[PRE REVIEW]: statsExpressions: R Package for Tidy Dataframes and Expressions with Statistical Details #3111

whedon · 2021-03-14T20:00:46Z

Submitting author: @IndrajeetPatil (Indrajeet Patil)
Repository: https://github.com/IndrajeetPatil/statsExpressions
Version: 1.0.0
Editor: @mikldk
Reviewers: @humanfactors, @tomfaulkenberry
Managing EiC: Arfon Smith

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

whedon · 2021-03-14T20:00:49Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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 · 2021-03-14T20:02:02Z

Failed to discover a Statement of need section in paper

whedon · 2021-03-14T20:02:05Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.19 s (379.5 files/s, 62590.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               34            658           1405           4388
Markdown                        10            466              0           1603
Rmd                              4            322            700            609
XML                              1              0              2            441
YAML                            11             83              7            422
JSON                             1              0              0            399
TeX                              1             27              0            144
CSS                              1              5              0             20
SVG                              8              0              0              8
-------------------------------------------------------------------------------
SUM:                            71           1561           2114           8034
-------------------------------------------------------------------------------


Statistical information for the repository 'edad175370fc19625aa0965d' was
gathered on 2021/03/14.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Indrajeet Patil                 18           704            704          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments

whedon · 2021-03-14T20:02:13Z

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

OK DOIs

- 10.21105/joss.02815 is OK
- 10.21105/joss.02445 is OK
- 10.5281/zenodo.3952174 is OK
- 10.21105/joss.01412 is OK
- 10.21105/joss.02306 is OK
- 10.5281/zenodo.2074621 is OK
- 10.21105/joss.01541 is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- 10.3758/s13428-019-01246-w may be a valid DOI for title: Robust Statistical Methods in R Using the WRS2 Package
- 10.31234/osf.io/yqxfr may be a valid DOI for title: The JASP guidelines for conducting and reporting a Bayesian analysis
- 10.32614/rj-2016-001 may be a valid DOI for title: metaplus: An R Package for the Analysis of Robust Meta-Analysis and Meta-Regression

INVALID DOIs

- None

whedon · 2021-03-14T20:02:24Z

PDF failed to compile for issue #3111 with the following error:

/app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/author.rb:72:in block in build_affiliation_string': Problem with affiliations for Indrajeet Patil, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/author.rb:71:in each'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/author.rb:71:in build_affiliation_string' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/author.rb:17:in initialize'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:205:in new' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:205:in block in parse_authors'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:202:in each' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:202:in parse_authors'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:93:in initialize' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in new'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in set_paper' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:58:in prepare'
from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:131:in <top (required)>' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `

'

arfon · 2021-03-14T21:00:10Z

@IndrajeetPatil - this PR should fix your paper compilation IndrajeetPatil/statsExpressions#81

arfon · 2021-03-14T21:00:34Z

@whedon invite @karthik as editor

👋 @karthik - would you be able to edit this submission for JOSS?

whedon · 2021-03-14T21:00:37Z

@karthik has been invited to edit this submission.

IndrajeetPatil · 2021-03-17T10:56:04Z

Potential reviewers:

RMHogervorst
cimentadaj
martinju
humanfactors

Will suggest a few more if none of them can review the submission.

karthik · 2021-03-19T00:52:50Z

@arfon Currently don't have bandwidth to edit this but let me know if you can't find anyone else to take over.

IndrajeetPatil · 2021-03-19T15:33:51Z

@arfon Are we allowed to make suggestions about possible editors as well?

If yes, I can suggest the following people:

Will suggest a few more if none of them can edit the submission.

IndrajeetPatil · 2021-03-19T21:28:03Z

@whedon generate pdf

whedon · 2021-03-19T21:28:39Z

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

IndrajeetPatil · 2021-03-25T12:18:16Z

Hi everyone, any update on the submission?

I have suggested both possible editors and reviewers.
Please let me know if I can do anything else on my end to expedite the process. :)

arfon · 2021-03-25T16:11:40Z

@IndrajeetPatil - apologies for the slow progress here. As our existing editors are a little overloaded I'm going to mark this submission as waitlisted for now. As and when an editor becomes available, we'll go ahead and assign one.

