[REVIEW]: LinRegOutliers: A Julia package for detecting outliers in linear regression #2892

whedon · 2020-12-08T14:17:24Z

Submitting author: @jbytecode (Mehmet Hakan Satman)
Repository: https://github.com/jbytecode/LinRegOutliers
Version: v0.8.5
Editor: @mikldk
Reviewers: @salleuska, @rMassimiliano
Archive: 10.5281/zenodo.4419418

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Markdown: [![status](https://joss.theoj.org/papers/a4fc555d2ef4bafb3ff61c5326b530dc/status.svg)](https://joss.theoj.org/papers/a4fc555d2ef4bafb3ff61c5326b530dc)

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Reviewer instructions & questions

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Review checklist for @salleuska

Conflict of interest

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@jbytecode) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
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

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

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
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 @rMassimiliano

Conflict of interest

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@jbytecode) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
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

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

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
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?

The text was updated successfully, but these errors were encountered:

whedon · 2020-12-08T14:17:27Z

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

⚠️ JOSS reduced service mode ⚠️

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whedon · 2020-12-08T14:18:05Z

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

whedon · 2020-12-08T14:18:28Z

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

OK DOIs

- 10.1016/B978-0-08-051581-6.50070-2 is OK
- 10.1137/141000671 is OK
- 10.2307/2531498 is OK
- 10.1111/j.2517-6161.1992.tb01449.x is OK
- 10.1080/01621459.1993.10476407 is OK
- 10.1080/01621459.1994.10476872 is OK
- 10.1111/j.2517-6161.1994.tb01988.x is OK
- 10.1111/j.2517-6161.1995.tb02051.x is OK
- 10.1080/03610929708831988 is OK
- 10.1016/s0167-9473(98)00021-8 is OK
- 10.1016/S0167-9473(99)00101-2 is OK
- 10.1016/S0167-9473(02)00291-8 is OK
- 10.1080/02664760500163599 is OK
- 10.1080/01966324.2006.10737673 is OK
- 10.1109/ACC.2009.5160229 is OK
- 10.1016/S0167-9473(99)00029-8 is OK
- 10.1080/01621459.1984.10477105 is OK
- 10.1007/978-3-642-58250-9_27 is OK
- 10.1002/wics.19 is OK
- 10.1080/00401706.1999.10485670 is OK
- 10.5539/ijsp.v2n3p101 is OK
- 10.14419/ijasp.v3i1.4439 is OK
- 10.1007/s11590-020-01565-4 is OK
- 10.2307/1268249 is OK
- 10.1080/03610918.2011.598989 is OK

MISSING DOIs

- None

INVALID DOIs

- None

mikldk · 2020-12-08T14:18:41Z

@salleuska, @rMassimiliano: Thanks for agreeing to review. Please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If possible create issues (and cross-reference) in the submission's repository to avoid too specific discussions in this review thread.

If you have any questions or concerns please let me know.

mikldk · 2020-12-14T10:11:03Z

@salleuska, @rMassimiliano, would you mind giving a brief status of your progress?

mikldk · 2020-12-21T08:46:30Z

@salleuska, @rMassimiliano, would you mind giving a brief status of your progress?

whedon · 2020-12-22T14:17:41Z

👋 @salleuska, please update us on how your review is going.

whedon · 2020-12-22T14:17:41Z

👋 @rMassimiliano, please update us on how your review is going.

salleuska · 2020-12-28T16:03:26Z

@mikldk Sorry for the late, I am working on this, and plan to get back to you with the review by the end of the week.

salleuska · 2020-12-31T12:55:23Z

Comments on the software repository

I have some concerns regarding documentation of functions and examples, but I think these can be easily addressed by the author. My main concern is that the documentation should be expanded. Although each of the methods seems well referenced, few sentences describing what is the base idea of each algorithm would be helpful in my opinion. This also should help to clarify why some functions return different outputs (Array vs Dictionary) and what each element of the Dictionary is.

I'll open a few more detailed issues in the repository to reference here, and make a separate comment related to Software Paper checklist.

