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`rbioacc`: an `R`-package to analyze toxicokinetic data #499

Closed sandrinecharles closed 2 years ago

sandrinecharles commented 2 years ago

Reviewers: Submitting Author Name: Sandrine Charles Submitting Author Github Handle: !--author1-->@sandrinecharles<!--end-author1-- Other Package Authors Github handles: (comma separated, delete if none) @aursiber, @virgile-baudrot Repository: https://github.com/aursiber/rbioacc Version submitted: Submission type: Standard Editor: TBD Reviewers: TBD

Archive: TBD Version accepted: TBD Language: en

Package: rbioacc
Title: Inference and Prediction of ToxicoKinetic (TK) Models
Version: 1.1-0
Authors@R: c(
    person("Virgile", "Baudrot", role = "aut", email = "virgile.baudrot@posteo.net"),
    person("Sandrine", "Charles", role = "aut"),
    person("Ophélia", "Gestin", role = "ctb"),
    person("Mélina", "Kaag", role = "aut"),
    person("Christelle", "Lopes", role = "ctb"),
    person("Gauthier", "Multari", role = "ctb"),
    person("Alain", "Pavé", role = "ctb"),
    person("Aude", "Ratier", role = "aut"),
    person("Aurélie", "Siberchicot", role = c("aut", "cre"), email = "aurelie.siberchicot@univ-lyon1.fr")
    )
Description: The MOSAICbioacc application is a turnkey package providing bioaccumulation
    factors (BCF/BMF/BSAF) from a toxicokinetic (TK) model fitted to
    accumulation-depuration data. It is designed to fulfil the requirements
    of regulators when examining applications for market authorization of active
    substances. See Ratier et al. (2021) <doi:10.1101/2021.09.08.459421>.
URL: https://github.com/aursiber/rbioacc
BugReports: https://github.com/aursiber/rbioacc/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Biarch: true
Depends: 
    R (>= 3.5.0)
Imports: 
    ggplot2,
    methods,
    Rcpp,
    rstan (>= 2.18.1),
    rstantools (>= 2.1.1),
    ggmcmc,
    GGally,
    loo,
    stringr,
    stats,
    zoo
LinkingTo: 
    BH (>= 1.66.0),
    Rcpp,
    RcppEigen (>= 0.3.3.3.0),
    RcppParallel (>= 5.0.1),
    rstan (>= 2.18.1),
    StanHeaders (>= 2.18.0)
SystemRequirements: GNU make
Config/testthat/edition: 3
Suggests: 
    knitr,
    rmarkdown,
    testthat
VignetteBuilder: knitr

Scope

Technical checks

Confirm each of the following by checking the box.

This package:

Publication options

MEE Options - [X] 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. - [X] 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

ropensci-review-bot commented 2 years 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 2 years ago

Error (500). The editorcheck service is currently unavailable

mpadge commented 2 years ago

@sandrinecharles Sorry about that, we are trying to diagnose what went wrong. Checks should appear soon.

sandrinecharles commented 2 years ago

@mpadge no problem, this is not really urgent. By the way, I already submitted to MEE, and only after I saw that it is not recommended to do in this order. Sorry...

ropensci-review-bot commented 2 years ago

Checks for rbioacc (v1.1-0)

