openalexR: an R package to interface with the OpenAlex API

trangdata commented 1 year ago

Date accepted: 2023-02-23

Submitting Author Name: Trang Le Submitting Author Github Handle: !--author1-->@trangdata@massimoaria@ldecicco-USGS<!--end-editor-- Reviewers: @BriannaLind, @pachadotdev

Due date for @BriannaLind: 2022-12-22 Due date for Due date for @pachadotdev: 2023-01-24

Archive: TBD Version accepted: TBD Language: en

Paste the full DESCRIPTION file inside a code block below:

Type: Package
Package: openalexR
Title: Getting Bibliographic Records from 'OpenAlex' Database Using 'DSL'
    API
Version: 1.0.2
Authors@R: c(
    person(given = "Massimo",
           family = "Aria",
           role = c("aut", "cre", "cph"),
           email = "aria@unina.it",
           comment = c(ORCID = "0000-0002-8517-9411")),
    person(given = "Corrado",
           family = "Cuccurullo",
           role = c("ctb"),
           email = "cuccurullocorrado@gmail.com",
           comment = c(ORCID = "0000-0002-7401-8575")),       
    person(given = "Trang",
           family = "Le",
           role = "aut",
           email = "grixor@gmail.com",
           comment = c(ORCID = "0000-0003-3737-6565"))
    )
Description: A set of tools to extract bibliographic content from
    'OpenAlex' database using API <https://docs.openalex.org/api/>.
License: MIT + file LICENSE
URL: https://github.com/massimoaria/openalexR,
    https://massimoaria.github.io/openalexR/
BugReports: https://github.com/massimoaria/openalexR/issues
Imports: 
    curl,
    httr,
    jsonlite,
    progress,
    tibble
Suggests: 
    testthat (>= 3.0.0),
    dplyr,
    knitr,
    rmarkdown,
    tidyr,
    purrr,
    ggplot2,
    covr
VignetteBuilder: 
    knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.1
Config/testthat/edition: 3
Depends: 
    R (>= 2.10)

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.):
- [x] data retrieval
- [ ] data extraction
- [ ] data munging
- [ ] data deposition
- [ ] data validation and testing
- [ ] workflow automation
- [ ] version control
- [ ] citation management and bibliometrics
- [ ] scientific software wrappers
- [ ] field and lab reproducibility tools
- [ ] database software bindings
- [ ] geospatial data
- [ ] text analysis
Explain how and why the package falls under these categories (briefly, 1-2 sentences): The package interacts with the OpenAlex API. Similar packages in the same category are rcrossref and rotl.
Who is the target audience and what are scientific applications of this package? Anyone who wants to work in R to interact with the OpenAlex API to acquire information on publications, authors, etc., including researchers in the field of bibliometrics, text mining, etc. We include several example analyses in our README.
Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category? Please see the detailed answer here with a detailed table of comparison and examples of code differences.
(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research? Yes.
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. https://github.com/ropensci/software-review/issues/557
Explain reasons for any pkgcheck items which your package is unable to pass. N/A. Passed all checks.

Technical checks

Confirm each of the following by checking the box.

[x] I have read the rOpenSci packaging guide.
[x] I have read the author guide and I expect to maintain this package for at least 2 years or to find a replacement.

This package:

[x] does not violate the Terms of Service of any service it interacts with.
[x] has a CRAN and OSI accepted license.
[x] contains a README with instructions for installing the development version.
[x] includes documentation with examples for all functions, created with roxygen2.
[x] contains a vignette with examples of its essential functions and uses.
[x] has a test suite.
[x] has continuous integration, including reporting of test coverage.

