CRediTas: a tiny package to generate CRediT authors statements #576
Comments
|
Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type |
|
🚀 Editor check started 👋 |
Checks for credit (v0.1.0)git hash: 5c151c4f
Important: All failing checks above must be addressed prior to proceeding (Checks marked with 👀 may be optionally addressed.) Package License: MIT + file LICENSE 1. Package DependenciesDetails of Package Dependency Usage (click to open)
The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.
Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table. basefor (3), data.frame (2), drop (1), if (1), length (1), ncol (1), nrow (1), seq_len (1), T (1) creditcreate_template (1), read_template (1) statsdf (2) utilsread.csv2 (1), write.csv2 (1) NOTE: No imported packages appear to have associated function calls; please ensure with author that these 'Imports' are listed appropriately. 2. Statistical PropertiesThis package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing. Details of statistical properties (click to open)
The package has:
Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the The final measure (
2a. Network visualisationClick to see the interactive network visualisation of calls between objects in package 3.
|
| id | name | conclusion | sha | run_number | date |
|---|---|---|---|---|---|
| 4253501958 | R-CMD-check | success | 5c151c | 6 | 2023-02-23 |
3b. goodpractice results
R CMD check with rcmdcheck
rcmdcheck found no errors, warnings, or notes
Test coverage with covr
Package coverage: 100
Cyclocomplexity with cyclocomp
No functions have cyclocomplexity >= 15
Static code analyses with lintr
lintr found the following 2 potential issues:
| message | number of times |
|---|---|
| Lines should not be more than 80 characters. | 2 |
4. Other Checks
Details of other checks (click to open)
✖️ The following function name is duplicated in other packages:
-
read_templatefrom onbrand
Package Versions
| package | version |
|---|---|
| pkgstats | 0.1.3 |
| pkgcheck | 0.1.1.11 |
Editor-in-Chief Instructions:
Processing may not proceed until the items marked with ✖️ have been resolved.
|
All items marked with ✖️ have been resolved. |
|
@ropensci-review-bot check package |
|
Thanks, about to send the query. |
|
🚀 Editor check started 👋 |
Checks for credit (v0.1.0)git hash: fa36ab55
(Checks marked with 👀 may be optionally addressed.) Package License: MIT + file LICENSE 1. Package DependenciesDetails of Package Dependency Usage (click to open)
The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.
Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table. basefor (3), data.frame (2), drop (1), if (1), length (1), ncol (1), nrow (1), seq_len (1), T (1) creditcreate_template (1), read_template (1) statsdf (2) utilsread.csv2 (1), write.csv2 (1) NOTE: No imported packages appear to have associated function calls; please ensure with author that these 'Imports' are listed appropriately. 2. Statistical PropertiesThis package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing. Details of statistical properties (click to open)
The package has:
Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the The final measure (
2a. Network visualisationClick to see the interactive network visualisation of calls between objects in package 3.
|
| id | name | conclusion | sha | run_number | date |
|---|---|---|---|---|---|
| 4253778554 | R-CMD-check | success | fa36ab | 10 | 2023-02-23 |
3b. goodpractice results
R CMD check with rcmdcheck
rcmdcheck found no errors, warnings, or notes
Test coverage with covr
Package coverage: 100
Cyclocomplexity with cyclocomp
No functions have cyclocomplexity >= 15
Static code analyses with lintr
lintr found the following 6 potential issues:
| message | number of times |
|---|---|
| Avoid library() and require() calls in packages | 1 |
| Lines should not be more than 80 characters. | 5 |
4. Other Checks
Details of other checks (click to open)
✖️ The following function name is duplicated in other packages:
-
read_templatefrom onbrand
Package Versions
| package | version |
|---|---|
| pkgstats | 0.1.3 |
| pkgcheck | 0.1.1.11 |
Editor-in-Chief Instructions:
This package is in top shape and may be passed on to a handling editor
|
@ropensci-review-bot check package (I added some sanity checks to a function) |
|
I'm sorry human, I don't understand that. You can see what commands I support by typing:
|
|
@ropensci-review-bot check package |
|
Thanks, about to send the query. |
|
🚀 Editor check started 👋 |
Checks for credit (v0.1.0)git hash: ca2d4ce9
(Checks marked with 👀 may be optionally addressed.) Package License: MIT + file LICENSE 1. Package DependenciesDetails of Package Dependency Usage (click to open)
The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.
Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table. basefor (3), data.frame (2), nrow (2), seq_len (2), character (1), drop (1), file (1), if (1), length (1), ncol (1), T (1), vapply (1) creditcheck_cras_table (1), create_template (1), drop_authors (1), read_template (1) statsdf (2) utilsread.csv2 (1) NOTE: No imported packages appear to have associated function calls; please ensure with author that these 'Imports' are listed appropriately. 2. Statistical PropertiesThis package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing. Details of statistical properties (click to open)
The package has:
Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the The final measure (
2a. Network visualisationClick to see the interactive network visualisation of calls between objects in package 3.
|
| id | name | conclusion | sha | run_number | date |
|---|---|---|---|---|---|
| 4260817751 | R-CMD-check | NA | ca2d4c | 12 | 2023-02-24 |
3b. goodpractice results
R CMD check with rcmdcheck
rcmdcheck found no errors, warnings, or notes
Test coverage with covr
Package coverage: 100
Cyclocomplexity with cyclocomp
No functions have cyclocomplexity >= 15
Static code analyses with lintr
lintr found the following 3 potential issues:
| message | number of times |
|---|---|
| Avoid library() and require() calls in packages | 1 |
| Lines should not be more than 80 characters. | 2 |
4. Other Checks
Details of other checks (click to open)
✖️ The following function name is duplicated in other packages:
-
read_templatefrom onbrand
Package Versions
| package | version |
|---|---|
| pkgstats | 0.1.3 |
| pkgcheck | 0.1.1.11 |
Editor-in-Chief Instructions:
This package is in top shape and may be passed on to a handling editor
|
@jospueyo thanks a lot for your submission! I'm discussing the scope with the editors board. To increase the chance they will see the merit of {credit} you might want to unpack in README why the task this package solves is a tedious one. README says it's tedious but it's not immediately obvious how. |
|
@maurolepore I just pushed this explanation. |
|
Thanks for the explanation and for your patience. I discussed with other editors and find this package to be in scope. I'll start looking for a handling editor. |
|
@ropensci-review-bot assign @emilyriederer as editor |
|
Assigned! @emilyriederer is now the editor |
|
Hi @jospueyo ! I'm delighted to be handling this from the editorial side. I'm traveling for work W-F so I may be a bit slower to respond, but I thought I'd share some initial feedback to get us started. Thanks again and I look forward to working together. Editor checks:
Editor commentsThis is a very clean submission, and it feels close to being ready for reviewers! I notice a few small opportunities before we do the hand-off.
|
|
|
Thanks @jospueyo ! I like the Documentation updates a lot. My mistake on the License -- I somehow saw the |
|
@ropensci-review-bot seeking reviewers |
|
Please add this badge to the README of your package repository: [](https://github.com/ropensci/software-review/issues/576)Furthermore, if your package does not have a NEWS.md file yet, please create one to capture the changes made during the review process. See https://devguide.ropensci.org/releasing.html#news |
|
I addressed all comments of @msperlin. You can see all changes in news: https://github.com/jospueyo/CRediTas/blob/master/NEWS.md |
Thanks @jospueyo. Great work. LEt me know if I can help any further. |
|
📆 @zambujo you have 2 days left before the due date for your review (2023-04-04). |
Package ReviewPlease check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide
DocumentationThe package includes all the following forms of documentation:
Functionality
Estimated hours spent reviewing: 5
Review CommentsCRediTas, which presents itself as a tiny R package, gathers a few functions designed to help authors in providing detailed information about the 14 contributor roles defined by CRediT. Essentially, the package provides a few functions to convert an author-contribution matrix in CRediT statements-like format. The matrix can be more easily shared and edited among the authors in a spreadsheet-like manner before producing the corresponding text with the authors and their contributions. Although the previous review already significantly improved the package, I have a few additional suggestions (of which implementing non-important ones is left to the criteria of the the author):
template_create <- function(authors, roles = roles_get()){
df <- data.frame(Authors = authors)
mat <- matrix(0, nrow = length(authors), ncol = length(roles))
colnames(mat) <- roles
return(cbind(df, mat))
}In the long run, I would also think of adding a couple of extra features:
|
Responses to @zambujo:
|
|
For the long run suggestions, I will keep those in mind. I liked both ideas from @zambujo. The second one is especially interesting for epistemological research. I also have in mind an option to facilitate copy&paste in MS word, currently the bold is missed on the way to MS word. Any contributions will be welcome! ;) |
I agree. |
|
