We would like to thank the editors for their comments and suggestions. We have made considerable changes to both the submission as well as the package based on the feedback provided. Below we address and discuss each of the issues provided.
We have restructured the document and added text describing more specifically how a computational component list’s structure maps to the that of an R Markdown document. We have also added an example of the ld_cc_dendro() function earlier in the document to illustrate the correspondence between the list and the document.
The progression of the examples has also been revised so that the example builds progressively in complexity and sophistication. We hope that this change allows the reader to digest successively more elaborate concepts and functionality facilitated by the package. However, the goal of the package is to address the presentation of results in the context described. It is not meant to address how those results are derived. We have added emphasis to this in Section 5.
The advantages and limitations of both the automated reproducible document generation and package are given in Section 1 and the discussion in Section 6. Section 5 and 6 describe those situations for which the package has been shown useful.
The comment concerning the “monolithicness”" of the presentation is somewhat difficult to understand. We provide one example that progressively uses more of the packages functionality along with a simplified example where the package is being used for several clinical trials in both academia and industry. Furthermore, and earlier version of the manuscript was sufficient for analysts (intermediate R users) to create reproducible docucments for reporting to clinicians with little to no extra instruction.
The manuscript needs to be spell-checked and proofread. The manuscript in its current form is not suitable for review.
A print method should be added for listdown objects.
As replication material an R script, e.g., by purling the Rmd file and editing the R script output such that it is in a human readable form, needs to be provided.
supplemental-materials directory.The submitted package version and the version on CRAN are out of sync. An updated version should be submitted to JSS.
Appendix 1 can be omitted, but rather included in plain text form in a standalone file in the supplementary material.
For referring to subsections, do not use Subsection x.y, just Section x.y.
The code presented in the manuscript should not contain comments within the verbatim code. Instead the comments should be made in the normal LaTeX text.
For the code layout in R publications, we typically distinguish input/output using Sinput/Soutput (or equivalently CodeInput/CodeOutput). Unless there are special reasons to format it differently, the input should use the text width (up to 76 or 77 characters) and be indented by two spaces, e.g.,
As a reminder, please make sure that , and have been used for highlighting throughout the paper (including titles and references), except where explicitly escaped.
Springer-Verlag (not: Springer) ysis.” In Compstat, pp. 575–580. Springer.
Please make sure that all software packages are cite’d properly.
All references should be in title style.
Please make sure that the files needed to replicate all code/examples within the manuscript are included in a standalone replication script