Publication options

[x] 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

- [ ] The package is novel and will be of interest to the broad readership of the journal. - [ ] The manuscript describing the package is no longer than 3000 words. - [ ] You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see [MEE's Policy on Publishing Code](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/journal-resources/policy-on-publishing-code.html)) - (*Scope: Do consider MEE's [Aims and Scope](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/aims-and-scope/read-full-aims-and-scope.html) for your manuscript. We make no guarantee that your manuscript will be within MEE scope.*) - (*Although not required, we strongly recommend having a full manuscript prepared when you submit here.*) - (*Please do not submit your package separately to Methods in Ecology and Evolution*)

Code of conduct

[x] I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

ropensci-review-bot commented 1 year ago

Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type @ropensci-review-bot help for help.

ropensci-review-bot commented 1 year ago

:rocket:

Editor check started

:wave:

ropensci-review-bot commented 1 year ago

Checks for openalexR (v1.0.2)

git hash: c0d32fea

:heavy_check_mark: Package is already on CRAN.
:heavy_check_mark: has a 'codemeta.json' file.
:heavy_check_mark: has a 'contributing' file.
:heavy_check_mark: uses 'roxygen2'.
:heavy_check_mark: 'DESCRIPTION' has a URL field.
:heavy_check_mark: 'DESCRIPTION' has a BugReports field.
:heavy_check_mark: Package has at least one HTML vignette
:heavy_check_mark: All functions have examples.
:heavy_check_mark: Package has continuous integration checks.
:heavy_check_mark: Package coverage is 92.4%.
:heavy_check_mark: R CMD check found no errors.
:heavy_check_mark: R CMD check found no warnings.

Package License: MIT + file LICENSE

1. Package Dependencies

Details 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. |type |package | ncalls| |:----------|:---------|------:| |internal |base | 227| |internal |openalexR | 67| |internal |utils | 16| |internal |stats | 12| |internal |graphics | 2| |internal |methods | 2| |imports |httr | 5| |imports |jsonlite | 2| |imports |curl | NA| |imports |progress | NA| |imports |tibble | NA| |suggests |testthat | NA| |suggests |dplyr | NA| |suggests |knitr | NA| |suggests |rmarkdown | NA| |suggests |tidyr | NA| |suggests |purrr | NA| |suggests |ggplot2 | NA| |suggests |covr | NA| |linking_to |NA | NA| 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()', and examining the 'external_calls' table.

base

list (62), c (23), lapply (16), do.call (15), length (14), if (11), for (7), unlist (7), vector (6), mode (5), paste (5), is.null (4), lengths (4), names (3), rbind.data.frame (3), by (2), duplicated (2), max (2), min (2), nrow (2), rbind (2), rep (2), search (2), sort (2), switch (2), unique (2), url (2), which (2), as.character (1), ceiling (1), environment (1), format (1), grepl (1), intersect (1), is.na (1), logical (1), mapply (1), merge (1), paste0 (1), seq_along (1), seq.int (1), strsplit (1), tolower (1), vapply (1)

openalexR

oa_fetch (13), oa_progress (7), au_collapse (5), subs_na (5), empty_list (3), oa_request (3), SR (3), abstract_build (2), api_request (2), append_flt (2), cfg (2), oa_entities (2), simple_rapply (2), asl (1), authors2df (1), concepts2df (1), get_auth_position (1), id_type (1), institutions2df (1), isValidEmail (1), oa_email (1), oa_query (1), oa_random (1), oa_snowball (1), oa2bibliometrix (1), oa2df (1), prepend (1), shorten_oaid (1), shorten_orcid (1)

utils

data (16)

stats

filter (11), setNames (1)

httr

content (2), GET (1), modify_url (1), user_agent (1)

graphics

text (2)

jsonlite

fromJSON (2)

methods

as (2)

