README.md

In virgile-baudrot/rstanTKTD: Bayesian fitting of the General Unified Threshold model of Survival (GUTS) for data in ecotoxicology

gutsRstan is a library developped for calibration of TKTD (Toxicokinetics-Toxicodynamics) models GUTS (General Unified Threshold models of Survival) with the Bayesian language Stan.

Build status for development version

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How to Install

Installing gutsRstan on Windows

For further information about the installation, you can have a look at the installation of the rstan package: - github rstan wiki: installing RStan on Windows

R prerequisites

R version 3.0.2 or later is required (as it is for r).

The latest stable version of R is available from - https://www.r-project.org/

Dowload and Install Rtools

Rtools can be downloaded from - https://cran.r-project.org/bin/windows/Rtools/ Note that latest version of Rtools have compatibility with R version 3.3.x and later.

During installation, just take attention that the C++ compiler included in Rtools is allowed to be used by R.

Once reloaded a new R session, check that Rtools can be used in R:

> Sys.getenv("PATH")

Should return something like:

[1] "c:\\\\Rtools\\\\bin;c:\\\\Rtools\\\\gcc-4.6.3\\\\bin;...

Check also that g++ can be call from R:

> system('g++ -v')

Should return something like:

Using built-in specs.
COLLECT_GCC=c:\Rtools\GCC-46~1.3\bin\G__~1.EXE
COLLECT_LTO_WRAPPER=c:/rtools/gcc-46~1.3/bin/../libexec/gcc/i686-w64-mingw32/4.6.3/lto-wrapper.exe
Target: i686-w64-mingw32
Configured with: /data/gannet/ripley/Sources/mingw-test3/src/gcc/configure --host=i686-w64-mingw32 --build=x86_64-linux-gnu --target=i686-w64-mingw32 --with-sysroot=/data/gannet/ripley/Sources/mingw-test3/mingw32mingw32/mingw32 --prefix=/data/gannet/ripley/Sources/mingw-test3/mingw32mingw32/mingw32 --with-gmp=/data/gannet/ripley/Sources/mingw-test3/mingw32mingw32/prereq_install --with-mpfr=/data/gannet/ripley/Sources/mingw-test3/mingw32mingw32/prereq_install --with-mpc=/data/gannet/ripley/Sources/mingw-test3/mingw32mingw32/prereq_install --disable-shared --enable-static --enable-targets=all --enable-languages=c,c++,fortran --enable-libgomp --enable-sjlj-exceptions --enable-fully-dynamic-string --disable-nls --disable-werror --enable-checking=release --disable-win32-registry --disable-rpath --disable-werror CFLAGS='-O2 -mtune=core2 -fomit-frame-pointer' LDFLAGS=
Thread model: win32
gcc version 4.6.3 20111208 (prerelease) (GCC)

Installing gutsRstan

From the github repository of gutsRstan, the following command should work:

install.packages("devtools")
library("devtools")
install_github("virgile-baudrot/gutsRstan")

Or from the source tar.gz file available in your download repository (~\\ is the path to your repository gutsRstan_0.1.0.tar.gz).

install.packages("~\\gutsRstan_0.1.0.tar.gz", repos = NULL, type = "source")

# Or once the package will be on CRAN
# install.packages("gutsRstan")

Installing gutsRstan on Mac and Linux

For further information about the installation, you can have a look at the installation of the rstan package: - github rstan wiki: installing RStan on Mac or Linux

You should install Rcpp from CRAN:

install.packages("Rcpp")

Then, you can install gutsRstan from the github repository of gutsRstan, the following command should work:

install.packages("devtools")
library("devtools")
install_github("virgile-baudrot/gutsRstan")

Or from the source tar.gz file available in your download repository (~// is the path to your repository gutsRstan_0.1.0.tar.gz):

install.packages("~//gutsRstan_0.1.0.tar.gz", repos = NULL, type = "source")

# Or once the package will be on CRAN
# install.packages("gutsRstan")

Restart R and check the toolchain:

fx <- inline::cxxfunction( signature(x = "integer", y = "numeric" ) , '
    return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;
' )

fx( 2L, 5 ) # should be 10

Compilation

Compilation (for command-line users)

• cd to source directory
• Build from sources (creates vignette and archive) R CMD build .
• Build and install R CMD INSTALL --build .
• Build and install building vignettes with R interpreter: devtools::install(build_vignettes = TRUE)
• Check the package R CMD check --as-cran gutsRstan_X.X.X.tar.gz
• Update package description/NAMESPACE
• under the R interpreter: roxygen2::roxygenise(".")
• Generate documentation
• reference manual: R CMD Rd2pdf --output=documentation .
• re-build reference manual: rm documentation | R CMD Rd2pdf --output=documentation .
• vignettes (using the R interpreter): devtools::document(roclets=c('rd', 'collate', 'namespace', 'vignette'))
• Run unit tests
• under the R interpreter: devtools::test()

Compilation (with RStudio)

• need devtools, ROxygen2 v5.0.1 or higgher
• RStudio builder configuration:
• Project Options : enable Use devtools package... enable Generate documentation... ROxygen options...: all enable exeptVignettesandSource and binary package build`
• update Documentation (no vignette, only NAMESPACE and Rd) Document or Ctrl + Shift + D
• build the source file : More : Build Source Package

virgile-baudrot/rstanTKTD documentation built on May 29, 2019, 9:57 a.m.