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Short Installation Instructions

installation.Rmd

Installation 

# requires the 'remotes' package
remotes::install_github("icpm-kth/uqsa")

Alternatively, download a release tar.gz or zip file and run

R CMD INSTALL uqsa*.{tar.gz,zip}

Prerequisites

The R package uqsa contains examples that in addition to the normal package dependencies also use

  • reshape2, ggplot2;
  • the R package icpm-kth/SBtabVFGEN, used to generate vector field files from SBtab files (it can be installed by running remotes::install_github("icpm-kth/SBtabVFGEN"));
    • SBtabVFGEN benefits from having libSBML installed with R bindings; this is not a hard dependency, but required for export to SBML, L2V4.
    • hdf5r is also of (very minor) optional benefit.
  • the R package icpm-kth/rgsl, used to solve ODEs in C using functions from the GNU scientific library (gsl) (you can install it by running remotes::install_github("icpm-kth/rgsl")).
    • you also need to install the GNU Scientific Library itself (the rgsl package was tested on MACOS and some GNU Linux platforms [debian, ubuntu])
  • The auto-generation of code, be it GSL odeiv2 compatible code or R code for each model is done using the shell script in icpm-kth/RPN-derivative; that package has several backends for analystic (symbolc) math (the thing that computer algebra systems do)

Note on Model code

Strictly speaking auto-generation of code is not required, the user can also hand-craft the model code and just not use any of the SBtab related functionality. This package only requires either R code for deSolve or C code for gsl_odeiv2 (https://www.gnu.org/software/gsl/doc/html/ode-initval.html)

All user visible functions have a manual (e.g. run > ?ABCMCMC in R)