**NOTE:** Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.

2. Statistical Properties

This 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: - code in R (100% in 8 files) and - 2 authors - 4 vignettes - 2 internal data files - 5 imported packages - 16 exported functions (median 36 lines of code) - 54 non-exported functions in R (median 8 lines of code) --- Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages The following terminology is used: - `loc` = "Lines of Code" - `fn` = "function" - `exp`/`not_exp` = exported / not exported All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by [the `checks_to_markdown()` function](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) The final measure (`fn_call_network_size`) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile. |measure | value| percentile|noteworthy | |:------------------------|-----:|----------:|:----------| |files_R | 8| 50.7| | |files_vignettes | 4| 95.3| | |files_tests | 8| 88.2| | |loc_R | 858| 63.8| | |loc_vignettes | 583| 81.6| | |loc_tests | 363| 68.2| | |num_vignettes | 4| 96.6|TRUE | |data_size_total | 4058| 66.2| | |data_size_median | 2029| 68.7| | |n_fns_r | 70| 66.8| | |n_fns_r_exported | 16| 60.6| | |n_fns_r_not_exported | 54| 69.6| | |n_fns_per_file_r | 6| 73.8| | |num_params_per_fn | 2| 11.9| | |loc_per_fn_r | 14| 42.4| | |loc_per_fn_r_exp | 36| 70.0| | |loc_per_fn_r_not_exp | 8| 26.4| | |rel_whitespace_R | 23| 70.2| | |rel_whitespace_vignettes | 28| 79.4| | |rel_whitespace_tests | 16| 59.8| | |doclines_per_fn_exp | 46| 58.1| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 63| 70.9| | ---

2a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

3. `goodpractice` and other checks

Details of goodpractice checks (click to open)

#### 3a. Continuous Integration Badges [![R-CMD-check.yaml](https://github.com/massimoaria/openalexR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/massimoaria/openalexR/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:--------------------------|:----------|:------|----------:|:----------| | 3420154650|pages build and deployment |success |3a012b | 38|2022-11-08 | | 3420037823|pkgcheck |success |c0d32f | 2|2022-11-08 | | 3420182325|pkgdown |NA |c4e6ce | 88|2022-11-08 | | 3420182323|R-CMD-check |NA |c4e6ce | 73|2022-11-08 | | 3420182324|test-coverage |NA |c4e6ce | 30|2022-11-08 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) rcmdcheck found no errors, warnings, or notes #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 92.42 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) The following functions have cyclocomplexity >= 15: function | cyclocomplexity --- | --- oa_request | 19 works2df | 16 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 74 potential issues: message | number of times --- | --- Avoid library() and require() calls in packages | 9 Lines should not be more than 80 characters. | 65

Package Versions

|package |version | |:--------|:--------| |pkgstats |0.1.1.66 | |pkgcheck |0.1.0.32 |

Editor-in-Chief Instructions:

This package is in top shape and may be passed on to a handling editor

annakrystalli commented 1 year ago

Thanks for submitting @trangdata! 🎉

I'm in the process of assigning a handling editor.

In the meantime, it appears there's a minor discrepancy in the version stated in the submission and pasted DESCRIPTION (1.0.1) and the actual current package version (1.0.2). Would you mind correcting and double-checking the pasted DESCRIPTION is up to date?

trangdata commented 1 year ago

Thanks so much @annakrystalli! 🌻

it appears there's a minor discrepancy in the version stated in the submission and pasted DESCRIPTION (1.0.1) and the actual current package version (1.0.2).

Ah my bad. I forgot to update the version. Edited now.

annakrystalli commented 1 year ago

@ropensci-review-bot assign @ldecicco-USGS as editor

ropensci-review-bot commented 1 year ago

Assigned! @ldecicco-USGS is now the editor

ldecicco-USGS commented 1 year ago

Editor checks:

[x] Documentation: The package has sufficient documentation available online (README, pkgdown docs) to allow for an assessment of functionality and scope without installing the package. In particular,
- [ ] Is the case for the package well made?
- [ ] Is the reference index page clear (grouped by topic if necessary)?
- [ ] Are vignettes readable, sufficiently detailed and not just perfunctory?
[x] Fit: The package meets criteria for fit and overlap.
[x] Installation instructions: Are installation instructions clear enough for human users?
[x] Tests: If the package has some interactivity / HTTP / plot production etc. are the tests using state-of-the-art tooling?
[ ] Contributing information: Is the documentation for contribution clear enough e.g. tokens for tests, playgrounds?
[x] License: The package has a CRAN or OSI accepted license.
[x] Project management: Are the issue and PR trackers in a good shape, e.g. are there outstanding bugs, is it clear when feature requests are meant to be tackled?

