excluder: checks for exclusion criteria in online data #455
Comments
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@ropensci-review-bot check package |
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Thanks, about to send the query. |
Checks for excluder (v0.2.2)git hash: 1d8446c9
Important: All failing checks above must be addressed prior to proceeding Package License: GPL (>= 3) 1. 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
The final measure (
1a. Network visualisationInteractive network visualisation of calls between objects in package can be viewed by clicking here 2.
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| name | conclusion | sha | date |
|---|---|---|---|
| pkgdown | success | 1d8446 | 2021-07-26 |
| R-CMD-check | success | 1d8446 | 2021-07-26 |
| test-coverage | success | 1d8446 | 2021-07-26 |
3b. goodpractice results
R CMD check with rcmdcheck
R CMD check generated the following note:
- checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘qualtRics’, ‘rgeolocate’
Test coverage with covr
Package coverage: 81.79
Cyclocomplexity with cyclocomp
The following function have cyclocomplexity >= 15:
| function | cyclocomplexity |
|---|---|
| check_duplicates | 19 |
Static code analyses with lintr
lintr found the following 201 potential issues:
| message | number of times |
|---|---|
| Lines should not be more than 80 characters. | 201 |
Package Versions
| package | version |
|---|---|
| pkgstats | 0.0.0.265 |
| pkgcheck | 0.0.1.367 |
Editor-in-Chief Instructions:
This package may be submitted
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The only check that failed was "Package does not have a 'contributing.md' file". Does this mean that the package should not have a contributing.md file? So should I just remove the file and remove all references to Contributing to this package? |
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Thanks for the submission @JeffreyRStevens! Sorry for a bit of a delay as we were working out our new automated diagnostics bot, which your review is the first to use, and you just found a bug in! Your |
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Ah, OK--no problem. Glad to be a guinea pig to help debug! |
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@JeffreyRStevens, it's my pleasure to be the handling editor of your submission. Editor checks:
Editor commentsCongratulations! The bot and I are very happy to see the package meets rOpenSci's guidelines 👍. I'll start looking for reviewers. Note the following minor issues. You might want to consider before the review:
❯ checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘qualtRics’, ‘rgeolocate’
# Good
dupl_ip <- TRUE
if (identical(dupl_ip, TRUE)) {
message("Do something.")
}
#> Do something.
# Good
dupl_ip <- TRUE
stopifnot(length(dupl_ip) == 1L)
if (dupl_ip) {
message("Do something.")
}
#> Do something.
# Fragile
dupl_ip <- c(TRUE, FALSE) # This might be accidentally non-atomic
if (dupl_ip == TRUE) {
message("Do something.")
}
#> Warning in if (dupl_ip == TRUE) {: the condition has length > 1 and only the
#> first element will be used
#> Do something.Created on 2021-08-07 by the reprex package (v2.0.0)
check-mark-exclude:
Note: Using an external vector in selections is ambiguous.
i Use `all_of(location_col)` instead of `location_col` to silence this message.
i See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
Reviewers: Due date: |
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@ropensci-review-bot seeking reviewers |
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Please add this badge to the README of your package repository: [](https://github.com/ropensci/software-review/issues/455)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 |
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@JeffreyRStevens, could you suggest two or three potential reviewers? Although I wouldn't pick more than one, your list will inform the type of expertise you think would be useful when reviewing {excluder}. I'll also use other criteria as described in How to look for reviewers. |
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@maurolepore thank you for your speedy initial review of {excluder}. I have pushed some changes to address your comments.
Thank you again for your careful review, and let me know if I missed something. |
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Thanks @JeffreyRStevens for responding quickly.
