Referee report of "mathml: Translate R Expressions to MathML and LaTeX".

• Id: 2023-47

General

This article presents a recent package for typesetting equations differently than the usual way offered by markup syntax in Markdown. Its main advantage is that it allows typesetting some mathematical R code directly. Usually, with R Markdown, it builds on Pandoc support for Math and requires writing Math syntax directly, not converting R code to Math directly. This is new and interesting for documents heavily relying on math expressions for the code and the typeset content. The article is rather technical, which can make it quite scoped to interested readers, but not to any R Journal readers. It explains the technical implementation and then demos the usage through simple examples and a long case study. It is unfortunate that code can't be reproduced directly from the paper examples without accessing the companion R file. Overall, despite being highly technical in its form, I believe the usage and advantage are clear. Readers will know if they could be interested in becoming users too. Especially for PDF publication.

Detailed comments

• The article is quite technical about the package and how it works. It even requires some external software (Prolog), but it is not mentioned as a requirement (not even on the CRAN page or Github repo README). It would be better to make it clear that R alone is not enough.

  Response: In the revision, it is now made explicit that the package needs either SWI-Prolog installed on the system or R package rswipl.

• The technical background part is interesting, but I feel it is quite complicated for a direct user of the package reading this to understand how it will help. I wonder if it would not be better to leave technicals for after the "How to Use" part (called Package mathml in practice)

  Response: In the revision, the technical implementation has been moved to the suggested place.

• The introduction says: \> The R extension of the markdown language (Xie, Dervieux, and Riederer 2020) enables reproducible statistical reports with nice typesetting in HTML, Microsoft Word, and Latex. This is a bit confusing, as there is the rmarkdown package and also a markdown package. The reference points to the R Markdown Cookbook, so the reader can guess, but this is not the "R Markdown Definitive Guide," which would be the correct reference to rmarkdown package documentation. Citing the package itself would be the most accurate, I believe. I think this introduction can be made less confusing.

  Response: Thank you for pointing this out, this has been corrected in the revised manuscript.

• Paper is using "RMarkdown" whereas convention should probably be "R Markdown" (with a space) as found in the R Markdown Cookbook or R Markdown Definitive Guide (https://bookdown.org/yihui/rmarkdown-cookbook/software-info.html and https://bookdown.org/yihui/rmarkdown/software-info.html) rmarkdown (with lowercase and no space) is the package name. "R Markdown" is correctly used once in the conclusion. The usage should be made coherent throughout the article to use "R Markdown"

  Response: This has been corrected in the revised manuscript.

• I find it sometimes hard to follow the examples, as they are hidden in the source.

  > We can include the output in a RMarkdown document by specifying results = "asis" in the R code chunk of RMarkdown, as is done in all examples below.
  
  It is not really shown how, without probably looking at the article code source.
  It is assumed that the reader is a knowledgeable rmarkdown or knitr user.
  This can be made more clear if this is indeed the case.

  Response: It is now made clear that the target audience has some basic knowledge of rmarkdown and knitr. Moreover, a code snippet with a R code chunk is presented in the introduction.

  > The R function mathout() has been defined in the preamble of this article; it wraps a call to mathml() for HTML output and mathjax() for LaTeX output.
  
  Same here.
  The function `mathout()` is mentioned but not shown.
  We have to open the R source file to understand.
  This also assumes some form of expertise from the readers.
  This could be made more clear or point to more resources to help non-knowledgeable users understand.
  Overall, is it really worth adding those details without an example?
  This adds to the already-existing technical complexity.
  A reader could try reproducing the code by copying and pasting, but it won't work.
  (And I did try it.)

  Response: mathout() has been added to the list of functions of the package, so that copy-pasting the examples now works.

• As said earlier, a system requirement seems to be needed. Package won't work without it (it errors and also adds a warning about missing software). The CRAN page does not mention it either, and we derive the need for it from the dependency on Prolog. I think the article could be more specific about this.

  Response: It is actually sufficient to have R package rswipl installed or SWI-Prolog on the system. To our knowledge, it is not possible to give alternative system requirements in a package. However, we improved the error message from R package rolog to explicitly remind the user what is to be done if Prolog is not found.

• In conclusion, distill (Allaire et al. 2018) is cited as a package for displaying mathematical formulas. I am not sure to see the direct relation \> It extends the current features of R and existing packages for displaying mathematical formulas in R (Murrell and Ihaka 2000; Allaire et al. 2018). Maybe this needs checking to see if the reference is still applicable where it is.

  Response: The reviewer is correct, the reference is a bit far from the topic and has been removed.

Code

• A simple try of the package will lead to an error.

  ``` r
  library(mathml)
  #> Le chargement a nécessité le package : rolog
  #> Warning in fun(libname, pkgname): swipl not found in the PATH. Please set
  #> SWI_HOME_DIR accordingly or install R package rswipl.
  #> Warning in rolog::consult(system.file("pl/mathml.pl", package = pkgname)):
  #> swipl not found in the PATH. Please set SWI_HOME_DIR accordingly or install R
  #> package rswipl. term <- quote(pbinom(k, N, p)) term
  #> pbinom(k, N, p) mathjax(term)
  #> Warning in rolog::once(call("r2mathjax", term, expression(X), flags), options =
  #> list(preproc = list(rolog::preproc, : swipl not found in the PATH. Please set
  #> SWI_HOME_DIR accordingly or install R package rswipl.
  #> Error in t$X: $ operator is invalid for atomic vectors
  ```
  
  This is a bit unfortunate.
  Package improvement to make?
  Probably improving correct setup checks and error messages would be helpful.
  Adding more warnings about requirements to the article would be good.
  It seems package `rswipl` could be used to avoid installing Prolog, but I needed to search for this specifically from the error message shown.
  not a great user experience in my opinion, especially when discovering the MathML package while reading this article.

  Response: The welcome message of the underlying package rolog has been revised to make it more informative and helpful in case of missing requirements, as well as the package DESCRIPTION and the readme on github.

• Why is the mathout() function not part of the package? A reader will definitely want to try it while reading, and it would also make it easier to have this included. Using this mathml in a R Markdown document will make sense if the function offered by the package handles the different formats.

  Response: mathout() has been added to the list of functions of the package, so that copy-pasting the examples now works.

• I think the package should have functions that better support its usage in 'knitting' context. knitr provides tools like `knitr::asis_output()` and Custom Printing Method. These should be used so that calling mathml(term) in a chunk will work without knowing more about setting flags Currently, results = "asis" is needed, and mathml(term, flags = list(cat=TRUE)) needs to be used. This can definitely be improved with a knit_print() method.

  Response: A knit_print method has been added, as suggested.