Editor comments

ldecicco-USGS commented 1 year ago

Hi @trangdata ! The package looks great! I'll try to find some editors as soon as possible

trangdata commented 1 year ago

Thank you so much @ldecicco-USGS. 🪴 And you mean reviewers right? 😅

ldecicco-USGS commented 1 year ago

😆Yup!

ldecicco-USGS commented 1 year ago

@ropensci-review-bot assign @BriannaLind as reviewer

ropensci-review-bot commented 1 year ago

@BriannaLind added to the reviewers list. Review due date is 2022-12-22. Thanks @BriannaLind for accepting to review! Please refer to our reviewer guide.

rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more.

ropensci-review-bot commented 1 year ago

@BriannaLind: If you haven't done so, please fill this form for us to update our reviewers records.

BriannaLind commented 1 year ago

Sorry for the delay team - I am diving into the review, will get back asap

ldecicco-USGS commented 1 year ago

It turns out I had assigned the review to a fake account that was impersonating the actual reviewer. I'm verifying he's still interested in reviewing. Sorry for the delay @trangdata !

ldecicco-USGS commented 1 year ago

@ropensci-review-bot assign @pachadotdev as reviewer

ropensci-review-bot commented 1 year ago

@pachadotdev added to the reviewers list. Review due date is 2023-01-24. Thanks @pachadotdev for accepting to review! Please refer to our reviewer guide.

rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more.

ldecicco-USGS commented 1 year ago

Hi @pachadotdev and @BriannaLind , checking in to see if you could update us on an approximate timeline for when you'll be able to do the review.

pachadotdev commented 1 year ago

Hi @pachadotdev and @BriannaLind , checking in to see if you could update us on an approximate timeline for when you'll be able to do the review.

hi i finished the wilsonfreitas review last weekend i can check this one on monday

ropensci-review-bot commented 1 year ago

:calendar: @pachadotdev you have 2 days left before the due date for your review (2023-01-24).

BriannaLind commented 1 year ago

Should have it done by the middle/end of the week!

From: Pachá @.> Sent: Friday, January 20, 2023 10:39 AM To: ropensci/software-review @.> Cc: Lind, Brianna (Contractor) @.>; Mention @.> Subject: [EXTERNAL] Re: [ropensci/software-review] openalexR: an R package to interface with the OpenAlex API (Issue #560)

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hi i finished the wilsonfreitas review last weekend i can check this one on monday

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BriannaLind commented 1 year ago

Package Review (1)

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

Briefly describe any working relationship you have (had) with the package authors.
[x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (if you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

[x] A statement of need: clearly stating problems the software is designed to solve and its target audience in README
[x] Installation instructions: for the development version of package and any non-standard dependencies in README
[x] Vignette(s): demonstrating major functionality that runs successfully locally
[x] Function Documentation: for all exported functions
[x] Examples: (that run successfully locally) for all exported functions
[x] Community guidelines: including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

Functionality

[x] Installation: Installation succeeds as documented.
[x] Functionality: Any functional claims of the software been confirmed.
[x] Performance: Any performance claims of the software been confirmed.
[x] Automated tests: Unit tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.
[x] Packaging guidelines: The package conforms to the rOpenSci packaging guidelines.

Estimated hours spent reviewing: 6

[x] Should the author(s) deem it appropriate, I agree to be acknowledged as a package reviewer ("rev" role) in the package DESCRIPTION file.