Outputdevtools::load_all()
#> ℹ Loading excluder
packageVersion("excluder")
#> [1] '0.2.2'
gert::git_log(max = 1)
#> # A tibble: 1 × 6
#> commit author time files merge message
#> * <chr> <chr> <dttm> <int> <lgl> <chr>
#> 1 d99bc23850c3f… Jeffrey R. Ste… 2021-08-08 15:06:45 29 FALSE "Change all te…
devtools::check()
#> ℹ Updating excluder documentation
#> ℹ Loading excluder
#> Warning: [/home/mauro/git/excluder/R/check_duplicates.R:9] @details Link
#> to unavailable package: qualtRics::fetch_survey. there is no package called
#> 'qualtRics'
#> Warning: [/home/mauro/git/excluder/R/check_duration.R:9] @details Link to
#> unavailable package: qualtRics::fetch_survey. there is no package called
#> 'qualtRics'
#> Warning: [/home/mauro/git/excluder/R/check_ip.R:9] @details Link to unavailable
#> package: qualtRics::fetch_survey. there is no package called 'qualtRics'
#> Warning: [/home/mauro/git/excluder/R/check_location.R:9] @details Link to
#> unavailable package: qualtRics::fetch_survey. there is no package called
#> 'qualtRics'
#> Warning: [/home/mauro/git/excluder/R/check_preview.R:9] @details Link to
#> unavailable package: qualtRics::fetch_survey. there is no package called
#> 'qualtRics'
#> Warning: [/home/mauro/git/excluder/R/check_progress.R:9] @details Link to
#> unavailable package: qualtRics::fetch_survey. there is no package called
#> 'qualtRics'
#> Warning: [/home/mauro/git/excluder/R/check_resolution.R:10] @details Link
#> to unavailable package: qualtRics::fetch_survey. there is no package called
#> 'qualtRics'
#> Warning: [/home/mauro/git/excluder/R/qualtrics_numeric.R:3] @description Link
#> to unavailable package: rgeolocate::ip2location. there is no package called
#> 'rgeolocate'
#> Warning: [/home/mauro/git/excluder/R/qualtrics_raw.R:3] @description Link
#> to unavailable package: rgeolocate::ip2location. there is no package called
#> 'rgeolocate'
#> Warning: [/home/mauro/git/excluder/R/qualtrics_text.R:3] @description Link
#> to unavailable package: rgeolocate::ip2location. there is no package called
#> 'rgeolocate'
#> Warning: [/home/mauro/git/excluder/R/remove_label_rows.R:7] @details Link
#> to unavailable package: qualtRics::fetch_survey. there is no package called
#> 'qualtRics'
#> Writing NAMESPACE
#> Writing NAMESPACE
#> ── Building ──────────────────────────────────────────────────────── excluder ──
#> Setting env vars:
#> • CFLAGS : -Wall -pedantic
#> • CXXFLAGS : -Wall -pedantic
#> • CXX11FLAGS: -Wall -pedantic
#> ────────────────────────────────────────────────────────────────────────────────
#> checking for file ‘/home/mauro/git/excluder/DESCRIPTION’ ... ✓ checking for file ‘/home/mauro/git/excluder/DESCRIPTION’
#> ─ preparing ‘excluder’:
#> checking DESCRIPTION meta-information ... ✓ checking DESCRIPTION meta-information
#> ─ installing the package to build vignettes
#> creating vignettes ... ✓ creating vignettes (2.6s)
#> ─ checking for LF line-endings in source and make files and shell scripts
#> ─ checking for empty or unneeded directories
#> ─ building ‘excluder_0.2.2.tar.gz’
#>
#> ── Checking ──────────────────────────────────────────────────────── excluder ──
#> Setting env vars:
#> • _R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
#> • _R_CHECK_CRAN_INCOMING_REMOTE_ : FALSE
#> • _R_CHECK_CRAN_INCOMING_ : FALSE
#> • _R_CHECK_FORCE_SUGGESTS_ : FALSE
#> • NOT_CRAN : true
#> ── R CMD check ─────────────────────────────────────────────────────────────────
#> * using log directory ‘/tmp/Rtmpcusbks/excluder.Rcheck’
#> * using R version 4.1.0 (2021-05-18)
#> * using platform: x86_64-pc-linux-gnu (64-bit)
#> * using session charset: UTF-8
#> * using options ‘--no-manual --as-cran’
#> * checking for file ‘excluder/DESCRIPTION’ ... OK
#> * this is package ‘excluder’ version ‘0.2.2’
#> * package encoding: UTF-8
#> * checking package namespace information ... OK
#> * checking package dependencies ... OK
#> * checking if this is a source package ... OK
#> * checking if there is a namespace ... OK
#> * checking for executable files ... OK
#> * checking for hidden files and directories ... OK
#> * checking for portable file names ... OK
#> * checking for sufficient/correct file permissions ... OK
#> * checking whether package ‘excluder’ can be installed ... OK
#> * checking installed package size ... OK
#> * checking package directory ... OK
#> * checking for future file timestamps ... OK
#> * checking ‘build’ directory ... OK
#> * checking DESCRIPTION meta-information ... OK
#> * checking top-level files ... NOTE
#> Non-standard files/directories found at top level:
#> ‘mid-guppy_reprex.R’ ‘mid-guppy_reprex.md’ ‘ok-coqui_reprex.R’
