Submission tidyqpcr - Quantitative PCR analysis in the tidyverse #470

ewallace · 2021-10-07T16:48:10Z

Date accepted: 2022-06-10
Submitting Author Name: Edward Wallace
Submitting Author Github Handle: @ewallace
Other Package Authors Github handles: @DimmestP
Repository: https://github.com/ewallace/tidyqpcr
Version submitted: 0.3.0
Submission type: Standard
Editor: @jooolia
Reviewers: @kelshmo

Due date for @kelshmo: 2021-11-19

Archive: TBD
Version accepted: TBD

Paste the full DESCRIPTION file inside a code block below:

Package: tidyqpcr
Type: Package
Title: Quantitative PCR Analysis with the Tidyverse
Version: 0.3
Authors@R: c(person("Edward", "Wallace", email = "Edward.Wallace@ed.ac.uk", role = c("aut", "cre")),
             person("Sam", "Haynes", email = "samuel.haynes10@gmail.com", role = c("ctb")))
Description: This package is for reproducible quantitative PCR (qPCR) analysis using packages from the tidyverse, notably dplyr and ggplot2. It normalizes (by ddCq), summarizes, and plots pre-calculated Cq data, and plots raw amplification and melt curves from Roche LightCycler machines. It does NOT (yet) calculate Cq data from amplification curves.
Depends: 
    R (>= 3.1.0),
    tibble,
    tidyr
Imports:
    rlang,
    dplyr,
    ggplot2,
    readr,
    forcats,
    assertthat,
    lifecycle
Suggests: knitr, 
    rmarkdown, 
    tidyverse,
    cowplot,
    testthat
VignetteBuilder: knitr
License: Apache License 2.0 + file LICENSE
LazyData: true
RoxygenNote: 7.1.1
Encoding: UTF-8
URL: https://github.com/ewallace/tidyqpcr, https://ewallace.github.io/tidyqpcr/
BugReports: https://github.com/ewallace/tidyqpcr/issues
Language: en-GB

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
- data munging
- data deposition
- 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):

tidyqpcr is an R package that empowers scientists to conduct reproducible, flexible, and best-practice compliant quantitative polymerase chain reaction (qPCR) analysis.

tidyqpcr offers a standardised user interface and structure for qPCR analysis, within the tidyverse paradigm of spreadsheet-like rectangular data frames and generic functions that build up complex analyses in a series of simple steps.

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

Any molecular biologist or bioinformatician who needs to design or analyse a qPCR experiment.

Quantitative PCR is among the most common techniques in biological and biomedical re-
search, used for the quantification of DNA and RNA.

Standardised and open-source qPCR analysis pipelines will encourage best-practices in the reporting of qPCR results, improve the evaluation of qPCR experiments and ultimately lead to increased confidence in conclusions based on qPCR data.

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

Some open-source libraries for qPCR analysis are available, notably qpcR (Spiess, 2018) and pcr (Ahmed & Kim, 2018). qpcR is a feature rich qPCR analysis package relying on an object-oriented approach using S4 classes. pcr is a less extensive qPCR analysis package based on the tidyverse suite of generic data-science tools using the paradigm of tidy data (spreadsheet-like rectangular data frames). However, available packages either assume extensive prior R knowledge, overlook best-practices in qPCR experiments, or lack extensive documentation. There remains a need for a qPCR analysis package that integrates with the user-friendly tidyverse, encourages the use of MIQE best-practice compliant experimental design, and provides detailed example analysis pipelines as R vignettes.

(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?
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.

We presented tidyqpcr on the rOpenSci discussion page which Stefanie Butland and Sean Hughes kindly responded to. In response to @seaaan ’s comments we improved the vignettes, stuck to a consistent function naming convention and added functionality to calculate ddCq. We intend to add further functionality in future versions including: support for absolute quantification, support for multiple targets per well, and enabling the use of the plater package.

In email correspondence with Stefanie, we believe Julia Gustavsen would be a perfect editor for our project as they reviewed Sean’s plater package. As for reviewers, we think someone with experience in conducting assays for RNA/DNA quantification and normalisation would be of benefit because of the emphasis on experimental design best-practices.

Technical checks

Confirm each of the following by checking the box.

