An R package for the inference of physiologically-based toxicokinetics model
library("rstantools")
rstan_create_package(path = 'rPBK')
See further information here rstantools
Use this to add a new dependency
usethis::use_package("ggplot2")
usethis::use_package("testthat")
Additional dependencies used in the Vignette
usethis::use_package("loo", "Suggests")
Use this to add a data to be used in the package
usethis::use_data(dataCompartment4)
usethis::use_data(dataMaleGammarusSingle)
Use this to add a test function. ADD A TEST FILE TO EVERY NEW R FILE!
usethis::use_test("data.R")
usethis::use_test("dataPBK.R")
usethis::use_test("fitPBK.R")
usethis::use_test("plotFIT.R")
usethis::use_test("plotPPC.R")
usethis::use_test("predictPBK.R")
Add vignette
usethis::use_vignette("Examples")
remove files from building
usethis::use_build_ignore("[.]so", escape = FALSE)
usethis::use_build_ignore("[.]o", escape = FALSE)
Before 'Documentation' and 'Clear and Rebuild' and within 'Configure Build Tools...' untick 'use devtools package function if available'. Keep 'Generate Configuration with Roxygen'
- to load all internal function of a package during dev:
devtools::load_all()
To make the package lighter, we have to remove the vignettes: see file .Rbuildignore
Sometimes, there is an Error to recompile during development after change of .stan files.
A solution is to remove the rPBK
folder in R repository of the win-library (see the path written in the error message).
An other solution is to build the package from the terminal using R CMD -preclean INSTALL rPBK
from parent directory of rPBK
.
- S3 Object System: https://adv-r.had.co.nz/S3.html
- Google's R Style Guide: https://google.github.io/styleguide/Rguide.html
- testthat: https://github.com/r-lib/testthat
- covr: https://github.com/r-lib/covr
- to add a package
xxr
:usethis::use_package("xxr")
- to add data set
datar
:usethis::use_data(datar)
example(source) # defines the sourceDir() function
try(roxygen2::roxygenize(load_code = sourceDir), silent = TRUE)
roxygen2::roxygenize()
pkgbuild::compile_dll() # to preform a fake R CMD install
roxygen2::roxygenize() # to update the documentation
devtools::install()
Test and Check the package
devtools::test()
devtools::check()
then to build the package:
devtools::build()
If the archive produce (rPBK_X.Y.Z.tar.gz
) is in the workspace of the container (outside RPBK), then move the archive:
mv rPBK_X.Y.Z.tar.gz rPBK
Check as CRAN
R CMD check --as-cran
or from command line, but not working very well to be send to CRAN:
R CMD INSTALL --preclean --no-configure --build .
R CMD INSTALL --preclean --build .