#> ‘ok-coqui_reprex.spin.R’ ‘ok-coqui_reprex.spin.Rmd’
#> * checking for left-over files ... OK
#> * checking index information ... OK
#> * checking package subdirectories ... OK
#> * checking R files for non-ASCII characters ... OK
#> * checking R files for syntax errors ... OK
#> * checking whether the package can be loaded ... OK
#> * checking whether the package can be loaded with stated dependencies ... OK
#> * checking whether the package can be unloaded cleanly ... OK
#> * checking whether the namespace can be loaded with stated dependencies ... OK
#> * checking whether the namespace can be unloaded cleanly ... OK
#> * checking loading without being on the library search path ... OK
#> * checking dependencies in R code ... OK
#> * checking S3 generic/method consistency ... OK
#> * checking replacement functions ... OK
#> * checking foreign function calls ... OK
#> * checking R code for possible problems ... NOTE
#> collapse_exclusions: no visible binding for global variable
#> ‘exclusions’
#> Undefined global functions or variables:
#> exclusions
#> * checking Rd files ... OK
#> * checking Rd metadata ... OK
#> * checking Rd line widths ... OK
#> * checking Rd cross-references ... NOTE
#> Packages unavailable to check Rd xrefs: ‘qualtRics’, ‘rgeolocate’
#> * checking for missing documentation entries ... OK
#> * checking for code/documentation mismatches ... OK
#> * checking Rd \usage sections ... OK
#> * checking Rd contents ... OK
#> * checking for unstated dependencies in examples ... OK
#> * checking contents of ‘data’ directory ... OK
#> * checking data for non-ASCII characters ... OK
#> * checking LazyData ... OK
#> * checking data for ASCII and uncompressed saves ... OK
#> * checking installed files from ‘inst/doc’ ... OK
#> * checking files in ‘vignettes’ ... OK
#> * checking examples ... OK
#> * checking for unstated dependencies in ‘tests’ ... OK
#> * checking tests ...
#> Running ‘testthat.R’
#> OK
#> * checking for unstated dependencies in vignettes ... OK
#> * checking package vignettes in ‘inst/doc’ ... OK
#> * checking re-building of vignette outputs ... OK
#> * checking for non-standard things in the check directory ... OK
#> * checking for detritus in the temp directory ... OK
#> * DONE
#>
#> Status: 3 NOTEs
#> See
#> ‘/tmp/Rtmpcusbks/excluder.Rcheck/00check.log’
#> for details.
#> ── R CMD check results ───────────────────────────────────── excluder 0.2.2 ────
#> Duration: 56.5s
#>
#> > checking top-level files ... NOTE
#> Non-standard files/directories found at top level:
#> ‘mid-guppy_reprex.R’ ‘mid-guppy_reprex.md’ ‘ok-coqui_reprex.R’
#> ‘ok-coqui_reprex.spin.R’ ‘ok-coqui_reprex.spin.Rmd’
#>
#> > checking R code for possible problems ... NOTE
#> collapse_exclusions: no visible binding for global variable
#> ‘exclusions’
#> Undefined global functions or variables:
#> exclusions
#>
#> > checking Rd cross-references ... NOTE
#> Packages unavailable to check Rd xrefs: ‘qualtRics’, ‘rgeolocate’
#>
#> 0 errors ✓ | 0 warnings ✓ | 3 notes xSession infosessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.1.0 (2021-05-18)
#> os Ubuntu 20.04.2 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/Mazatlan
#> date 2021-08-10
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> ! package * version date lib source
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#> askpass 1.1 2019-01-13 [1] CRAN (R 4.1.0)
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#> devtools 2.4.2 2021-06-07 [1] CRAN (R 4.1.0)
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#> dplyr 1.0.7 2021-06-18 [1] CRAN (R 4.1.0)
#> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0)
#> P excluder * 0.2.2 2021-08-07 [?] local
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#> hms 1.1.0 2021-05-17 [1] CRAN (R 4.1.0)
#> htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.1.0)
#> iptools 0.6.1 2018-12-09 [1] RSPM (R 4.1.0)
#> janitor 2.1.0 2021-01-05 [1] CRAN (R 4.1.0)
#> knitr 1.33 2021-04-24 [1] CRAN (R 4.1.0)
#> lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.1.0)
#> lubridate 1.7.10 2021-02-26 [1] CRAN (R 4.1.0)
#> magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.0)
#> maps 3.3.0 2018-04-03 [1] RSPM (R 4.0.3)
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#> rmarkdown 2.10 2021-08-06 [1] CRAN (R 4.1.0)
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#>
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#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library
#>
#> P ── Loaded and on-disk path mismatch.
Thanks for your work and suggestions for reviewers. |
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Many thanks for the clarifications and help, @maurolepore.
