ldecicco-USGS
commented
3 years ago Hi @dbarneche ! Thanks for your submission. I'll be the editor for this process. The "fit" for the package and rOpenSci looks great, a very suitable package.
The first step is the "editor checks". Once this is completed, I'll be asking around for reviewers.
Editor checks:
- [x] Documentation: The package has sufficient documentation available online (README, pkgdown docs) to allow for an assessment of functionality and scope without installing the package.
- [x] Fit: The package meets criteria for fit and overlap
- [x] Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
- [x] License: The package has a CRAN or OSI accepted license
- [x] Repository: The repository link resolves correctly
Editor comments
The standard devtools::check() resulted in:
> checking package dependencies ... NOTE
Suggests orphaned package: 'ggmap'
> checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' imports not declared from:
'dplyr' 'tidyr'
0 errors v | 0 warnings v | 2 notes xA standard tool we use is goodpractice::gp(), which resulted in:
Preparing: rcmdcheck
── GP dataaimsr ────────────────────────────────────────────────────
It is good practice to
✖ write unit tests for all functions, and all
package code in general. 80% of code lines are covered
by test cases.
R/aims_data.R:169:NA
R/aims_data.R:170:NA
R/aims_data.R:171:NA
R/aims_data.R:176:NA
R/aims_data.R:177:NA
... and 22 more lines
✖ avoid long code lines, it is bad for
readability. Also, many people prefer editor windows
that are about 80 characters wide. Try make your lines
shorter than 80 characters
R\aims_data.R:29:1
✖ fix this R CMD check NOTE: '::' or ':::'
imports not declared from: 'dplyr' 'tidyr'Coverage looks pretty good:
covr::package_coverage()
dataaimsr Coverage: 80.00%
R/zzz.R: 0.00%
R/aims_data.R: 80.00%
R/page_data.R: 88.24%
R/helpers.R: 90.32%
R/filter_values.R: 90.91%
R/aims_data_doi.R: 100.00%
R/expose_attributes.R: 100.00%You suggest tidyverse, which is typically not recommended:
https://www.tidyverse.org/blog/2018/06/tidyverse-not-for-packages/
Because some package installations will install all suggested packages, suggesting tidyverse could be a major undertaking for your users. Glancing though your vignettes, it looks like you could suggest just dplyr and tidyr, and probably purrr if you consider dropping the plyr::llply suggestion and replace it with purrr:mapdf.
On that note, plyr is a package you'll probably want to avoid if possible. If you are already steering your users towards tidyverse, I think it's not a stretch to drop the plyr suggestion and move to a purrr alternative.
Many of the help file (.Rd generated from roxygen) don't have working examples, which is always helpful for users.
Due to the nature of the package, you may want to have a look here for additional testing strategies: https://books.ropensci.org/http-testing/index.html
So with that being said, I'll start the process for finding reviewers, but I'd encourage you to consider the above comments in the meantime.
You can add the rOpenSci 'under review' badge to your README:
You may use rodev::use_review_badge(), rodev::use_review_badge(428). Badge URL is https://badges.ropensci.org/428_status.svg.
Full link should be:
[](https://github.com/ropensci/software-review/issues/428)
dbarneche
karthik
boshek
techisdead
ropensci-review-bot
Submitting Author: Diego R. Barneche (@dbarneche)
Other Authors: AIMS Datacentre team: (Jeffrey L. Sheehan, Greg Coleman, Mark Rehbein) Repository: https://github.com/open-AIMS/dataaimsr Version submitted: 1.0.2 Editor: @ldecicco-USGS Reviewers: @boshek Reviewers: @techisdead Archive: TBD
Version accepted: TBD
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.):
Explain how and why the package falls under these categories (briefly, 1-2 sentences):
dataaimsris an R package written to provide open access to decades of field measurements of atmospheric and oceanographic parameters around the coast of Australia, conducted by the Australian Institute of Marine Science (AIMS). The package communicates with the recently-developed AIMS Data Platform API via an API key.Who is the target audience and what are scientific applications of this package?
The data retrieval functions within
dataaimsrare designed to be useful to any researcher interested in long-term, instrument-based marine environmental data from tropical Australia.Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category? No because the datasets have been always maintained internally at AIMS. This is the first attempt of the institute to make it broadly available via an R package.
(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research? N/A
If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted. N/A
Technical checks
Confirm each of the following by checking the box.
This package:
Publication options
[X] 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? If so:
MEE Options
- [ ] 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. - [ ] 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