I have read the guide for authors and rOpenSci packaging guide.

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, created with roxygen2.
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 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?
Do you wish to submit an Applications Article about your package to Journal of Open Source Software?

We have included a paper.md file in the repository as per JOSS instructions to authors.

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.

The text was updated successfully, but these errors were encountered:

ropensci-review-bot · 2021-10-07T16:48:11Z

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

ropensci-review-bot · 2021-10-07T16:48:16Z

🚀

Editor check started

👋

ropensci-review-bot · 2021-10-07T16:57:05Z

Checks for tidyqpcr (v0.3)

git hash: 4bce0332

✔️ Package name is available
✖️ does not have a 'CITATION' file.
✔️ has a 'codemeta.json' file.
✖️ does not have a 'contributing' file.
✔️ uses 'roxygen2'.
✔️ 'DESCRIPTION' has a URL field.
✔️ 'DESCRIPTION' has a BugReports field.
✔️ Package has at least one HTML vignette
✖️ These functions do not have examples: [calculate_deltacq_bysampleid.Rd].
✖️ Package has no continuous integration checks.
✔️ Package coverage is 79.7%.
✔️ R CMD check found no errors.
✔️ R CMD check found no warnings.

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

Package License: Apache License 2.0 + 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 R (100% in 6 files) and
1 authors
4 vignettes
no internal data file
7 imported packages
28 exported functions (median 8 lines of code)
28 non-exported functions in R (median 11 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	6	35.8
files_vignettes	4	94.3
files_tests	5	78.5
loc_R	339	32.0
loc_vignettes	1014	93.7
loc_tests	368	65.9
num_vignettes	4	96.0	TRUE
n_fns_r	56	52.0
n_fns_r_exported	28	74.9
n_fns_r_not_exported	28	40.8
n_fns_per_file_r	5	60.4
num_params_per_fn	3	33.1
loc_per_fn_r	10	40.0
loc_per_fn_r_exp	8	19.7
loc_per_fn_r_not_exp	11	51.8
rel_whitespace_R	10	22.3
rel_whitespace_vignettes	35	97.8	TRUE
rel_whitespace_tests	23	86.5
doclines_per_fn_exp	36	42.9
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	10	24.0

1a. Network visualisation

Interactive network visualisation of calls between objects in package can be viewed by clicking here

2. `goodpractice` and other checks

Details of goodpractice and other checks (click to open)

3b. `goodpractice` results

`R CMD check` with rcmdcheck

R CMD check generated the following notes:

checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE
installed size is 12.7Mb
sub-directories of 1Mb or more:
doc 2.8Mb
extdata 9.7Mb
checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
Apache License 2.0 + file LICENSE

R CMD check generated the following check_fails:

no_description_depends
rcmdcheck_not_permitted_license_restrictions
rcmdcheck_hidden_files_and_directories
rcmdcheck_reasonable_installed_size

Test coverage with covr

Package coverage: 79.72

Cyclocomplexity with cyclocomp

No functions have cyclocomplexity >= 15

Static code analyses with lintr

lintr found the following 85 potential issues:

message	number of times
Lines should not be more than 80 characters.	85

Package Versions

package	version
pkgstats	0.0.2.3
pkgcheck	0.0.2.53

Editor-in-Chief Instructions:

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

noamross · 2021-10-08T16:39:36Z

@ropensci-review-bot assign @jooolia as editor

ropensci-review-bot · 2021-10-08T16:39:38Z

Assigned! @jooolia is now the editor

DimmestP · 2021-10-13T15:17:32Z

@ropensci-review-bot help

ropensci-review-bot · 2021-10-13T15:17:33Z

Hello @DimmestP, here are the things you can ask me to do:


# List all available commands
@ropensci-review-bot help

# Show our Code of Conduct
@ropensci-review-bot code of conduct

DimmestP · 2021-10-13T15:29:17Z

Helpful!
@noamross or @jooolia

Hello!! Thank you for spending your time helping us improve tidyqpcr.

I have added a few commits to the main tidyqpcr repo that I think solve the remaining issues. How can I get the review bot to check again?

What is the process that it uses to check for function examples? I ran covr::package_coverage(type = "examples") locally and got 83.96% coverage. The 'missing' examples are from functions that are variations of other functions (which are documented with examples) and are linked together with a @describeIn tag. See scale_x_log2nice and scale_x_log10nice in the plot_helpers.R file.

jooolia · 2021-10-15T08:57:08Z

@ropensci-review-bot check package

ropensci-review-bot · 2021-10-15T08:57:09Z

Thanks, about to send the query.

ropensci-review-bot · 2021-10-15T08:57:12Z

🚀

Editor check started

👋

ropensci-review-bot · 2021-10-15T08:57:46Z

Checks for tidyqpcr (v0.3)

git hash: 737cca43

✔️ Package name is available
✔️ has a 'CITATION' file.
✔️ has a 'codemeta.json' file.
✔️ has a 'contributing' file.
✔️ uses 'roxygen2'.
✔️ 'DESCRIPTION' has a URL field.
✔️ 'DESCRIPTION' has a BugReports field.
✔️ Package has at least one HTML vignette
✔️ All functions have examples.
✔️ Package has continuous integration checks.
✔️ Package coverage is 79.7%.
✔️ R CMD check found no errors.
✔️ R CMD check found no warnings.

Package License: Apache License 2.0 + 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 R (100% in 6 files) and
1 authors
4 vignettes
no internal data file
7 imported packages
28 exported functions (median 8 lines of code)
28 non-exported functions in R (median 11 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	6	35.8
files_vignettes	0	0.0	TRUE
files_tests	5	78.5
loc_R	339	32.0
loc_tests	368	65.9
num_vignettes	4	96.0	TRUE
n_fns_r	56	52.0
n_fns_r_exported	28	74.9
n_fns_r_not_exported	28	40.8
n_fns_per_file_r	5	60.4
num_params_per_fn	3	33.1
loc_per_fn_r	10	40.0
loc_per_fn_r_exp	8	19.7
loc_per_fn_r_not_exp	11	51.8
rel_whitespace_R	9	19.3
rel_whitespace_tests	23	86.5
doclines_per_fn_exp	48	60.4
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	10	24.0

1a. Network visualisation

Interactive network visualisation of calls between objects in package can be viewed by clicking here

2. `goodpractice` and other checks

Details of goodpractice and other checks (click to open)

3a. Continuous Integration Badges

GitHub Workflow Results

name	conclusion	sha	date
.github/workflows/draft-pdf.yml	success	737cca	2021-10-13
fair-software	success	737cca	2021-10-13
R-CMD-check	success	737cca	2021-10-13

3b. `goodpractice` results

`R CMD check` with rcmdcheck

R CMD check generated the following notes:

checking installed package size ... NOTE
installed size is 12.7Mb
sub-directories of 1Mb or more:
doc 2.8Mb
extdata 9.7Mb
checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
Apache License 2.0 + file LICENSE
checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
CITATION.cff
Most likely ‘inst/CITATION’ should be used instead.

R CMD check generated the following check_fails:

no_description_depends
rcmdcheck_not_permitted_license_restrictions
rcmdcheck_citation_file_at_standard_place
rcmdcheck_reasonable_installed_size

Test coverage with covr

Package coverage: 79.72

Cyclocomplexity with cyclocomp

No functions have cyclocomplexity >= 15

Static code analyses with lintr

lintr found the following 94 potential issues:

message	number of times
Lines should not be more than 80 characters.	94

Package Versions

package	version
pkgstats	0.0.2.16
pkgcheck	0.0.2.86

Editor-in-Chief Instructions:

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

jooolia · 2021-10-15T10:25:03Z

Hi @DimmestP,
I re-ran the checks and all looks good. I will start looking for reviewers.

Regarding the examples, there is no pre-set % that we require (as far as I know and from re-reading the packaging guide), right now it is stated as "Include extensive examples in the documentation", so I will let the reviewers comment on whether they think some functions are missing examples or not.

Thanks! Julia

mpadge · 2021-10-15T10:30:06Z

@jooolia The above check is all ✔️, including

✔️ All functions have examples.

jooolia · 2021-10-15T10:37:28Z

ha you are right @mpadge! thanks for pointing that out.

jooolia · 2021-10-29T16:42:25Z

@ropensci-review-bot add @kelshmo to reviewers

ropensci-review-bot · 2021-10-29T16:42:27Z

@kelshmo added to the reviewers list. Review due date is 2021-11-19. Thanks @kelshmo for accepting to review! Please refer to our reviewer guide.

ropensci-review-bot · 2021-10-29T16:42:29Z

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

jooolia · 2021-11-19T10:19:34Z

@ropensci-review-bot add @wolski to reviewers

ropensci-review-bot · 2021-11-19T10:19:37Z

@wolski added to the reviewers list. Review due date is 2021-12-10. Thanks @wolski for accepting to review! Please refer to our reviewer guide.

ewallace · 2022-06-08T13:38:29Z

Hi @jooolia,

Thank you for this thorough check, it has helped a lot and given us more opportunity for improvements. @DimmestP and I have addressed these:

plot_helpers. Given the minimal use of these functions and that their capabilities are now in the scales package, we removed these in pull request https://github.com/ewallace/tidyqpcr/pull/183
URLs. Fixed in https://github.com/ewallace/tidyqpcr/pull/184
Tests. Addressed in https://github.com/ewallace/tidyqpcr/pull/185
dplyr joins. Addressed in https://github.com/ewallace/tidyqpcr/pull/182

We hope that's everything for the review process? Let us know.

Also we are open to suggestions as to whether it is better to share via CRAN or via Bioconductor. I really don't know.

jooolia · 2022-06-10T07:02:09Z

@ropensci-review-bot submit review #470 (comment) time 12

jooolia · 2022-06-10T07:27:57Z

Dear @ewallace and @DimmestP,
Thanks for all your hard work. 👍 This looks good to me. Since @kelshmo has already approved I will approve this and we can move forward with the next steps.

Regarding CRAN vs. Bioconductor, my personal opinion is that it depends on your targeted users, dependencies and perhaps future plans for the package. Many rOpenSci packages are on CRAN. Right now I am aware (thanks to @maelle 's help) of two rOpenSci pacakges that are on Bioconductor: https://docs.ropensci.org/genbankr/ and https://github.com/YuLab-SMU/treeio . Both CRAN and Bioconductor have their own "gotchas" as detailed in dev guide sections 1.16 and 1.17 https://devguide.ropensci.org/building.html?q=bioconductor#bioconductor-gotchas

jooolia · 2022-06-10T07:28:33Z

@ropensci-review-bot approve tidyqpcr

ropensci-review-bot · 2022-06-10T07:28:35Z

Approved! Thanks @ewallace for submitting and @kelshmo for your reviews! 😁

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.
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Fix all links to the GitHub repo to point to the repo under the ropensci organization.
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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.

Last but not least, you can volunteer as a reviewer via filling a short form.

ewallace · 2022-06-15T14:00:11Z

@ropensci-review-bot finalize transfer of tidyqpcr

ropensci-review-bot · 2022-06-15T14:00:16Z

Transfer completed.
The tidyqpcr team is now owner of the repository and the author has been invited to the team

ewallace · 2022-06-15T14:37:28Z

ewallace · 2022-06-22T10:12:54Z

@ropensci-review-bot give codecov access to ropensci/tidy

ropensci-review-bot · 2022-06-22T10:12:55Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@ropensci-review-bot help

mpadge · 2022-06-22T10:34:56Z

@ewallace We're just tring to find out why help isn't working there. Regardless, codecov access should be automatic with your first push to the repo in the ropensci org. I checked there and it's all set up properly. We'll fix the help issue in the meantime. Thanks.

ewallace · 2022-06-22T10:36:42Z

Thank you @mpadge!

