[REVIEW]: phylosmith: an R-package for reproducible and efficient microbiome analysis with phyloseq-objects

[whedon]

Submitting author: @schuyler-smith (Schuyler Smith)
Repository: https://github.com/schuyler-smith/phylosmith/
Version: 0.99.0
Editor: @karthik
Reviewer: @joey711
Archive: 10.5281/zenodo.3251024

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/4d4780ab16c487764ebe108fa6bcdc2c"><img src="http://joss.theoj.org/papers/4d4780ab16c487764ebe108fa6bcdc2c/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/4d4780ab16c487764ebe108fa6bcdc2c/status.svg)](http://joss.theoj.org/papers/4d4780ab16c487764ebe108fa6bcdc2c)

Reviewers and authors:

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.)

Reviewer instructions & questions

@joey711, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @karthik know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @joey711

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (0.99.0)?
• Authorship: Has the submitting author (@schuyler-smith) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @joey711 it looks like you're currently assigned as the reviewer for this paper 🎉.

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For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[karthik]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

OK DOIs

- 10.1371/journal.pone.0061217 is OK

MISSING DOIs

- https://doi.org/10.1371/journal.pcbi.1005871 may be missing for title: Ten simple rules for biologists learning to program
- https://doi.org/10.1038/nature11234 may be missing for title: Structure, function and diversity of the healthy human microbiome

INVALID DOIs

- None

[schuyler-smith]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

OK DOIs

- 10.1371/journal.pone.0061217 is OK
- 10.1371/journal.pcbi.1005871 is OK
- 10.1038/nature11234 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[schuyler-smith]

@karthik I just want to check to make sure that everything is set for this on my end, or if there is anything that I can/need to do. Thank you!

[karthik]

@schuyler-smith All good at your end. We're just waiting for the review to come in.

[karthik]

Pinged reviewer over email on 06/05

[joey711]

Functionality confirmed.

[joey711]

Also tested the co_occurrence function, which was re-implemented with Rcpp for performance. Can confirm the performance. I did not test accuracy.

Speaking of accuracy, that function in particular could use some unit tests to establish a baseline of analytical accuracy. A few other functional unit tests wouldn't hurt.

[joey711]

Main deficiencies to address:

• (1) Installation. The documented installation code is insufficient. The phyloseq package is released through bioconductor, and is not installed automatically as a dependency through the indicated devtools::install_github("phylosmith") command. More importantly, there are other deeply-implied dependencies related to the Rcpp compilation. I was able to resolve this with the following Dockerfile code, starting with an official bioconductor release image (see below).
• (2) Unit tests. There are none.

Dockerfile code:

FROM bioconductor/release_core2

# Install phyloseq 
RUN Rscript -e 'if(!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")}; BiocManager::install("phyloseq")'

RUN Rscript -e 'install.packages("devtools")'

RUN apt-get update && apt-get install -y --no-install-recommends libudunits2-dev
RUN Rscript -e 'install.packages("units")'

RUN Rscript -e 'install.packages("RcppEigen")'
RUN Rscript -e 'install.packages("RcppParallel")'
RUN Rscript -e 'install.packages("Rtsne")'

# ggforce
RUN apt-get install -y --no-install-recommends libgdal-dev
RUN Rscript -e 'install.packages("ggforce")'

# Install phylosmith
RUN Rscript -e 'devtools::install_github("schuyler-smith/phylosmith")'

# To run R from the command line:
# docker run -ti --user bioc bioconductor/release_core2 R
# docker run -e PASSWORD=rstudio1 -p 8787:8787 phylosmith

[joey711]

Otherwise looks good. @karthik I'm not sure what to do next? I think author will find it is in their own best interest to address these two minor issues. Afterward, it seems to meet all the criteria and I'm happy to get out of the way.

[schuyler-smith]

@joey711 Thank you for the review!
I was aware of the installation dependencies, from dealing with travis-ci, but wasn't sure how convoluted I should make the instructions vs let the user install dependencies on a need-to-need basis. I updated the instructions to include all the dependencies I included in the travis file, and the ones you listed for your installation. Hopefully it's clear and complete!

The unit tests I was admittedly not sure how to include, but had thought about. I am sure I have wasted a lot of my own time by not adding them sooner. I will look into including them!

[schuyler-smith]

@karthik I addressed the installation documentation issues, hopefully to a satisfactory level. I will hope to add the unit tests in the near future. If they are needed, please let me know and I will make it a priority.

Is there anything I need to do for the next steps?

[schuyler-smith]

@karthik also curious of what the next steps actually are, namely when doi's get assigned so that my labmate can cite. Thanks again for all the help!

[karthik]

Thanks @joey711 for this review! @schuyler-smith I'm just returning from a trip so I'll need a day to look over the changes and recommend next steps. I'll update this thread shortly.

[karthik]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[karthik]

@whedon check references

[whedon]

PDF failed to compile for issue #1442 with the following error:

Error reading bibliography ./paper.bib (line 15, column 9):
unexpected ","
expecting white space
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

[danielskatz]

The first ref should have DOI https://doi.org/10.1038/nature09944 added
The fourth ref should have DOI http://dx.doi.org/10.18637/jss.v040.i08 added

there could also be more...

[schuyler-smith]

@danielskatz you are correct, I found a couple other DOIs. I think i blindly trusted the google scholar bib citations. Hopefully it looks better.

[schuyler-smith]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[danielskatz]

ok, looks good now - thanks

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

OK DOIs

- 10.1371/journal.pone.0061217 is OK
- 10.18637/jss.v040.i08 is OK
- 10.1371/journal.pcbi.1005871 is OK
- 10.1038/nature11234 is OK
- 10.1038/nature07540 is OK
- 10.1038/nature09944 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#785

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#785, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01442 joss-papers#786
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01442
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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