cran-comments.md
In sahu27/sahu: Population Life Course Exposure to Health Effects Modeling

1) Citing a reference.

WE are in the process of putting a manuscript together for the methods used in the package. There is no authoratative source on the methods here that can be cited easily. Once the publication gets accepted, we will update the package with that information. In the meantime we have added a reference in description to a book that provides a good overview of PBPK modeling and its applications.

2) No copyright holder provided

Appropriate copyright holder has been added to the description file

This is a resubmission. Following are the responses to concerns raised by the reviewers

1) Is there some reference about the method you can add in the Description field in the form Authors (year) ?

*We currently do not have a publication for this package and so cannot add anything to the reference field

2)We see in one of your C files:

/* rapidPBPK.model.c for R deSolve package

If it is for deSolve, is it from their authors? Have you added authors and copyright information in Authors@R field?

*The C file is created by us specifically for the package. It is written in the format that deSolve package can accept to simulate it. However it is not from that package and hence we have not added authors from that package.

The copyright has been switched from GPL-3 to MIT. This is more suitable with the intention of the package and the liscense has been updated to reflect the new license

4) There are not enough examples in the Rd files.

*Examples have been added to every function that will be called directly by the user. Rest of the functions should not be called by the user directly and so no examples will be addded for those

This is a resubmission and makes the following changes 1) Examples have been added to main functions that launch shiny interfaces to run the analysis. They are defined as dontrun. 2) A sentence has been added to the function description and package description informing the users that all analysis can only be run using the user interface.

This is a resubmision and makes the following changes based on reviewer comments: 1) Space added after periods in package description 2) Acronyms and package names enclosed by single quotes instead of double quotes 3) Vignette added that explains basic setup needed to start using the package. Since all functions in the package are run through the interactive Shiny interface, the vignette does not actually execute any code.

This is a resubmission. The last version submitted had a period missing at the end of the description. Causing it to error out. This version is spell checked for accuracy.

This is a resubmission. In this version I have addressed two concerns raised during the previous review. Specifically

No packages are a part of the Depends field in the description. The namespace and imports were reorganised to ensure the package still works
The description has been updated.

This is a resubmission. In this version I have fixed the two warnings that were a part of the previous submission. This version now has

Import functions corrected to avoid replacing previously imported functions
Complete documentation for all exported functions.

local OS X install, R 3.5.0
local windows install
win-builder (devel and release)

0 errors | 2 warnings | 1 note

checking whether package 'plethem' can be installed ... WARNING Warning: replacing previous import 'shiny::runExample' by 'shinyjs::runExample' when loading 'plethem' Warning: replacing previous import 'shiny::dataTableOutput' by 'DT::dataTableOutput' when loading 'plethem' This is expected and agreeable since the function from DT improves upon the function from Shiny.
checking Rd \usage sections ... WARNING Certain functions have undocumented arguments. These functions are external modules that run the user interface. They need to be exported for the UI to work, but should not be called by the users. Their description and title explains that clearly.
checking package dependencies ... NOTE Depends: includes the non-default packages: 'shiny' 'shinyjs' 'ggplot2' 'V8' 'shinyBS' 'shinyWidgets' 'httk' 'miniUI' 'shinydashboard' 'rstudioapi' Adding so many packages to the search path is excessive and importing selectively is preferable.