I admit that I have less familiarity with Julia packages than R, and what I am suggesting is what is typically done in R. If @mikldk or @rMassimiliano have some different view, please let me know.

salleuska · 2020-12-31T14:07:54Z

Software paper

I think that the paper does not require major changes in the structure or language. I have just a few minor comments

Summary. ``Our package covers a significant portion of the literature on fitting with outliers'' -> Our package [..] on (linear regression | model fitting) with outliers
Statement of need. I wonder if the methods can be listed or tabulated according to the 4 categories mentioned in the previous section (diagnostics, direct methods, robust methods, multivariate). This should help in navigating between the many methods.
Installation and basic usage. It is explained that some methods may return additional information, but there is no documentation or reference to what this information is. I think it would be better this information to be documented in the package as suggested in my previous issues. If not should be made clear that one has to look into the paper related to the method.

jbytecode · 2020-12-31T22:05:40Z

Dear reviewer @salleuska,

Thank you for your valuable suggestions, corrections, and comments. We will implement them. Thank you.

jbytecode · 2021-01-02T11:45:31Z

@whedon generate pdf

whedon · 2021-01-02T11:46:06Z

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

jbytecode · 2021-01-02T11:46:18Z

@whedon check references

whedon · 2021-01-02T11:46:34Z

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

OK DOIs

- 10.1016/B978-0-08-051581-6.50070-2 is OK
- 10.1137/141000671 is OK
- 10.2307/2531498 is OK
- 10.1111/j.2517-6161.1992.tb01449.x is OK
- 10.1080/01621459.1993.10476407 is OK
- 10.1080/01621459.1994.10476872 is OK
- 10.1111/j.2517-6161.1994.tb01988.x is OK
- 10.1111/j.2517-6161.1995.tb02051.x is OK
- 10.1080/03610929708831988 is OK
- 10.1016/s0167-9473(98)00021-8 is OK
- 10.1016/S0167-9473(99)00101-2 is OK
- 10.1016/S0167-9473(02)00291-8 is OK
- 10.1080/02664760500163599 is OK
- 10.1080/01966324.2006.10737673 is OK
- 10.1109/ACC.2009.5160229 is OK
- 10.1016/S0167-9473(99)00029-8 is OK
- 10.1080/01621459.1984.10477105 is OK
- 10.1007/978-3-642-58250-9_27 is OK
- 10.1002/wics.19 is OK
- 10.1080/00401706.1999.10485670 is OK
- 10.5539/ijsp.v2n3p101 is OK
- 10.14419/ijasp.v3i1.4439 is OK
- 10.1007/s11590-020-01565-4 is OK
- 10.2307/1268249 is OK
- 10.1080/03610918.2011.598989 is OK

MISSING DOIs

- None

INVALID DOIs

- None

jbytecode · 2021-01-02T11:55:25Z

Dear reviewer @salleuska,

Methods are consistently returning a Dict object even the result includes only one item.
All exported methods have now Description and Output sections in their documentation. In the former, we give a short and brief introduction, how it runs, what does it do, etc., without getting deep into the details. In the latter, we present what the method returns and what is the meaning of these items.
Examples.md is updated.
Documentation is updated.
Summary is fixed.
Statement of field section is changed a little bit. There are now 5 categories, including the visual methods, and listed in separate tables, each for diagnostics, direct methods, robust methods, methods for multivariate data, and visual methods.

I think, these changes cover all your suggestions. Please, let me know, if there is anything missing or wrong.

Thank you.

rMassimiliano · 2021-01-02T17:12:15Z

I really like the new example section. I have some comments on the main paper and on the example section in the repository in the following. I tested the code on Julia 1.5.3 on Ubuntu.

Paper
Following line-by-line the code in the section Installation and basic usage, the examples at line 70 and 71 return Array not Dict. Make sure the results shown in the paper are consistent with the code in the repository.

Repository (examples.md)

Sebert & Montgomery & Rollier (1998) Algorithm:

smr98(reg); ## return `Array` not `Dict`

Peña and Yohai (1995)
I would change 'suspected subsets' into 'subset of potential outliers'.
in the code snippets I think py95(reg)["outliers"] should be py95(reg)

py95(reg)
Dict{Any,Any} with 2 entries:
  "outliers"       => [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14]
  "suspected.sets" => Set([[14, 13], [43, 54, 24, 38, 22], Int64[], [58, 66, 32,…

While the current version would return

py95(reg)["outliers"]
14-element Array{Int64,1}:
  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14

Least Trimmed Squares Regression
I would add the code to reproduce the plot in a snippet (or a link to a separate file if too long)

jbytecode · 2021-01-02T17:56:21Z

Dear reviewer @rMassimiliano,

Thank you very much for your comments.