📆 @msperlin you have 2 days left before the due date for your review (2023-04-06). |
|
Many thanks @jospueyo: great to see the changes. If i/o functionality is to be kept, then I'd like to extend my suggestion of not setting In And to help beginners, it might be a good idea to include path nomalization with Eg.: template_create <- function(authors, file, roles = roles_get()) {
df <- data.frame(Authors = authors)
mat <- matrix(0, nrow = length(authors), ncol = length(roles))
colnames(mat) <- roles
df <- cbind(df, mat)
if (is.missing(file)) return(df)
file <- normalizePath(file)
write.csv2(df, file, row.names = FALSE)
invisible()
}Last, consider updating the error message in |
|
@msperlin - It looks like you're satisfied with the responses to your feedback? If so, can you please document your approval with our {Final Approval Form](https://devguide.ropensci.org/approval2template.html) ? (Same for @zambujo once you're satisfied with the discussion!) |
Reviewer ResponseFinal approval (post-review)
Estimated hours spent reviewing: 2 |
|
Thank you for these final insights, @zambujo! I followed all your suggestions except using I also updated the NEWS, which I forgot in the last review. Best wishes! |
Reviewer ResponseFinal approval (post-review)
Estimated hours spent reviewing: 1 |
|
@ropensci-review-bot submit review #576 (comment) time 5 |
|
Logged review for zambujo (hours: 5) |
|
@ropensci-review-bot submit review #576 (comment) time 1.5 |
|
Logged review for msperlin (hours: 1.5) |
ropensci-review-bot
added
4/review(s)-in-awaiting-changes
and removed
3/reviewer(s)-assigned
labels
|
Thanks to @zambujo and @msperlin for their thoughtful reviews and @jospueyo for his fast follow-ups! I'm happy to say it looks like we are ready to approve this package 🎉 @jospueyo , I'll submit the "formal approval" now. Please make sure to read the instructions the bot shares carefully! There's a lot of great information in there regarding repo transfer and package promotion. |
|
@ropensci-review-bot approve CRediTas |
|
Approved! Thanks @jospueyo for submitting and @zambujo, @msperlin for your reviews! 😁 To-dos:
Should you want to acknowledge your reviewers in your package DESCRIPTION, you can do so by making them Welcome aboard! We'd love to host a post about your package - either a short introduction to it with an example for a technical audience or a longer post with some narrative about its development or something you learned, and an example of its use for a broader readership. If you are interested, consult the blog guide, and tag @ropensci/blog-editors in your reply. They will get in touch about timing and can answer any questions. We maintain an online book with our best practice and tips, this chapter starts the 3d section that's about guidance for after onboarding (with advice on releases, package marketing, GitHub grooming); the guide also feature CRAN gotchas. Please tell us what could be improved. Last but not least, you can volunteer as a reviewer via filling a short form. |
|
I'm sorry human, I don't understand that. You can see what commands I support by typing:
|
|
@ropensci-review-bot finalize transfer of CRediTas |
|
Transfer completed. |
I completed all tasks. I will think about the post. Probably in a few weeks. I also volunteered as a reviewer, although I have a lot to learn. |
|
Hi, @jospueyo (rOpenSci Community Manager here). If you want to, I can invite you to our Slack workspace. I will need your email. You can send it to [email protected]. |
Date accepted: 2023-04-11
Submitting Author Name: Josep Pueyo-Ros
Due date for @zambujo: 2023-04-04Submitting Author Github Handle: @jospueyo
Repository: https://github.com/jospueyo/CRediTas
Version submitted: 0.1.0
Submission type: Standard
Editor: @emilyriederer
Reviewers: @zambujo, @msperlin
Due date for @msperlin: 2023-04-06
Archive: TBD
Version accepted: TBD
Language: en
Scope
Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):
Explain how and why the package falls under these categories (briefly, 1-2 sentences):
The package facilitates the creation of CRediT author statements, which are mandatory for many journals and encourage good practices in coauthoring scientific publications.
The target audience are authors of scientific publications. There are not scientific applications of this package. It helps in the good practices of open science.
There are not as far as I know
Not applicable
If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.
Explain reasons for any
pkgcheckitems which your package is unable to pass.Long lines in test-write_cras.R because I compare a string with a generated text file. If I break the lines I cannot compare both.
Avoid T and F in write_cras.R: I do not use T or F, in line 1, there is "CRediT" which confounds the algorithm.
Technical checks
Confirm each of the following by checking the box.
This package:
Publication options
Do you intend for this package to go on CRAN?
Do you intend for this package to go on Bioconductor?
Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:
MEE Options
Code of conduct
The text was updated successfully, but these errors were encountered: