[PRE REVIEW]: Tidytacos: An R package for analyses on taxonomic composition of microbial communities

[editorialbot]

Submitting author: !--author-handle-->@wsmets<!--end-author-handle-- (Wenke Smets) Repository: https://github.com/LebeerLab/tidytacos Branch with paper.md (empty if default branch): master Version: v0.3.0 Editor: !--editor-->@diazrenata<!--end-editor-- Reviewers: @kelly-sovacool, @david-barnett Managing EiC: Kristen Thyng

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (491.2 files/s, 283944.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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SVG                              2              0              0          16171
R                               25            637           1386           2277
Markdown                         5             53              0            989
TeX                              1             26              0            233
YAML                             5             28             17            149
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SUM:                            38            744           1403          19819
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 910

[editorialbot]

Failed to discover a valid open source license

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.7287/peerj.preprints.1318v1 may be a valid DOI for title: A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing
- 10.3390/microorganisms9091797 may be a valid DOI for title: Current applications of absolute bacterial quantification in microbiome studies and decision-making regarding different biological questions
- 10.1101/2022.08.16.504148 may be a valid DOI for title: Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome
- 10.1128/spectrum.02420-21 may be a valid DOI for title: Bacterial succession and community dynamics of the emerging leaf phyllosphere in spring
- 10.1128/spectrum.01755-22 may be a valid DOI for title: The Greenhouse Phyllosphere Microbiome and Associations with Introduced Bumblebees and Predatory Mites
- 10.3389/fmicb.2017.02372 may be a valid DOI for title: Comparing the healthy nose and nasopharynx microbiota reveals continuity as well as niche-specificity
- 10.1038/s41598-020-64705-x may be a valid DOI for title: Impact of a lactobacilli-containing gel on vulvovaginal candidosis and the vaginal microbiome
- 10.1128/msphere.00239-22 may be a valid DOI for title: Impacts of menstruation, community type, and an oral yeast probiotic on the vaginal microbiome
- 10.1128/msystems.00056-21 may be a valid DOI for title: Case-control microbiome study of chronic otitis media with effusion in children points at streptococcus salivarius as a pathobiont-inhibiting species
- 10.1016/j.xcrm.2022.100521 may be a valid DOI for title: Selective targeting of skin pathobionts and inflammation with topically applied lactobacilli
- 10.1186/s42523-019-0010-6 may be a valid DOI for title: The microbiome of the invertebrate model host Galleria mellonella is dominated by Enterococcus
- 10.2139/ssrn.3422481 may be a valid DOI for title: Lactobacilli have a niche in the human nose
- 10.3389/fnut.2022.916607 may be a valid DOI for title: Spontaneous riboflavin-overproducing Limosilactobacillus reuteri for biofortification of fermented foods
- 10.1016/j.isci.2021.103306 may be a valid DOI for title: Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples
- 10.1016/j.isci.2021.102978 may be a valid DOI for title: The nasal mutualist Dolosigranulum pigrum AMBR11 supports homeostasis via multiple mechanisms
- 10.1016/j.biortech.2022.128285 may be a valid DOI for title: Boosting aerobic microbial protein productivity and quality on brewery wastewater: Impact of anaerobic acidification, high-rate process and biomass age
- 10.1021/acs.est.9b06404.s001 may be a valid DOI for title: Return-sludge treatment with endogenous free nitrous acid limits nitrate production and N2O emission for mainstream partial nitritation/Anammox
- 10.1039/d1ew00525a may be a valid DOI for title: Piloting carbon-lean nitrogen removal for energy-autonomous sewage treatment
- 10.1016/j.biortech.2021.125996 may be a valid DOI for title: Oxygen control and stressor treatments for complete and long-term suppression of nitrite-oxidizing bacteria in biofilm-based partial nitritation/anammox
- 10.1038/s41564-023-01500-0 may be a valid DOI for title: A citizen-science-enabled catalogue of the vaginal microbiome and associated factors

INVALID DOIs

- None

[kthyng]

Hi @wsmets and thanks for your submission. Looking at your note and the package (forked from another repo and having progressed quite a bit from there but still tied to the original repo, and language in the readme "For most functions it is still very basic; this will be improved in the future") it sounds like this package isn't ready to be reviewed. When we ask for reviewer time it is expected that the package is robust and presented its best polished form, everything is ready for outside eyes. Do you need to take more time to wrap up some work before we would send this for review?

We also require a valid open source license.

[wsmets]

Thanks for your input. We've addressed all your points, but are still working on improving function descriptions. We will let you know when we are ready!

[kthyng]

@wsmets Thanks for your response. My comment was more of a general one asking you to consider if the package is mature enough for review rather than a list of points to address. What do you mean?

[wsmets]

Well, with addressing points I meant that we added an open source licence, removed the fork to the original repo, we improved function descriptions, and removed the comment from readme relating to function descriptions. We understand your concern, but are confident our package is mature enough for release into the world and therefore also for review.

[kthyng]

@wsmets Ok then, I will add this to our waitlist since all relevant editors are occupied. Thanks for your patience.

[kthyng]

I'm sorry for the continued delay — things are moving slowly through the holidays.

[kthyng]

We still don't have a relevant editor available, but we are expecting to on-board some new editors in the next few weeks so I expect this submission to be taking up by one of them.

[SWittouck]

Great @kthyng , thank you for the update!

[kthyng]

Hi @mikemahoney218 any chance this is near your wheelhouse to edit?

[kthyng]

@editorialbot invite @mikemahoney218 as editor

[editorialbot]

Invitation to edit this submission sent!

[mikemahoney218]

Sorry @kthyng and @SWittouck , I think this is a bit too far afield for me -- I don't have any experience with microbes and last touched a microscope during my second year of undergrad. I need to turn this one down unfortunately.

[kthyng]

@AoifeHughes might you be able to edit this submission?

[kthyng]

@editorialbot invite @AoifeHughes as editor

[editorialbot]

Invitation to edit this submission sent!

[kthyng]

@diazrenata Could you edit this submission?

[kthyng]

@editorialbot invite @diazrenata as editor

[editorialbot]

Invitation to edit this submission sent!

[diazrenata]

@editorialbot assign me as editor

[editorialbot]

Assigned! @diazrenata is now the editor

[diazrenata]

@david-barnett and @kelly-sovacool: Would you be available, and interested, in reviewing this JOSS submission on microbial community data?

[kelly-sovacool]

@diazrenata Yes, sign me up

[diazrenata]

@kelly-sovacool Fantastic - thank you!

[diazrenata]

@editorialbot add @kelly-sovacool as reviewer

[editorialbot]

@kelly-sovacool added to the reviewers list!

[david-barnett]

@david-barnett and @kelly-sovacool: Would you be available, and interested, in reviewing this JOSS submission on microbial community data?

@diazrenata I'm in 👍

[diazrenata]

@david-barnett Fantastic! I'll add you.

[diazrenata]

@editorialbot add @david-barnett as reviewer

[editorialbot]

@david-barnett added to the reviewers list!

[diazrenata]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6313.