Parametric Ordinary Differential Equations Model of Growth, Death, and Respiration of Macroinvertebrate and Algae Taxa

Numerically solve and plot solutions of a parametric ordinary differential equations model of growth, death, and respiration of macroinvertebrate and algae taxa dependent on pre-defined environmental factors. The model (version 1.0) is introduced in Schuwirth, N. and Reichert, P., (2013) . This package includes model extensions and the core functions introduced and used in Kattwinkel, M. et al. (2016) , Mondy, C. P., and Schuwirth, N. (2017) , and Paillex, A. et al. (2017) .


Developers instructions for building, installing and testing Streambugs R package sources.

Installation

Prerequisites

You need a C compiler (recommended GCC >= 5 or LLVM >= 7); cf.

$ gcc --version

You also need an R (>= 3.0.2) installation on your computer; run:

$ R

which should download, build and install all R tools needed to build C/C++ based packages.

Attention

installing above R packages, together with all suggested dependencies (the dependencies=TRUE keword argument), takes some time, especially for the devtools package. You might opt for not installing suggested dependencies, and install the missing ones as you discover them.

Build, install and test

Run R shell and load devtools library:

$ R
> library(devtools)

To create docs, build package and install it run in this folder:

> devtools::document()
> pkg_src = devtools::build()
> install.packages(pkg_src, repos=NULL, type="source")

Run tests

To run tests, with the package as a working directory, run:

> devtools::test()

Check for CRAN submission

To check for CRAN submission, with the package as a working directory, run:

> devtools::check()
Check archive for submission

Build will create a zipped TAR file ../streambugs_PKGVER.tar.gz, where PKGVER is the current package version. You can check this package for CRAN submission by running in shell:

$ R CMD check --as-cran ../streambugs_$(VERSION).tar.gz

This creates the streambugs.Rcheck/ folder which contains also a PDF file streambugs-manual.pdf, that is the R vignette of the package.

Equivalently, from R shell, after the build, run:

> devtools::check(pkg_src)

Cleanup

Remove build, packaging files, and CRAN check folder, i.e., relative to this folder, following files:

src/*.o
src/*.so
man/*.Rd
../streambugs_0.1.tar.gz
streambugs.Rcheck/

To uninstall the package from your system run in R shell:

> remove.packages("streambugs")

News

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("streambugs")

1.0 by Nele Schuwirth, a year ago


http://www.eawag.ch/en/department/siam/projects/streambugs/


Report a bug at https://github.com/trybik/streambugs/issues


Browse source code at https://github.com/cran/streambugs


Authors: Peter Reichert , Mikolaj Rybinski , Nele Schuwirth


Documentation:   PDF Manual  


GPL-3 license


Imports deSolve

Suggests testthat

System requirements: C99


See at CRAN