misc/README_Developers.md

In Novartis/xgxr: Exploratory Graphics for Pharmacometrics

xgxr

How to update/test/use package

• Developing the package: Run _Package_Setup.R. This will update the documentation, reinstall the package, and rebuild the vignette.
• Installing the package for use in your project: follow the directions below, also here. There are a few options.
• Option 1: Install directory from CRAN using install.packages("xgxr", lib = "./"). If you want it in your default library, you can delete the lib option.
• Option 2: Install directly from Github to a local repository with the following command: devtools::install_github("Novartis/xgxr", args = c('--library="./"')). If you want to install it in your default library path, you can delete the "args" option.

• Option 3: Download the package as a tar.gz file and then type: install.packages("xgxr_1.0.4.tar.gz", repos = NULL, lib = "./", type = "source")

  `` * **Last Resort Failsafe:** If you want to copy code from xGx exploratory graphics webpage but are unable to install thexgxrpackage, you can use an older version of the website that does not make use of thexgxr` package. http://opensource.nibr.com/xgx_v1

Your contribution

• If you will be helping to contribute, we make an effort to follow the tidyverse style guide.

Overview for how R packages (including this one) are organized

Functions

Functions are located in the "R" folder. When creating a new function, copy an existing one and follow the same format, with the documentation in the header When creating a new function, make sure to also add example code and some code to the vignette. * For the function to be visible after the package is loaded, make sure to have the @export line.

Datasets

Sample datasets are stored in the the data folder as ".Rda" files and also, for convenience, in the inst/extdata folder as csv files. Code for generating some of these datasets is stored in the data_create folder. And the Single Ascending Dose PKPD dataset came from [https://github.com/dpastoor/PKPDdatasets/blob/master/R/PKPDdatasets.R#L31]

Documentation

Documentation is located in the "man" folder. Do not edit this folder. Instead, edit the documentation within the function header and the documentation will be automatically created [as described here] (https://CRAN.R-project.org/web/packages/roxygen2/vignettes/roxygen2.html).

Vignettes

Vignettes are documents that show how a package can be used. They are located in the "vignettes" folder. Build them using the devtools::build_vignettes() function.

Description files

• The DESCRPTION file is where you list the dependencies on any other packages.
• The NAMESPACE file lists which packages are exported. It should not be edited because it's automatically generated by the devtools::document() command

Here are some links for learning more about packages

• Hilary Parker's brief intro
• Hadley Wickham's book
• Developing package with Rstudio
• Getting a package onto CRAN

Coveralls.io for testing

Visit coveralls.io if later, we get to the point where we want to look at unit test coverage.

Novartis/xgxr documentation built on Oct. 20, 2023, 4:35 a.m.