Submission: chlorpromazineR

[eebrown]

Submitting Author: Eric Brown (@eebrown)
Repository: https://github.com/eebrown/chlorpromazineR
Version submitted: 0.1.0
Editor: @karthik
Reviewer 1: @chasemc
Reviewer 2: @fboehm
Archive: TBD
Version accepted: TBD

---

• Paste the full DESCRIPTION file inside a code block below:

Package: chlorpromazineR
Title: Convert Antipsychotic Doses to Chlorpromazine Equivalents
Version: 0.1.0
Authors@R: 
    c(person(given = "Eric",
             family = "Brown",
             role = c("aut", "cre"),
             email = "eb@ericebrown.com"),
      person(given = "Parita",
             family = "Shah",
             role = "aut"),
      person(given = "Julia",
             family = "Kim",
             role = "aut"))
Description: As different antipsychotic medications have different potencies,
    the doses of different medications cannot be directly compared. Various
    strategies are used to convert doses into a common reference so that
    comparison is meaningful. Chlorpromazine (CPZ) has historically been used
    as a reference medication into which other antipsychotic doses can be
    converted, as "chlorpromazine-equivalent doses". Using conversion keys
    generated from widely-cited scientific papers (Gardner et. al 2010
    <https://doi.org/10.1176/appi.ajp.2009.09060802>, Leucht et al. 2016
    <https://doi.org/10.1093/schbul/sbv167>), antipsychotic doses are converted
    to CPZ (or any specified antipsychotic) equivalents. The use of the package
    is described in the included vignette. Not for clinical use.
URL: https://github.com/eebrown/chlorpromazineR
BugReports: https://github.com/eebrown/chlorpromazineR/issues
Depends: R (>= 3.5)
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests: 
    knitr,
    rmarkdown,
    testthat,
    covr
VignetteBuilder: knitr

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.):

  • data retrieval
  • data extraction
  • database access
  • data munging
  • data deposition
  • reproducibility
  • geospatial data
  • text analysis

• Explain how and why the package falls under these categories (briefly, 1-2 sentences):

(See #306 - accepted presubmission inquiry) This package falls within "data munging" by virtue of its main feature - to convert antipsychotic doses into a common reference equivalent. It fosters reproducibility as the current practice is typically to reference the source paper without showing the conversion method (which if done manually, though simple, is prone to error). This improves accuracy and transparency.

• Who is the target audience and what are scientific applications of this package?

Researchers in psychiatry/neuroscience involving antipsychotic medications often need to calculate equivalent doses, which is why the papers describing such methods are widely cited. Yet, there is no R package that facilitates this.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?

None to our knowledge.

• If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

#306 @noamross

Technical checks

Confirm each of the following by checking the box. This package:

• does not violate the Terms of Service of any service it interacts with.
• has a CRAN and OSI accepted license.
• contains a README with instructions for installing the development version.
• includes documentation with examples for all functions.
• contains a vignette with examples of its essential functions and uses.
• has a test suite.
• has continuous integration, including reporting of test coverage using services such as Travis CI, Coveralls and/or CodeCov.

Publication options

• Do you intend for this package to go on CRAN?
• Do you wish to automatically submit to the Journal of Open Source Software? If so:

JOSS Options

• The package has an obvious research application according to JOSS's definition.
  • The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
  • The package is deposited in a long-term repository with the DOI:
  • (Do not submit your package separately to JOSS)

• 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)
• (Scope: Do consider MEE's Aims and Scope 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

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

[karthik]

Editor checks:

• Fit: The package meets criteria for fit and overlap
• Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
• License: The package has a CRAN or OSI accepted license
• Repository: The repository link resolves correctly
• Archive (JOSS only, may be post-review): The repository DOI resolves correctly
• Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?

---

Editor comments

👋 @eebrown! I'll be your editor on this submission. A goodpractice report on your packages comes out mostly clean! Once I assign reviewers, we'll take a deeper dive through your package. Here are some small housekeeping things to do in the meantime.

• Add a badge to your repo. It will update as the review progresses and change to 'reviewed' once accepted.

[![](https://badges.ropensci.org/307_status.svg)](https://github.com/ropensci/onboarding/issues/307)

I'd encourage you to register for an ORCID and add it to your description for each author. See more here

• There is a small typo in the README.

With this package, he hope:

he should be we?

I'll start looking for reviewers now. If you have suggestions on people who might be qualified to review this (but have no conflict of interest), feel free to suggest names.

[eebrown]

Thanks, @karthik! I've updated the DESCRIPTION and README files.

[eebrown]

Hi @karthik. Any luck finding any reviewers?

[karthik]

Eric: I'm very embarrassed to have dropped the ball on this amidst late May/June travels. I'm now actively seeking reviewers and will update the thread within a week. I'll make sure to keep this on a fast track the rest of the way. Again, apologies for my tardiness.