Review Comments

Sorry for the delay in reviewing - I am also quite new to git hub and at first had some trouble navigating and following instructions with the package reviewer. Very cool package - I am looking forward to playing around with it more!

I ran the set up and tutorial in the readme of http://github.com/massimoria/openalexR. The first example executed fine, but instead of the nice display shown in the tutorial I had a bunch of (kind of ugly tabsets). I tried reinstalling knitr package, but that 'help. That happened for all of the 'works' and 'author' examples. The rest of the tutorial worked well, except several times I had to install packages that were not shown in the script but were necessary (this included ggraph, ggtext, and word cloud). As with most scripts, R did not want to play nice until all packages were updated to the most recent version.

trangdata commented 1 year ago

Hi @BriannaLind, first of all, thank you so much for spending your time reviewing the package. ❤️ ✨ I appreciate your comments!

The first example executed fine, but instead of the nice display shown in the tutorial I had a bunch of (kind of ugly tabsets).

Ah this is interesting. I'm not sure what's going on with knitr, but you're right: we should separate oa_fetch() and the lines to display the output dataframe, so that the user can still see the output any other ways. I will update the readme.

The rest of the tutorial worked well, except several times I had to install packages that were not shown in the script but were necessary (this included ggraph, ggtext, and word cloud)

We had a few discussions regarding finding a balance between adding dependencies and making the user separately install things. We decided to keep the package minimal with few dependencies since most use cases won't require additional packages. When the user wants more specific analyses, e.g., snowballing, we expect them to install ggraph separately. The examples were to show the variety of use cases for openalexR, so we didn't think attaching, for example, wordcloud, as an Imports was necessary. However, if you think these examples should be moved to a different place than the readme, we will consider the suggestion!

Thanks again for the constructive feedback! 🌱

BriannaLind commented 1 year ago

@trangdata yay! I'm glad it was helpful!

I think its totally fine for users to install extra packages separately - I mostly was thinking of a 'new R user' who is going to want to really work through your examples and copy and paste the script ---that it would be nice to have library(XXX) above the code snippet to reduce frustration.

pachadotdev commented 1 year ago

hi @trangdata I; ll try to have my review done by Thu

trangdata commented 1 year ago

I think its totally fine for users to install extra packages separately - I mostly was thinking of a 'new R user' who is going to want to really work through your examples and copy and paste the script ---that it would be nice to have library(XXX) above the code snippet to reduce frustration.

@BriannaLind ah gotcha! That makes sense. I'll keep this in mind when updating the readme.

ll try to have my review done by Thu

@pachadotdev Thank you!!! I'm excited to hear your feedback! 🙌🏽

maurolepore commented 1 year ago

Dear all,

My EiC rotation just started and I'm checking the status of open issues. I don't mean to intrude but to save you time. So while I'm here I note the second review might be ready soon.

@pachadotdev, any updates?

pachadotdev commented 1 year ago

Dear all,

My EiC rotation just started and I'm checking the status of open issues. I don't mean to intrude but to save you time. So while I'm here I note the second review might be ready soon.

@pachadotdev, any updates?

hi! I can send it by tonight

pachadotdev commented 1 year ago

ready how do I upload this?

ldecicco-USGS commented 1 year ago

Hi @pachadotdev - copy and paste the text in the comments. If there are any formatting issues I can take a look and see how to fix it up.

pachadotdev commented 1 year ago

Package Review (1)

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

Briefly describe any working relationship you have (had) with the package authors.
[x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (if you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

[x] A statement of need: clearly stating problems the software is designed to solve and its target audience in README

[x] Installation instructions: for the development version of package and any non-standard dependencies in README
[x] Vignette(s): demonstrating major functionality that runs successfully locally
[x] Function Documentation: for all exported functions
[x] Examples: (that run successfully locally) for all exported functions
[x] Community guidelines: including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

Functionality

[x] Installation: Installation succeeds as documented.
[x] Functionality: Any functional claims of the software been confirmed.
[x] Performance: Any performance claims of the software been confirmed.
[x] Automated tests: Unit tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.
[x] Packaging guidelines: The package conforms to the rOpenSci packaging guidelines.