I was sufficiently confused to put a discussion point on adding codecov access to the dev guide and/or making it easier to know who to ask for help https://discuss.ropensci.org/t/staff-admin-team-codecov/2982

(apologies, I deleted the failed
@ropensci-review-bot help
after deciding it wasn't working)

maelle · 2022-06-23T11:18:46Z

@ropensci-review-bot help

ropensci-review-bot · 2022-06-23T11:18:47Z

Hello @maelle, here are the things you can ask me to do:


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ewallace changed the title ~~tidyqpcr - Quantitative PCR analysis in the tidyverse~~ Submission tidyqpcr - Quantitative PCR analysis in the tidyverse Oct 7, 2021

ewallace mentioned this issue Oct 7, 2021

Draft rOpenSci submission ropensci/tidyqpcr#116

Closed

25 tasks

noamross mentioned this issue Oct 8, 2021

pkgcheck misses GitHub actions CI checks ropensci-review-tools/pkgcheck#87

Closed

ropensci-review-bot assigned jooolia Oct 8, 2021

ropensci-review-bot added the 1/editor-checks label Oct 8, 2021

jooolia added 2/seeking-reviewer(s) package topic:reproducibility and removed 1/editor-checks labels Oct 15, 2021

mpadge mentioned this issue Nov 2, 2021

canaper: Categorical Analysis of Neo- And Paleo-Endemism in R #475

Closed

11 tasks

jooolia added 4/review(s)-in-awaiting-changes and removed 5/awaiting-reviewer(s)-response labels Jun 3, 2022

This was referenced Jun 3, 2022

Fix URLs ropensci/tidyqpcr#179

Closed

Clean up tests ropensci/tidyqpcr#180

Closed

Specify by argument in joins ropensci/tidyqpcr#181

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ewallace mentioned this issue Jun 8, 2022

Response to jooolia 3rd review 2022-06-03 ropensci/tidyqpcr#186

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jooolia added 5/awaiting-reviewer(s)-response and removed 4/review(s)-in-awaiting-changes labels Jun 10, 2022

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ropensci-review-bot closed this as completed Jun 10, 2022

arfon mentioned this issue Jun 26, 2022

[REVIEW]: tidyqpcr: Quantitative PCR analysis in the tidyverse. openjournals/joss-reviews#4507

Closed

Submission tidyqpcr - Quantitative PCR analysis in the tidyverse #470

Submission tidyqpcr - Quantitative PCR analysis in the tidyverse #470

Comments

ewallace commented Oct 7, 2021 • edited by ropensci-review-bot Loading

Scope

Technical checks

Publication options

Code of conduct

ropensci-review-bot commented Oct 7, 2021

ropensci-review-bot commented Oct 7, 2021

ropensci-review-bot commented Oct 7, 2021

Checks for tidyqpcr (v0.3)

1. Statistical Properties

1a. Network visualisation

2. goodpractice and other checks

3b. goodpractice results

R CMD check with rcmdcheck

Test coverage with covr

Cyclocomplexity with cyclocomp

Static code analyses with lintr

Editor-in-Chief Instructions:

noamross commented Oct 8, 2021

ropensci-review-bot commented Oct 8, 2021

DimmestP commented Oct 13, 2021

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jooolia commented Oct 15, 2021

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ropensci-review-bot commented Oct 15, 2021

Checks for tidyqpcr (v0.3)

1. Statistical Properties

1a. Network visualisation

2. goodpractice and other checks

3a. Continuous Integration Badges

3b. goodpractice results

R CMD check with rcmdcheck

Test coverage with covr

Cyclocomplexity with cyclocomp

Static code analyses with lintr

Editor-in-Chief Instructions:

jooolia commented Oct 15, 2021

mpadge commented Oct 15, 2021

jooolia commented Oct 15, 2021

jooolia commented Oct 29, 2021

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jooolia commented Nov 19, 2021

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ewallace commented Jun 8, 2022

jooolia commented Jun 10, 2022

jooolia commented Jun 10, 2022

jooolia commented Jun 10, 2022

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ewallace commented Jun 15, 2022

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ewallace commented Jun 22, 2022

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mpadge commented Jun 22, 2022

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maelle commented Jun 23, 2022

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ewallace commented Oct 7, 2021 •

edited by ropensci-review-bot

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2. `goodpractice` and other checks

3b. `goodpractice` results

`R CMD check` with rcmdcheck

DimmestP commented Oct 13, 2021 •

edited

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2. `goodpractice` and other checks

3b. `goodpractice` results

`R CMD check` with rcmdcheck

ewallace commented Jun 15, 2022 •

edited

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ewallace commented Jun 22, 2022 •

edited

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