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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
::use_package("ggplot2")
usethis::use_package("testthat") usethis
Additional dependencies used in the Vignette
::use_package("loo", "Suggests") usethis
Use this to add a data to be used in the package
::use_data(dataCompartment4)
usethis::use_data(dataMaleGammarusSingle) usethis
Use this to add a test function. ADD A TEST FILE TO EVERY NEW R FILE!
::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") usethis
Add vignette
::use_vignette("Examples") usethis
remove files from building
::use_build_ignore("[.]so", escape = FALSE)
usethis::use_build_ignore("[.]o", escape = FALSE) usethis
Before ‘Documentation’ and ‘Clear and Rebuild’ and within ‘Configure Build Tools…’ untick ‘use devtools package function if available’. Keep ‘Generate Configuration with Roxygen’
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
.
xxr
:
usethis::use_package("xxr")
datar
:
usethis::use_data(datar)
example(source) # defines the sourceDir() function
try(roxygen2::roxygenize(load_code = sourceDir), silent = TRUE)
::roxygenize() roxygen2
::compile_dll() # to preform a fake R CMD install
pkgbuild::roxygenize() # to update the documentation
roxygen2::install() devtools
Test and Check the package
::test()
devtools::check() devtools
then to build the package:
::build() devtools
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 .
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.