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Software report:
github.com/AlDanial/cloc v 1.88 T=0.11 s (391.0 files/s, 198012.3 lines/s)
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SUM: 43 811 1491 19474
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 910
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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- None
MISSING DOIs
- 10.7287/peerj.preprints.1318 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
@kelly-sovacool, @david-barnett - Thank you for agreeing to review this submission! We'll continue the conversation on the review here.
In case it is helpful, here is the JOSS reviewers' guide: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html
Thank you both!
Hello all, 👋
I started to work through the reviewer checklist today. I have not completed my review of tidytacos but I have some questions and comments already.
Points 1 and 2 seem to me like practical issues worth addressing before proceeding with further review. Points 3 and 4 refer to issues with the manuscript and package documentation, which if addressed would make it easier to continue with a comprehensive and fair review of the package.
From the JOSS reviewer guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html#authorship
As part of the review process, you are asked to check whether the submitting author has made a ‘substantial contribution’ to the submitted software (as determined by the commit history)
Wenke Smets is the submitting author, but I did not find evidence of code contributions from this author.
From the commit history on github, I initially found only two commits from @wsmets, adding the manuscript for JOSS submission. https://github.com/LebeerLab/tidytacos/commits/dev?author=wsmets
I later found a couple more commits authored by "wsmets" but not linked to a github account (and so not easily searchable). What I found seemed to be small updates only to the documentation of several functions. https://github.com/LebeerLab/tidytacos/pull/17/commits/8ad017a838e93576823113e30b9a8fabf51e6a0a
@wsmets , is this a fair assessment of your contributions to tidytacos? If not, could you clarify what I missed?
It looks like the dev branch is quite active, and seems to include several features and documentation updates? It would be good to get clarity on the short term plans for this development. e.g. should this all be merged to master and tagged as a new version before further review?
From JOSS reviewer checklist :
State of the field: Do the authors describe how this software compares to other commonly-used packages?
From JOSS review criteria page:
Submissions that implement solutions already solved in other software packages are accepted into JOSS provided that they meet the criteria listed above and cite prior similar work. Reviewers should point out relevant published work which is not yet cited.
Currently the manuscript does not cite or mention similar work. tidytacos provides a generalist framework for handling data about the taxonomic composition of microbiomes, and facilitating the application of various relevant analyses and visualisations. Here are some R packages that address similar aims:
It would be great to see a few words added to the manuscript acknowledging related work. I think there is no need or space for an extensive comparison, but given that there are now so many related packages with overlapping functionality, it would be good to see some justification for the usefulness of tidytacos included in the paper. The philosophy section of the wiki claims that the simplicity of tidytacos' design provides some advantages over packages based around a more complex object structure e.g. phyloseq. I think this is a reasonable line of argument to expand upon in the paper.
From JOSS submission requirements:
Your software should be a significant contribution to the available open source software that either enables some new research challenges to be addressed or makes addressing research challenges significantly better (e.g., faster, easier, simpler).
I installed tidytacos from the master branch and ran all the wiki tutorial material locally.
https://github.com/LebeerLab/tidytacos/wiki/Tutorials
This tutorial started by demonstrating: making stacked bar charts; plotting observed ASV richness; making a 3D PCoA using Bray-Curtis dissimilarities computed on genus-level aggregated features. That worked fine, and it was mostly clear enough how I could make some simple changes to modify these procedures.
However, I have some suggestions for the documentation overall:
There appears to be a substantial amount of tidytacos functionality not covered by tutorial material. For example, there are several functions related to network analyses in the network.R file. These have minimal docs, without examples of use. Network analysis functionality is not mentioned in the manuscript either. I think there should be a more comprehensive structured overview available of the package's functionality available, to help guide new users. As well as adding tutorial material or other examples of use for more of the functionality, the authors could also consider structuring the reference page by theme, instead of listing all \~80 functions alphabetically.
In the Differential Abundance Analysis section of the tutorial wiki - the add_codifab and tacoplot_codifab functions are introduced. I do not recall seeing this approach for statistical analysis and visualisation before. It would be great to get a reference if this is an established method? Regardless, the method could be better described and justified in the documentation, as the details are currently unclear without looking at the underlying code. None of the codifab.R functionality is mentioned in the manuscript either.
@david-barnett, thank you for digging into the package and raising these points! @wsmets, could you respond to @david-barnett's questions (especially regarding package contributions, development plans, and documentation) before we proceed?
Hi @wsmets, just a quick re-up - have you had the chance to respond to @david-barnett's questions?
@david-barnett, @kelly-sovacool, and @diazrenata, thank you so much for taking the time to look into our tool and considering its publication! As a response to the first points raised by @david-barnett:
As for the limited contribution of the submitting author, I am actually new to GitHub and never tracked my changes to the package before. Besides the improvements to function descriptions, my greatest code contribution consists of four functions regarding the transformation of data to absolute abundances in case a spike was added. This is, to the best of our knowledge, an entirely new feature to the tools of amplicon sequencing analyses, but these four functions compared to the whole package remain a limited one. My other contributions consist more of giving user-based input, joining in meetings of package conceptualization, and supporting the organization and the writing of this publication, hence my role as submitting author. However, if these contributions are considered insufficient, we don’t mind changing the submitting author. @diazrenata, in that case, please let us know how we should proceed.
We are actively maintaining and expanding the package as user-based feedback comes in. We think the package can be reviewed as such, without considering the dev branch.
We think it is a valuable addition to mention existing work as you propose, and we are currently updating the manuscript to include the related packages.
We want to thank you for your patience while we are implementing your feedback in the package and the manuscript.