Estimated hours spent reviewing: 3.5

[x] Should the author(s) deem it appropriate, I agree to be acknowledged as a package reviewer ("rev" role) in the package DESCRIPTION file.

Review Comments

Sorry for the delay! The outputs look strange on Windows, but it works perfect on Ubuntu. After checking, it is because I had older pkgs on Windows.

pachadotdev commented 1 year ago

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

Briefly describe any working relationship you have (had) with the package authors.
[x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (if you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

[x] A statement of need: clearly stating problems the software is designed to solve and its target audience in README

[x] Installation instructions: for the development version of package and any non-standard dependencies in README
[x] Vignette(s): demonstrating major functionality that runs successfully locally
[x] Function Documentation: for all exported functions
[x] Examples: (that run successfully locally) for all exported functions
[x] Community guidelines: including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

Functionality

[x] Installation: Installation succeeds as documented.
[x] Functionality: Any functional claims of the software been confirmed.
[x] Performance: Any performance claims of the software been confirmed.
[x] Automated tests: Unit tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.
[x] Packaging guidelines: The package conforms to the rOpenSci packaging guidelines.

Estimated hours spent reviewing: 3.5

[x] Should the author(s) deem it appropriate, I agree to be acknowledged as a package reviewer ("rev" role) in the package DESCRIPTION file.

Review Comments

Sorry for the delay! The outputs look strange on Windows, but it works perfect on Ubuntu. After checking, it is because I had older pkgs on Windows.

ldecicco-USGS commented 1 year ago

@ropensci-review-bot submit review https://github.com/ropensci/software-review/issues/560#issuecomment-1419932073 time 3.5

ropensci-review-bot commented 1 year ago

Couldn't find entry for pachadotdev in the reviews log

ldecicco-USGS commented 1 year ago

@ropensci-review-bot submit review https://github.com/ropensci/software-review/issues/560#issuecomment-1409244254 time 6

ropensci-review-bot commented 1 year ago

Logged review for BriannaLind (hours: 6)

ldecicco-USGS commented 1 year ago

Thanks @pachadotdev and @BriannaLind for the reviews!

It seems like you both gave the package a test drive and things are looking pretty good. I don't see any major suggestions that were put forth yet to fix. Is that right? When I first looked at the package via the editor review, I also thought it was in pretty good shape!

If that's correct, @pachadotdev and @BriannaLind , could you use the Approval template and verify: https://devguide.ropensci.org/approval2template.html

BriannaLind commented 1 year ago

Reviewer Response

Final approval (post-review)

[x] The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 6

pachadotdev commented 1 year ago

Reviewer Response

Final approval (post-review)

[x] The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 3.5

ldecicco-USGS commented 1 year ago

@ropensci-review-bot approve openalexR

ropensci-review-bot commented 1 year ago

Approved! Thanks @trangdata for submitting and @BriannaLind, @pachadotdev for your reviews! :grin:

To-dos:

[ ] Transfer the repo to rOpenSci's "ropensci" GitHub organization under "Settings" in your repo. I have invited you to a team that should allow you to do so. You will need to enable two-factor authentication for your GitHub account. This invitation will expire after one week. If it happens write a comment @ropensci-review-bot invite me to ropensci/<package-name> which will re-send an invitation.
[ ] After transfer write a comment @ropensci-review-bot finalize transfer of <package-name> where <package-name> is the repo/package name. This will give you admin access back.
[ ] Fix all links to the GitHub repo to point to the repo under the ropensci organization.
[ ] Delete your current code of conduct file if you had one since rOpenSci's default one will apply, see https://devguide.ropensci.org/collaboration.html#coc-file
[ ] If you already had a pkgdown website and are ok relying only on rOpenSci central docs building and branding,
- deactivate the automatic deployment you might have set up
- remove styling tweaks from your pkgdown config but keep that config file
- replace the whole current pkgdown website with a redirecting page
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[ ] Increment the package version to reflect the changes you made during review. In NEWS.md, add a heading for the new version and one bullet for each user-facing change, and each developer-facing change that you think is relevant.
[ ] We're starting to roll out software metadata files to all rOpenSci packages via the Codemeta initiative, see https://docs.ropensci.org/codemetar/ for how to include it in your package, after installing the package - should be easy as running codemetar::write_codemeta() in the root of your package.
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Should you want to acknowledge your reviewers in your package DESCRIPTION, you can do so by making them "rev"-type contributors in the Authors@R field (with their consent).