In the paper, lines 70-71, the method smr98 (and all of the methods exported from the package) now return a Dict after pushing many commits. Could you please re-check? Or please tell me if I am unlucky missing something.
Peña and Yohai (1995) section is corrected.
A code snipped is added for drawing LTS line and Phone data.

rMassimiliano · 2021-01-03T11:35:23Z

Dear @jbytecode,
the functions on your repository https://github.com/jbytecode/LinRegOutliers are indeed updated and return Dict as expected.

However, the new version has not been added to Julia package registry JuliaRegistries/General. This is the version installed when using Pkg.add(), as suggested in the Installation section of the repo.

I would recommend to add the new version to JuliaRegistries/General, and also to change the package version, given that the return type of some functions is changed.

mikldk · 2021-01-05T09:05:06Z

@jbytecode There are some confusing about the tags/releases in your repository (v0.8.4 vs 0.8.4, see e.g. the diff).

If changed have been made since 0.8.4, then I recommend making this JOSS submission version 0.8.5 as the v prefix is not a part of the semantic versioning.

jbytecode · 2021-01-05T09:26:34Z

Dear editor @mikldk,

It is just because the v0.8.4 was automatically created by the tag bot after publishing the latest revision in Julia repos. So I set the name of release 0.8.4, without a v prefix.

Now, I am trying to create a new release, but zenodo throws an error of "New version's files must differ from all previous versions."

what to do now ?

edit: I created a small change and now I am trying to create a new release entry in zenodo.

jbytecode · 2021-01-05T10:06:59Z

Dear editor @mikldk,

It is okay.

The version is 0.8.5
Here is the DOI: 10.5281/zenodo.4419418
Here is the bagdet

mikldk · 2021-01-05T11:14:20Z

@whedon set 10.5281/zenodo.4419418 as archive

whedon · 2021-01-05T11:14:24Z

OK. 10.5281/zenodo.4419418 is the archive.

mikldk · 2021-01-05T11:14:32Z

@whedon set v0.8.5 as version

whedon · 2021-01-05T11:14:36Z

OK. v0.8.5 is the version.

mikldk · 2021-01-05T11:14:48Z

@whedon check references

whedon · 2021-01-05T11:15:13Z

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

OK DOIs

- 10.1016/B978-0-08-051581-6.50070-2 is OK
- 10.1137/141000671 is OK
- 10.2307/2531498 is OK
- 10.1111/j.2517-6161.1992.tb01449.x is OK
- 10.1080/01621459.1993.10476407 is OK
- 10.1080/01621459.1994.10476872 is OK
- 10.1111/j.2517-6161.1994.tb01988.x is OK
- 10.1111/j.2517-6161.1995.tb02051.x is OK
- 10.1080/03610929708831988 is OK
- 10.1016/s0167-9473(98)00021-8 is OK
- 10.1016/S0167-9473(99)00101-2 is OK
- 10.1016/S0167-9473(02)00291-8 is OK
- 10.1080/02664760500163599 is OK
- 10.1080/01966324.2006.10737673 is OK
- 10.1109/ACC.2009.5160229 is OK
- 10.1016/S0167-9473(99)00029-8 is OK
- 10.1080/01621459.1984.10477105 is OK
- 10.1007/978-3-642-58250-9_27 is OK
- 10.1002/wics.19 is OK
- 10.1080/00401706.1999.10485670 is OK
- 10.5539/ijsp.v2n3p101 is OK
- 10.14419/ijasp.v3i1.4439 is OK
- 10.1007/s11590-020-01565-4 is OK
- 10.2307/1268249 is OK
- 10.1080/03610918.2011.598989 is OK

MISSING DOIs

- None

INVALID DOIs

- None

mikldk · 2021-01-05T11:15:59Z

@whedon generate pdf

whedon · 2021-01-05T11:16:55Z

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

mikldk · 2021-01-05T11:18:53Z

@salleuska, @rMassimiliano Thank you very much for your effort in reviewing this paper!

mikldk · 2021-01-05T11:19:01Z

@whedon accept

whedon · 2021-01-05T11:19:05Z

Attempting dry run of processing paper acceptance...