git hash: e91a4f12

Important: All failing checks above must be addressed prior to proceeding

Package License: MIT + file LICENSE

1. 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 C/C++ Header (0% in 1 files), C++ (7% in 4 files) and R (93% in 22 files) - 5 authors - 2 vignettes - 9 internal data files - 11 imported packages - 40 exported functions (median 9 lines of code) - 85 non-exported functions in R (median 11 lines of code) - 4 C++ functions (median 26 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 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 | 22| 83.6| | |files_src | 4| 87.0| | |files_inst | 1| 97.7| | |files_vignettes | 2| 85.7| | |files_tests | 16| 94.9| | |loc_R | 1199| 72.8| | |loc_src | 92| 15.0| | |loc_inst | 0| 0.0|TRUE | |loc_vignettes | 190| 47.4| | |loc_tests | 405| 70.7| | |num_vignettes | 2| 89.2| | |data_size_total | 7746| 69.5| | |data_size_median | 533| 60.7| | |n_fns_r | 125| 81.6| | |n_fns_r_exported | 40| 84.0| | |n_fns_r_not_exported | 85| 80.5| | |n_fns_src | 4| 12.4| | |n_fns_per_file_r | 3| 53.4| | |n_fns_per_file_src | 0| 0.0|TRUE | |num_params_per_fn | 2| 11.9| | |loc_per_fn_r | 11| 32.3| | |loc_per_fn_r_exp | 9| 19.2| | |loc_per_fn_r_not_exp | 11| 35.4| | |loc_per_fn_src | 26| 79.6| | |rel_whitespace_R | 24| 79.7| | |rel_whitespace_src | 30| 23.9| | |rel_whitespace_vignettes | 35| 49.2| | |rel_whitespace_tests | 30| 76.2| | |doclines_per_fn_exp | 18| 10.4| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 59| 69.7| | ---

1a. Network visualisation

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

2. goodpractice and other checks

Details of goodpractice and other checks (click to open)

--- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following notes: 1. checking installed package size ... NOTE installed size is 104.3Mb sub-directories of 1Mb or more: libs 103.7Mb 2. checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. R CMD check generated the following check_fails: 1. no_import_package_as_a_whole 2. rcmdcheck_gnu_make_required 3. rcmdcheck_reasonable_installed_size #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 80.24 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) The following functions have cyclocomplexity >= 15: function | cyclocomplexity --- | --- predict_manual | 35 predict.fitTK | 31 equations | 15 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 273 potential issues: message | number of times --- | --- Avoid 1:length(...) expressions, use seq_len. | 6 Avoid 1:ncol(...) expressions, use seq_len. | 21 Avoid trailing semicolons, they are not needed. | 4 Avoid using sapply, consider vapply instead, that's type safe | 10 Lines should not be more than 80 characters. | 121 Use <-, not =, for assignment. | 111

Package Versions

|package |version | |:--------|:---------| |pkgstats |0.0.3.82 | |pkgcheck |0.0.2.205 |

Editor-in-Chief Instructions:

Processing may not proceed until the items marked with :heavy_multiplication_x: have been resolved.

ldecicco-USGS commented 2 years ago

Hi @sandrinecharles! Thanks for the submission.

I'm getting clarification on why it's recommended to complete the rOpenSci review before submitting to MEE. I suspect it's make it easier to make breaking changes based on the rOpenSci review.

As for the issues with the checks....

Our automated checks didn't initially work on this submission because your tests take in the order of hours, and they simply timed-out. The maintainer of our system was able to adjust the settings and let the tests run to completion. It took over 8 hours and I guess many of the tests failed.

We also note that you don't have any automated continuous integrated checks, as is required for a submission. Generally for me, the easiest way to add this on a GitHub repo is to use GitHub actions. I'd recommend starting with usethis::use_github_actions: https://usethis.r-lib.org/reference/github_actions.html

You should be able to run our checks locally with pkgcheck::pkgcheck() to confirm submission-readiness.

Again, thanks for the submission, I'm looking forward to testing out the package. I'm interested in the topic for how we could use it with water quality concentration data of various contaminants in the environment. It would be really helpful to expand the documentation in the README and vignette to describe how to modify the workflow to new data, and more details on who the intended audience is of the package.

emilyriederer commented 2 years ago

Hi there, @sandrinecharles ! I wanted to follow up on this issue. Were you still interested in addressing some of @ldecicco-USGS 's feedback and moving towards the review process? I added the "holding" tag since there hasn't been much recent discussion on this issue, but happy to continue the conversation as you wish. Thanks!

sandrinecharles commented 2 years ago

Hi @emilyriederer! Yes, we still want to consider feedback, but the engineer that should be in charge of this has quick how lab. This work is thus temporally suspended.

emilyriederer commented 2 years ago

Thanks for the update, @sandrinecharles ! We will leave this on hold for now.

emilyriederer commented 2 years ago

Hi @sandrinecharles ! We are doing a sweep of stale review issues. Since this review has been open and inactive for so long, much may have changed including author, editor, and reviewer bandwidth and ever-evolving rOpenSci best practices. As such, I'm closing this issue. If you still have interest and capacity, we would welcome you to open a new submission issue!