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@ropensci-review-bot add @juliasilge to reviewers |
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@juliasilge added to the reviewers list. Review due date is 2021-09-20. Thanks @juliasilge for accepting to review! Please refer to our reviewer guide. |
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@juliasilge: If you haven't done so, please fill this form for us to update our reviewers records. |
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@ropensci-review-bot add @jmobrien to reviewers |
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@jmobrien added to the reviewers list. Review due date is 2021-09-20. Thanks @jmobrien for accepting to review! Please refer to our reviewer guide. |
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@JeffreyRStevens, I'm thrilled that @juliasilge and @jmobrien accepted to review the excluder package. Note I look forward to working with you all. |
Package ReviewCongratulations to the author on this useful package for folks handling Qualtrics surveys. It will be convenient to have all these common checks in a consistent set of functions, and the messaging in the console is very nice. 🙌
DocumentationThe package includes all the following forms of documentation:
On documentation, I find some of the way the documentation works a bit confusing, especially when things go wrong for users. For example, if I have a dataset with no IP addresses or location information and I try to run However, when I look at the documentation for the function I used, I don't see anything about Functionality
Estimated hours spent reviewing: 2
Review Comments🎯 The function name 🎯 None of my real surveys have IP addresses so I was not able to check the iptools integration beyond the example survey data included in the package. 🎯 In the future, if you wanted to increase the polish of the console messages (once the nicest features of this package that I think will draw folks to use it), you might check out using cli. |
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@juliasilge thanks for your review. |
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I will have it in by later today, thanks.
…On Mon, Sep 27, 2021 at 2:18 PM Mauro Lepore ***@***.***> wrote:
@juliasilge <https://github.com/juliasilge> thanks for your review.
@jmobrien <https://github.com/jmobrien> when do you think you'll be able
to submit yours?
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I'm watching your discussion with the reviewers. Do you feel the ball is no longer on your court? If so I would ask the reviewers once again whether your changes sufficiently address any issues they raised in the review. Please confirm and I'll write a new comment with a We no longer review submissions to JOSS, but do mention the review -- I think you might get fast-tracking. |
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@maurolepore, yes, I think that I've addressed the reviewers concerns, and I'm waiting for their final approval. Thanks. |
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Dear reviewers, @jmobrien, do you have an estimate about when you might be able to confirm whether the changes made are sufficient to approve this package? @juliasilge, it seems your last concern (return visibly) has been addressed. Is there anything else you'd like to request or do you confirm the changes made are sufficient to approve this package? |
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Mauro, and Jeffrey, apologies--I've had a remarkable variety of unexpected
home and family issues come up over just this past week. I'm about to go
handle what I hope is the last of them, but I'll make it a priority to
finish everything tomorrow. Thanks for your patience.
…On Sat, Oct 30, 2021 at 8:37 PM Mauro Lepore ***@***.***> wrote:
Dear reviewers,
@jmobrien <https://github.com/jmobrien>, do you have an estimate about
when you might be able to confirm whether the changes made are sufficient
to approve this package?
@juliasilge <https://github.com/juliasilge>, it seems your last concern
(return visibly) has been addressed. Is there anything else you'd like to
request or do you confirm the changes made are sufficient to approve this
package?
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For me, the changes have addressed the issues I was interested in, and I approve it moving forward. ✅ |
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This looks much better. The modularization achieves a lot of the code streamlining I was hoping for, especially. I think I'm ready to approve, except for one maybe-bug and maybe 1 or 2 suggestions: 1. Small bug(?):
2. marking columns in Currently 3. Exclusions for Is the philosophy for having I'm not sure how you would want to approach an explicit feature for this, so I don't think adding one should hold up approval. Maybe something to consider for the future. Still, if this does fit the intended use for I think all of the above should be pretty trivial to implement, and ignore them if they don't fit your goals. Other than that, I think this is ready to go! Great work! |
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@jmobrien, @juliasilge, @maurolepore, I have a question for you all. |
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@JeffreyRStevens, I'm willing to help. Can you share the link to a branch or PR so I can pull it locally and reproduce the issue? |
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@maurolepore, many thanks! It is just on the main branch at https://github.com/JeffreyRStevens/excluder. |
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@JeffreyRStevens took a glance at it on your page. Just a thought, but I'm actually wondering if simplest solution to what you're facing may be to just make the The name being passed into (You could also do something similar using |
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Working with the current approach, might this work? I haven't tested it in a build and @JeffreyRStevens might know something better/more best-practices, but I think it's an option. keep_marked_column <- function(x, column, keep) {