whedon · 2021-01-05T11:19:55Z

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

OK DOIs

- 10.1016/B978-0-08-051581-6.50070-2 is OK
- 10.1137/141000671 is OK
- 10.2307/2531498 is OK
- 10.1111/j.2517-6161.1992.tb01449.x is OK
- 10.1080/01621459.1993.10476407 is OK
- 10.1080/01621459.1994.10476872 is OK
- 10.1111/j.2517-6161.1994.tb01988.x is OK
- 10.1111/j.2517-6161.1995.tb02051.x is OK
- 10.1080/03610929708831988 is OK
- 10.1016/s0167-9473(98)00021-8 is OK
- 10.1016/S0167-9473(99)00101-2 is OK
- 10.1016/S0167-9473(02)00291-8 is OK
- 10.1080/02664760500163599 is OK
- 10.1080/01966324.2006.10737673 is OK
- 10.1109/ACC.2009.5160229 is OK
- 10.1016/S0167-9473(99)00029-8 is OK
- 10.1080/01621459.1984.10477105 is OK
- 10.1007/978-3-642-58250-9_27 is OK
- 10.1002/wics.19 is OK
- 10.1080/00401706.1999.10485670 is OK
- 10.5539/ijsp.v2n3p101 is OK
- 10.14419/ijasp.v3i1.4439 is OK
- 10.1007/s11590-020-01565-4 is OK
- 10.2307/1268249 is OK
- 10.1080/03610918.2011.598989 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-01-05T11:20:05Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2012

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2012, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

jbytecode · 2021-01-05T11:27:34Z

@mikldk, @salleuska, and, @rMassimiliano, Thank you very much! Hope you all have a happy new year!

arfon · 2021-01-05T11:30:15Z

@whedon accept deposit=true

whedon · 2021-01-05T11:30:19Z

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

whedon · 2021-01-05T11:31:38Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2021-01-05T11:31:38Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02892 joss-papers#2013
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02892
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon · 2021-01-05T11:40:47Z

@salleuska, @rMassimiliano - many thanks for your reviews here and to @mikldk for editing this submission. JOSS relies upon the volunteer efforts of folks like yourselves and we simply couldn't do it without you!

@jbytecode - your paper is now accepted and published in JOSS ⚡🚀💥

whedon · 2021-01-05T11:40:51Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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whedon added Julia review TeX labels Dec 8, 2020

whedon assigned mikldk Dec 8, 2020

whedon mentioned this issue Dec 8, 2020

[PRE REVIEW]: LinRegOutliers: A Julia package for detecting outliers in linear regression #2884

Closed

whedon assigned salleuska Dec 9, 2020

This was referenced Dec 31, 2020

Documentation - 1. Functions jbytecode/LinRegOutliers#40

Closed

Documentation - 2. Examples jbytecode/LinRegOutliers#41

Closed

Consistency of objects returned from functions jbytecode/LinRegOutliers#42

Closed

whedon assigned rMassimiliano Jan 3, 2021

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Jan 5, 2021

whedon added accepted published Papers published in JOSS labels Jan 5, 2021

arfon closed this as completed Jan 5, 2021

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[PRE REVIEW]: Copulas.jl: A fully Distributions.jl-compliant copula package #6074

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[PRE REVIEW]: Kirstine.jl: A Julia Package for Bayesian Optimal Design of Experiments #6193

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[PRE REVIEW]: lintr: Static Code Analysis for R #7171

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[REVIEW]: LinRegOutliers: A Julia package for detecting outliers in linear regression #2892

[REVIEW]: LinRegOutliers: A Julia package for detecting outliers in linear regression #2892

Comments

whedon commented Dec 8, 2020 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @salleuska

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @rMassimiliano

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Dec 8, 2020

whedon commented Dec 8, 2020

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Comments on the software repository

salleuska commented Dec 31, 2020

Software paper

jbytecode commented Dec 31, 2020

jbytecode commented Jan 2, 2021

whedon commented Jan 2, 2021

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rMassimiliano commented Jan 2, 2021

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jbytecode commented Jan 5, 2021

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whedon commented Jan 5, 2021

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arfon commented Jan 5, 2021

whedon commented Jan 5, 2021

whedon commented Dec 8, 2020 •

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jbytecode commented Jan 2, 2021 •

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rMassimiliano commented Jan 3, 2021 •

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