[karthik]

Assigning @chasemc as reviewer 1. Please see guidelines here: https://devguide.ropensci.org/reviewerguide.html

[karthik]

Still seeking reviewer #2

[karthik]

Assigning @fboehm as reviewer 2
Please see guidelines here: devguide.ropensci.org/reviewerguide.html

[chasemc]

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

Chase's note- My review and inserted links correspond to the chlorpromazineR repository at git commit: f8a0f152fc57ec0afb0c60910a9764dee780508f

• 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:

• A statement of need clearly stating problems the software is designed to solve and its target audience in README
  • https://github.com/eebrown/chlorpromazineR/blame/master/README.md#L5-L11
• Installation instructions: for the development version of package and any non-standard dependencies in README
  • https://github.com/eebrown/chlorpromazineR/blame/master/README.md#L19
• Vignette(s) demonstrating major functionality that runs successfully locally
  • https://github.com/eebrown/chlorpromazineR/blob/master/vignettes/walkthrough.Rmd
• Function Documentation: for all exported functions in R help
  • https://github.com/eebrown/chlorpromazineR/tree/master/man
• Examples for all exported functions in R Help that run successfully locally
  • https://travis-ci.org/eebrown/chlorpromazineR/builds/536968685#L1026
• Community guidelines including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

For packages co-submitting to JOSS

• NA

Functionality

• Installation: Installation succeeds as documented.

Session info for installation test:

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2        ps_1.3.0          prettyunits_1.0.2 rprojroot_1.3-2
 [5] digest_0.6.20     crayon_1.3.4      withr_2.1.2       assertthat_0.2.1
 [9] R6_2.4.0          backports_1.1.4   magrittr_1.5      rlang_0.4.0
[13] cli_1.1.0         curl_4.0          fs_1.3.1          remotes_2.1.0
[17] testthat_2.2.1    callr_3.3.1       desc_1.2.0        devtools_2.1.0
[21] tools_3.6.1       glue_1.3.1        pkgload_1.0.2     compiler_3.6.1
[25] processx_3.4.1    pkgbuild_1.0.4    sessioninfo_1.1.1 memoise_1.1.0
[29] usethis_1.5.1

• Functionality: Any functional claims of the software been confirmed.

  • Vignette and examples were reproduced. Also, the unit tests are sufficient to ensure the authors are recieving expected results (e.g. hard-coded expected results are tested against).

• Performance: Any performance claims of the software been confirmed.

• Automated tests: Unit tests cover essential functions of the package
  and a reasonable range of inputs and conditions. All tests pass on my local machine.

==> devtools::test()

Loading chlorpromazineR
Testing chlorpromazineR
v |  OK F W S | Context
v |  19       | checking functions behave [0.1 s]
v |  10       | CPZ-equivalent conversion
v |  15       | checking key manipulation functions

== Results =============================
Duration: 0.3 s

OK:       44
Failed:   0
Warnings: 0
Skipped:  0

• Packaging guidelines: The package conforms to the rOpenSci packaging guidelines

Final approval (post-review)

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

Estimated hours spent reviewing: 5 (partly getting used to/reading rOpenSci procedure)

• 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

Community guidelines

• Contribution guidelines are missing.

Packaging guidelines

• Not sure if this is in the guidelines but I would recommend removing the license section from the README as it is not self-sufficient and may confuse potential users.

• "Brief demonstration usage" should be added to the README

  • https://devguide.ropensci.org/building.html#readme
  • Can probably just copy the example from chlorpromazineR::to_cpz()

I would suggest removing "age" from the vignettes/examples, as it suggests it might be used in the conversion. Alternately, change to another "metadata" that obviously wouldn't be used in dosing decisions, or make it clear that age isn't accounted for in the conversion.

Error Messages

Consider making a clear error message for likely things like someone providing a route that isn't accepted:

> to_cpz(example_oral, ap_label = "antipsychotic", dose_label = "dose", 
+        route = "nope")

Error in check_ap(x, key = key, ap_label = ap_label, route = route, route_label = route_label) : 
  object 'notfound' not found

Code Style
There are some places that could benefit from writing code in clearer style, such as using spaces- like here (not required but rOpenSci does recommend http://r-pkgs.had.co.nz/r.html). And, while not incorrect, it would make the code easier trace if that same section was broken into steps and/or code comments were added.

Previous Similar Work
There has been some previous similar work, the Stefan Leucht paper cited in this package (https://dx.doi.org/10.1093%2Fschbul%2Fsbv167) links to an excel tool "Antipsychotic dose conversion website.xls" available from:
http://www.cfdm.de/indexab2e.html?option=com_content&task=view&id=15&Itemid=29
While the Leucht paper is cited as a source of data, the tool is not and probably should be.

Overall
Otherwise, the package was well laid out and had low dependencies and therefore limited worry about future breaking changes.