Hi @wsmets, thanks for the update! It sounds like you've made contributions to the code and manuscript that aren't captured by GitHub's tracking, which I completely understand! Please let us know when you're done making modifications and we can proceed with review.
Hi @wsmets, just checking in on progress on the revisions to tidytacos?
Hi @diazrenata, thanks for checking in. We are working on it, but alternately went on holiday, had lab retreat and conferences. We hope to get back to you in the next 2 weeks!
Great! Thanks for the update!
On Thu, Apr 25, 2024 at 1:59 AM Wenke @.***> wrote:
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Hi @diazrenata https://github.com/diazrenata, thanks for checking in. We are working on it, but alternately went on holiday, had lab retreat and conferences. We hope to get back to you in the next 2 weeks!
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Dear @david-barnett, @kelly-sovacool, and @diazrenata,
Sorry for the delay, but we have further addressed the points raised by @david-barnett:
We adapted the text to include some of the most similar packages:
“tidytacos
offers similar functionalities as packages such as microViz (@barnett2021microviz), mia (@ernst1mia), and phyloseq (@mcmurdie2013phyloseq), but was designed specifically to be very accessible to researchers with limited R and general programming experience. To achieve this, tidytacos was embedded in the tidyverse framework, which provides a style of programming that is very intuitive for new (but also experienced) programmers and is often the starting point for many people learning R. Tidytacos is also very easy to install, since it has only the main tidyverse packages as dependencies for the vast majority of its functionality. Finally, tidytacos also serves the needs of researchers who are looking to implement some rarely used or new visualizations and methods of analysis.”
We have added tutorials for the network.R functions and for data processing, which can be found here: https://lebeerlab.github.io/tidytacos/articles/index.html
The “codifab” functions used to find taxa that are more or less abundant in one condition versus another, are based on a rather old but solid principle of differences between logratios first proposed by Aitchison. It is for example also used by ANCOM. We have expanded the descriptions of the functions “add_codifab” and “tacoplot_codifab” to improve interpretation of the results and added Aitchisons original paper. We furthermore added to the text of the manuscript: “and differentially abundant taxa can be determined with a method based on the logratio differences introduced by @aitchison1982statistical”
Dear @david-barnett, @kelly-sovacool, and @diazrenata, did you have an opportunity to look at our revised submission already?
@david-barnett 👋 When you have a moment, could you look over the revisions to "tidytacos"?
@kelly-sovacool 👋 Just checking in on the status of your review here?
@david-barnett 👋 When you have a moment, could you look over the revisions to "tidytacos"?
Hi, I'm currently quite swamped, but I'll probably be able to have a look in the week beginning 15th July
@kelly-sovacool 👋 Just checking in on the status of your review here?
I plan on getting to this in the next couple weeks!
@kelly-sovacool and @david-barnett - just checking in to see how things are going and when you may have the chance to revisit tidytacos
?
I will try to look today
@editorialbot generate pdf
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@david-barnett Great! Thanks!
I've completed a second round of review, which is the first time I assessed the software itself in depth. I'm pleased with the additional tutorial material available on the pkgdown website, and I still find the base design of tidytacos quite beginner-friendly. I worked through the quick start, stacked barplots, and data processing tutorials, which gave me a good walkthrough of the core functionality of the package. I encountered a few bugs when experimenting with the tools introduced in the tutorials and have filed GitHub issues for these.
My main criticism at this point concerns function-level documentation. Many functions are minimally described on their help pages with no examples of use. Additionally, many functions are not covered in the tutorials, making them difficult to use without reading the underlying code.
I would also like to see a more detailed description/justification of the required structure of the taxonomy table, such as which ranks must be included and the special treatment given to particular variables (e.g., species, taxon_id, sequence). This info would help prevent confusion when users try to import their own data into the tidytacos format.
Lastly, it would be beneficial to get R CMD check passing without warnings on the CI. There are currently documentation-related warnings, which are ignored.
The comparison with phyloseq in your getting started guide is quite compelling! Consider adding some of the points about the disadvantages of phyloseq's design to the paper and/or the homepage? https://lebeerlab.github.io/tidytacos/articles/getting-started.html
@kelly-sovacool Just checking in on your review here?
tidytacos is a compelling new R package for microbial ecology and microbiome analysis. The paper is well-written and makes a great case for the need the package fills in this space and its usefulness for novices and advanced users alike.
I found the package was easy to install (although there were minor warnings), and the vignettes are overall helpful for demonstrating the package's capabilities. However, there is a critical lack of detail on how users can import their own raw data into the package, as the getting started vignette links users to the source code directly. This is a significant barrier to entry for novice users who wish to analyze their own data. Additionally, as noted by @david-barnett, the documentation lacks examples for many of the functions.
While conducting my review of the package I opened up several issues. I separated these into lists of "Blocking issues" and "Suggestions" below. I leave it up to the discretion of the authors to decide whether to address the suggestions, but in my view the blocking issues do need to be addressed before publication.
Overall, this is a great package that will be a valuable addition to the field, it just needs minor updates before it will be fully ready for publication.
Thank you both so much for taking the time to look into this package more thoroughly! Your feedback is very valuable in improving our package, and we'll let you know when we got through all your points.
Hi @wsmets - just checking in on how revisions are going?
Hi @diazrenata, it's going well, but slow, since we have a bunch of other work on our plates. We hope to be done in a week or two.
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Thanks again for diving into the package, @david-barnett and @kelly-sovacool and giving us constructive feedback. Also, we appreciate your appreciation. We have looked into all your points of advice. All GitHub issues were addressed and closed. In short we:
We hope this satisfies everyone and, if not, are happy to receive any feedback.
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:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
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 Archive: Pending
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Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)
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@kelly-sovacool & @david-barnett, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @diazrenata know.
✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨
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