knitrdata: A tool for creating standalone Rmarkdown publications and reports

dmkaplan2000 commented 4 years ago

Submitting Author: @dmkaplan2000 Repository: dmkaplan2000/knitrdata Version submitted: 0.2.1 Editor: TBD Reviewer 1: TBD
Reviewer 2: TBD
Archive: TBD
Version accepted: TBD

Paste the full DESCRIPTION file inside a code block below:

Package: knitrdata
Type: Package
Title: Data Language Engine for 'knitr' / 'rmarkdown'
Version: 0.2.1
Authors@R: c(
  person("David M.", "Kaplan", role = c("aut", "cre", "cph"), email = "dmkaplan2000@gmail.com", comment = c(ORCID = "0000-0001-6087-359X", github = "dmkaplan2000"))
  )
Description: Implements a data language engine for incorporating data directly in 
    'rmarkdown' documents so that they can be made completely standalone.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/dmkaplan2000/knitrdata
Imports: knitr, base64enc
Suggests: gpg, rmarkdown
RoxygenNote: 7.1.0
VignetteBuilder: knitr

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
- [X] data extraction
- [ ] data munging
- [X] data deposition
- [X] workflow automataion
- [ ] 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):

knitrdata extends the capabilities of knitr to allow one to create chunks containing text and binary data directly in Rmarkdown documents. This opens the possibility of creating entirely self-contained Rmarkdown document capable of communicating data, methods, code, formatting and interpretation in a single document.

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

All scientific researchers aiming for computational reproducibility and open science.

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

Not to my knowledge.

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.

Technical checks

Confirm each of the following by checking the box.

[X] I have read the guide for authors and rOpenSci packaging guide.

This package:

[X] does not violate the Terms of Service of any service it interacts with.
[X] has a CRAN and OSI accepted license.
[X] contains a README with instructions for installing the development version.
[X] includes documentation with examples for all functions, created with roxygen2.
[X] contains a vignette with examples of its essential functions and uses.
[X] has a test suite.
[ ] has continuous integration, including reporting of test coverage using services such as Travis CI, Coveralls and/or CodeCov.

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 automatically submit to the Journal of Open Source Software? If so:

JOSS Options

- [ ] The package has an **obvious research application** according to [JOSS's definition](https://joss.readthedocs.io/en/latest/submitting.html#submission-requirements). - [ ] The package contains a `paper.md` matching [JOSS's requirements](https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain) with a high-level description in the package root or in `inst/`. - [ ] The package is deposited in a long-term repository with the DOI: - (*Do not submit your package separately to JOSS*)

[ ] Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:

MEE Options

- [X] The package is novel and will be of interest to the broad readership of the journal. - [X] The manuscript describing the package is no longer than 3000 words. - [X] 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

[X] I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

annakrystalli commented 4 years ago

Hello @dmkaplan2000 and thanks for your submission.

It is hard to evaluate package functionality from the current README. Could you please add more detail on what the package is and what it does in the README so that we can assess whether the package is in scope or not?

dmkaplan2000 commented 4 years ago

Hi,

I have beefed up the readme a bit, but I am not sure exactly what you are looking for. The main piece of information that was probably missing is that the package is an extension to knitr to create standalone Rmarkdown documents that can provide a single source for the contents of a paper.

If you are not satisfied with the modifications I have made, would you mind giving me a bit of a better idea of what you are looking for in the README? In the current README, I provide a brief description of what the package does, how to install it and how to use it, pointing to the package vignette for more details. The vignette is pretty detailed, so I didn't want to duplicate too much information in the README.

Thanks, David

On 5/29/20 15:45, Anna Krystalli wrote:

Hello @dmkaplan2000 https://github.com/dmkaplan2000 and thanks for your submission.

It is hard to evaluate package functionality from the current README. Could you please add more detail on what the package is and what it does in the README so that we can assess whether the package is in scope or not?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ropensci/software-review/issues/379#issuecomment-635980710, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEOYJPYVPIZJ22PJA75GDDRT6377ANCNFSM4NLHPSOA.

annakrystalli commented 4 years ago

Hi @dmkaplan2000,

Ultimately at this stage of the review, the editor in chief should be able to get a feel for the scope and function of the package from the README. The problem with the vignette is that the package needs to be installed and the docs built locally to be viewed, unless you include a pkgdown online version of the docs. That's not meant to happen at this stage.

