbytecode
Copy link

@editorialbot add @aalfons as reviewer

@editorialbot
Copy link
Collaborator Author

@aalfons added to the reviewers list!

@jbytecode
Copy link

@editorialbot start review

@editorialbot
Copy link
Collaborator Author

OK, I've started the review over in #7320.

@jbytecode
Copy link

The review starts at #7320, see you there.

@msalibian
Copy link

Dear @jbytecode,

I'm sorry I won't be able to help with this one. I'm over committed already, and don't expect it to get any better until January (when at least I end my term as Interim Dept Head!)

Sorry about this.

Matias

@jbytecode
Copy link

@msalibian - Hope to work in future works then. Thank you for the response.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@aalfons aalfons

@jbytecode jbytecode

@alemermartinez alemermartinez

Labels
C++ pre-review R TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
8 participants
@aalfons @crvernon @msalibian @jbytecode @tobiasschoch @alemermartinez @JiangmeiRubyXiong @editorialbot