col <- rlang::ensym(column)
if (identical(keep, FALSE)) {
x %>% dplyr::select(!!col)
} else {
x %>% dplyr::relocate(!!col)
}
} |
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My local experiment suggests that adding https://github.com/JeffreyRStevens/excluder/pull/5/files My suggestion is independent to the advice that @jmobrien shared. -- Also, while I'm here, you may simplify the keep <- FALSE
out <- "it's true"
if (!keep) {
out <- "it's false"
}
out
#> [1] "it's false"
keep <- TRUE
out <- "it's true"
if (!keep) {
out <- "it's false"
}
out
#> [1] "it's true"See https://speakerdeck.com/jennybc/code-smells-and-feels?slide=44 |
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Many thanks, @maurolepore and @jmobrien. I have merged @maurolepore's PR. I will tidy up a few things and then report back with a final summary soon. |
Is there anything else? |
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I have increased testing coverage with some additional tests. @jmobrien, does this meet your final approval? |
The way I interpret @jmobrien's comment is that he didn't need another round of review. You have addressed all his latest comments, so congratulations @JeffreyRStevens -- excluder is approved! And once again thanks @juliasilge and @jmobrien for your amazing work! I'll follow up soon with some more comments and instructions. |
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@ropensci-review-bot approve excluder |
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Approved! Thanks @JeffreyRStevens for submitting and @juliasilge, @jmobrien 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 @stefaniebutland in your reply. She 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. Please tell us what could be improved. Last but not least, you can volunteer as a reviewer via filling a short form. |
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@JeffreyRStevens I think the comment above includes everything you except two things:
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This is fantastic news! Many thanks @maurolepore, @juliasilge, and @jmobrien for the time and effort you have put into reviewing this package. It is soooo much better after your review, and I have learned a ton. |
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@maurolepore, I believe I have fully transitioned the package over to rOpenSci. The one remaining issue that I can't sort out is how to change the URL link in the About section of the GitHub page (https://github.com/ropensci/excluder) to https://docs.ropensci.org/excluder/. It is currently still linking to jeffreyrstevens.github.io/excluder even though I have changed all of the links in the repo. Do you know how to change this or will it just resolve on its own at some point? |
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@JeffreyRStevens I've made you admin of your repo again, so you should be able to make changes now. Admin rights are always lost during transfer, but we're working on a bot command for allowing package authors themselves to reclaim them. You'll get a smoother experience if you submit a second package. 😉 |
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Sorry @JeffreyRStevens and @maurolepore, my internet was out almost all of yesterday and I was dealing with that. But @maurolepore was correct about my stance. Just so it's explicit: I'm happy about the changes and am glad to see this approved! Congrats! |
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Many thanks @maelle and @maurolepore. I have now changed the URL. |
Date accepted: 2021-11-04
Due date for @juliasilge: 2021-09-20Submitting Author Name: Jeffrey Stevens
Submitting Author Github Handle: @JeffreyRStevens
Repository: https://github.com/JeffreyRStevens/excluder
Version submitted: 0.2.2
Submission type: Standard
Editor: @maurolepore
Reviewers: @juliasilge, @jmobrien
Due date for @jmobrien: 2021-09-20
Archive: TBD
Version accepted: TBD
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 falls under data munging because it processes data from Qualtrics or other online sources by checking for, marking, and excluding rows of data frames for common exclusion criteria (e.g., IP addresses outside of the United States or duplicate entries from the same location/IP address).
The target audience is data scientists using Qualtrics or other online systems to collect data from participants (e.g., Mechanical Turk workers). Ensuring good data quality from these participants can be tricky. For instance, while Mechanical Turk in theory screens workers based on location (e.g., if you want to restrict your participant pool to workers in the United States), this is not necessarily represented in the data. Finding the tools to screen for IP address location can be tricky, and this package simplifies checking for and excluding participants based on common data that Qualtrics reports such as geolocation, IP address, duplicate records from the same location, participant screen resolution, participant progress through the survey, and survey completion duration.
There are no similar packages to my knowledge. The {qualtRics} package at rOpenSci focuses on importing data from Qualtrics. The {MTurkR} package directly interfaces with the MTurk Requestor API, but the APIs have been deprecated and the package has been removed from CRAN.
Yes, it seems to comply with this guidance. Depending on the data that the user collects, there could be personally identifiable information accessed by this package. In particular, IP addresses that are recorded by Qualtrics can be processed with this package. Note that the package only works with personally identifiable information from data sets that already exist on the users' local file system, and the package does not collect or transmit data in any way. The package also includes a function
deidentify()that the user can use to strip location, IP address, language and even participant computer information (e.g., operating system, web browser, screen resolution) from the data frames to deidentify them.#454
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