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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.

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ldecicco-USGS commented 1 year ago

@trangdata Congratulations on the great package. Sorry the timing went a little longer than usual. The "bot" automatically closes this issue when the package gets approved, but we can still use the issue to communicate (or feel free to re-open it if you have any questions).

Let me know if you have any questions on the instructions above.

Once again, thanks for submitting to rOpenSci and great work! 🎉

trangdata commented 1 year ago

@ldecicco-USGS Thank you so much! ❤️ And huge thank you to the reviewers @pachadotdev and @BriannaLind for your valuable feedback! 🌈 Would you both be okay with us listing you as reviewers in our DESCRIPTION file?

On the first TODO: @ldecicco-USGS Could you please add (or ask the bot to add) @massimoaria to ropensci so he could transfer "ownership" of the repository, please? The package currently lives at https://github.com/massimoaria/openalexR. Thank you!

maelle commented 1 year ago

I sent an invitation to the organization to @massimoaria. Please ping me when the repo is transferred so that I might give @massimoaria admin access back.

Sorry for the clunkiness, it's only the second time in a short time we encounter this case https://github.com/ropensci-org/buffy/issues/98

massimoaria commented 1 year ago

Dear Maelle, I just transferred the openalexR repository to the rOpenSci organization.

Thanks a lot Massimo

⁣**** Dr. Massimo Aria Full Professor in Statistics for Social Sciences PhD in Computational Statistics Bibliometrix R-package creator K-Synth Academic Spin-Off co-founder Department of Economics and Statistics University of Naples Federico II Monte S. Angelo, via Cinthia I-80126 Napoli, Italy Room D-25, Sector D, 2nd Floor, Building 3 ph. +39 081675187 fax +39 081675009 mob. +39 392 1966384 email @.* https://www.massimoaria.com https://www.bibliometrix.org https://www.k-synth.unina.it https://scholar.google.it/citations?user=Qu66YZQAAAAJ https://orcid.org/0000-0002-8517-9411 http://www.researcherid.com/rid/O-7983-2015 https://www.researchgate.net/profile/Massimo_Aria **

Il giorno 24 feb 2023, alle ore 06:30, Maëlle Salmon @.***> ha scritto:

I sent an invitation to the organization to @massimoaria https://github.com/massimoaria. Please ping me when the repo is transferred so that I might give @massimoaria https://github.com/massimoaria admin access back.

Sorry for the clunkiness, it's only the second time in a short time we encounter this case ropensci-org/buffy#98 https://github.com/ropensci-org/buffy/issues/98 — Reply to this email directly, view it on GitHub https://github.com/ropensci/software-review/issues/560#issuecomment-1442831224, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD2H753KTTIRCVTQW4UFTKDWZBBRDANCNFSM6AAAAAAR2LR6UE. You are receiving this because you were mentioned.

maelle commented 1 year ago

Awesome, thanks! I've given you admin rights and write access to @trangdata but now that you have admin rights you can increase @trangdata's as needed.

trangdata commented 1 year ago

@massimoaria Any chance you could give me admin access so it's easier for me to make changes such as change the repo description url. Thank you! 🌱

massimoaria commented 1 year ago

Done!

ropensci / software-review