The README is important not just for us but for any user also. They will have a look at the README first. If they can't understand what the package does and how it is used they can't assess whether it's something they can make use of. They are unlikely to at that point install it and build the vignettes to find out more. The README is essentially the advertisement for your package. So anticipate what high-level information a user might want / need to know straight up. There are more specific recommendations in the rOpenSci packaging guide: https://devguide.ropensci.org/building.html#readme

The added demo definitely helps me understand how to use the package. I still have questions of what a good use case would be though and the full extent of its functionality. Eg for the example you give, I could just include something like the following and get a very similar result:

tibble::tribble(
  ~colA, ~colB,
  "a",   1,
  "b",   2,
  "c",   3
)
#> # A tibble: 3 x 2
#>   colA   colB
#>   <chr> <dbl>
#> 1 a         1
#> 2 b         2
#> 3 c         3

^{Created on 2020-05-29 by the reprex package (v0.3.0)}

Help me understand why or when in particular I should be considering your package instead.

dmkaplan2000 commented 4 years ago

Hi,

I just pushed a new version that includes several more examples that hopefully answer your questions.

Cheers, David

On 5/29/20 16:40, Anna Krystalli wrote:

Hi @dmkaplan2000 https://github.com/dmkaplan2000,

Ultimately at this stage of the review, the editor in chief should be able to get a feel for the scope and function of the package from the README. The problem with the vignette is that the package needs to be installed and the docs built locally to be viewed, unless you include a pkgdown online version of the docs. That's not meant to happen at this stage.

The README is important not just for us but for any user also. They will have a look at the README first. If they can't understand what the package does and how it is used they can't assess whether it's something they can make use of. They are unlikely to at that point install it and build the vignettes to find out more. The README is essentially the advertisement for your package. So anticipate what high-level information a user might want / need to know straight up. There are more specific recommendations in the rOpenSci packaging guide: https://devguide.ropensci.org/building.html#readme

The added demo definitely helps me understand how to use the package. I still have questions of what a good use case would be though and the full extent of its functionality. Eg for the example you give, I could just include something like the following and get a very similar result:

tibble::tribble( ~colA,~colB, "a",1, "b",2, "c",3 )

> # A tibble: 3 x 2

> colA colB

>

> 1 a 1

> 2 b 2

> 3 c 3

^Created on 2020-05-29 by the reprex package https://reprex.tidyverse.org (v0.3.0)

Help me understand why or when in particular I should be considering your package instead.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ropensci/software-review/issues/379#issuecomment-636010949, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEOYJODFVBZ6OI3SCNVDCDRT7CPXANCNFSM4NLHPSOA.

annakrystalli commented 4 years ago

Hi,

Thanks, that's much better! We'll discuss with the rest of the editors and get back to you shortly.

annakrystalli commented 4 years ago

Hello again @dmkaplan2000 .

After discussion, we decided that although interesting, the package is ultimately out of scope.

General tools for literate programming. (e.g., R markdown extensions) are out of scope and while exceptions might be made for extensions that have a very specific research application, we ultimately deemed knitrdata too general for the rOpenSci scope.

Thanks again for your submission.

dmkaplan2000 commented 4 years ago

Hi,

Thanks for your message. While I respect your decision, I do see among the list of packages on the rOpenSci website at least one package that has quite similar goals to mine - making use of knitr for science richer and more flexible - and that is a knitr extension, just like mine:

https://docs.ropensci.org/ezknitr/

There is also RefManageR which is for literate programming. I don't really see why those packages are within the ropensci scope, but mine is not.

Cheers, David

On 6/5/20 12:16, Anna Krystalli wrote:

Hello again @dmkaplan2000 https://github.com/dmkaplan2000 .

After discussion, we decided that although interesting, the package is ultimately out of scope.

General tools for literate programming. (e.g., R markdown extensions) are out of scope and while exceptions might be made for extensions that have a very specific research application, we ultimately deemed |knitrdata| too general for the rOpenSci scope.

Thanks again for your submission.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ropensci/software-review/issues/379#issuecomment-639388869, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEOYJNZ3WWJ6TQJFAVJNI3RVDAYVANCNFSM4NLHPSOA.

annakrystalli commented 4 years ago

Hi David,

Our scope definitions change over time. In the dev guide it does state that: “As this is a living document, these categories may change through time and not all previously onboarded packages would be in-scope today.”. This is the case with ezknitr which was reviewed 4 years ago.

As for RefManageR, it falls under the category "citation management and bibliometrics" which makes in scope.

I hope this clarifies our decision more.

Cheers

Anna

ropensci / software-review