IndrajeetPatil · 2021-04-12T15:31:27Z

Can this submission be reconsidered for review?

Two of my other submissions (both R packages) at JOSS were submitted after this submission and are already under review. So I am guessing someone might be available now to edit this submission?

arfon · 2021-04-12T18:48:14Z

Two of my other submissions (both R packages) at JOSS were submitted after this submission and are already under review. So I am guessing someone might be available now to edit this submission?

Not necessarily so. Please be patient.

arfon · 2021-04-23T09:25:48Z

@whedon invite @mikldk as editor

whedon · 2021-04-23T09:25:52Z

@mikldk has been invited to edit this submission.

mikldk · 2021-04-23T10:43:49Z

@whedon assign me as editor

whedon · 2021-04-23T10:43:53Z

OK, the editor is @mikldk

mikldk · 2021-04-23T10:45:02Z

@IndrajeetPatil Thanks for your submission. Can you briefly describe how this package differs e.g. from broom?

IndrajeetPatil · 2021-04-23T10:54:11Z

statsExpressions has wildly different goals than broom.

broom: convert regression and other modeling objects to dataframes
statsExpressions: provide consistent syntax to run different tests and extract dataframes and expressions

So statsExpressions doesn't work with objects, but rather provides functions to carry out different types of analyses.

statsExpressions is more opinionated than broom. For example, broom won't add any other information than present in underlying objects (e.g., it doesn't add effect sizes and their confidence intervals), while statsExpressions does.

broom::tidy(t.test(mtcars$wt, mu = 3))
#> # A tibble: 1 x 8
#>   estimate statistic p.value parameter conf.low conf.high method     alternative
#>      <dbl>     <dbl>   <dbl>     <dbl>    <dbl>     <dbl> <chr>      <chr>      
#> 1     3.22      1.26   0.218        31     2.86      3.57 One Sampl… two.sided

(df <- statsExpressions::one_sample_test(mtcars, wt, test.value = 3))
#> # A tibble: 1 x 11
#>      mu statistic df.error p.value method estimate conf.level conf.low conf.high
#>   <dbl>     <dbl>    <dbl>   <dbl> <chr>     <dbl>      <dbl>    <dbl>     <dbl>
#> 1     3      1.26       31   0.218 One S…    0.217       0.95   -0.129     0.566
#> # … with 2 more variables: effectsize <chr>, expression <list>

Additionally, statsExpressions provides dataframes containing expressions with statistical details. broom does no such thing.

library(ggplot2)

ggplot(mtcars, aes(wt)) + geom_histogram()  + 
  labs(subtitle = df$expression[[1]])
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

^{Created on 2021-04-23 by the reprex package (v2.0.0)}

IndrajeetPatil · 2021-04-23T10:54:32Z

Oh, forgot to say, thanks for accepting to edit this submission :)

mikldk · 2021-04-23T13:28:26Z

@RMHogervorst, @martinju: Would you be interested in reviewing this submission to The Journal of Open Source Software? Reviews are open and based on a checklist. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you have any questions or concerns please let me know.

IndrajeetPatil · 2021-04-23T15:03:00Z

I think you meant @RMHogervorst?

mikldk · 2021-04-24T05:11:14Z

Indeed.

martinju · 2021-04-26T00:28:36Z

@mikldk Thanks for the suggestion, but I don't have time for at least a couple of weeks.

mikldk · 2021-04-26T07:44:20Z

@Prof-ThiagoOliveira: Would you be interested in reviewing this submission to The Journal of Open Source Software? Reviews are open and based on a checklist. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you have any questions or concerns please let me know.

IndrajeetPatil · 2021-04-27T11:55:04Z

@mikldk Here are a few other reviewer suggestions:

Ohmaddi
russellpierce
mariacuellar
tomfaulkenberry
cimentadaj

Prof-ThiagoOliveira · 2021-04-27T14:24:12Z

Dear Mikkel, I am afraid I have to reject review this paper because I don't have enough time to review it accordingly this and next month. I am happy to receive more invitations in a couple of months. best regards, Thiago

…

________________________________ From: Mikkel Meyer Andersen ***@***.***> Sent: 26 April 2021 08:44 To: openjournals/joss-reviews ***@***.***> Cc: DE PAULA OLIVEIRA Thiago ***@***.***>; Mention ***@***.***> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: statsExpressions: R Package for Tidy Dataframes and Expressions with Statistical Details (#3111) This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe. @Prof-ThiagoOliveira<https://github.com/Prof-ThiagoOliveira>: Would you be interested in reviewing this submission to The Journal of Open Source Software<https://joss.theoj.org/>? Reviews are open and based on a checklist. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you have any questions or concerns please let me know. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#3111 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIGNHDIDULEDG5PTJPTAYUTTKUKWHANCNFSM4ZFKBRNQ>. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

mikldk · 2021-04-27T15:21:23Z

@ohmaddi: Would you be interested in reviewing this submission to The Journal of Open Source Software? Reviews are open and based on a checklist. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you have any questions or concerns please let me know.

IndrajeetPatil · 2021-04-30T05:33:58Z

@mikldk Maybe we can invite a few others and check their availability? Let me know if I should suggest more reviewers.

mikldk · 2021-05-03T07:37:00Z

@mariacuellar @russellpierce @tomfaulkenberry @cimentadaj @humanfactors Would you be interested in reviewing this submission to The Journal of Open Source Software? Reviews are open and based on a checklist. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you have any questions or concerns please let me know.

humanfactors · 2021-05-03T07:59:52Z

Happy to accept this review. Thanks for the information.

mikldk · 2021-05-03T08:11:49Z

@whedon add @humanfactors as reviewer

whedon · 2021-05-03T08:11:53Z

OK, @humanfactors is now a reviewer

mikldk · 2021-05-03T08:12:36Z

Thanks, @humanfactors . (We still need one more.)

humanfactors · 2021-05-03T08:29:59Z

@mikldk I would like to flag a potential perceived conflict of interest (i.e., to "avoid the appearance of conflicts of interest" as per JOSS policy). Both @IndrajeetPatil and I are members of the easystats contributor list and we both were CRAN co-authors on the bayestestR package (https://cran.r-project.org/web/packages/bayestestR/index.html) — though importantly, not on the manuscript related to the package.

If this is perceived as a possible COI, I would request this COI is waived on the basis that:

Indrajeet Patil and I have never co-authored a published manuscript, and do not have any prior or current collaborations related to publications. Nor do I see there to be any financial or academic benefits to me from this work that would prevent me from giving an impartial assessment of the work.
We are not personally or professionally antiquated
This project does not directly add to the easystats ecosystem

I place this here to be as thorough as possible and ensure I conform to policies.

mikldk · 2021-05-03T08:45:36Z

@humanfactors Thanks for flagging this. I agree that this is not a COI based on the description above.

tomfaulkenberry · 2021-05-03T09:42:31Z

@mikldk I'll be happy to review this. Thanks!

mikldk · 2021-05-03T09:49:50Z

@whedon add @tomfaulkenberry as reviewer

whedon · 2021-05-03T09:49:55Z

OK, @tomfaulkenberry is now a reviewer

mikldk · 2021-05-03T09:51:34Z

@whedon start review

whedon · 2021-05-03T09:51:38Z

OK, I've started the review over in #3236.

whedon added the pre-review label Mar 14, 2021

whedon added CSS R TeX labels Mar 14, 2021

arfon added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Mar 25, 2021

whedon assigned mikldk Apr 23, 2021

whedon unassigned mikldk May 3, 2021

whedon assigned humanfactors and mikldk May 3, 2021

whedon assigned humanfactors, mikldk and tomfaulkenberry and unassigned mikldk and humanfactors May 3, 2021

whedon closed this as completed May 3, 2021

[PRE REVIEW]: statsExpressions: R Package for Tidy Dataframes and Expressions with Statistical Details #3111

[PRE REVIEW]: statsExpressions: R Package for Tidy Dataframes and Expressions with Statistical Details #3111

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