NEWS

SBMLR 1.57.1

Added new function S4toS3() for converting S4 SBML models of rsbml into S3 SBMLR models.
Includes code from Vishak Venkateswaran's branch of SBMLR on github (July 2011). This is may allow it to read more models in http://www.ebi.ac.uk/biomodels-main/ I say may because I don't fully understand all of his codes, but add it in anyway.
Problem of libsbml allowing multiple args to multiplication operator was solved by using prod(). Similarly for sum(). Note that "*"() is strictly a binary operator.

Call my model object call SBMLR now to let SBML refer to rsbml's SBML object. Similary my simulate() is now sim() to keep it clear of rsbml's simulate().
SBMLR model files no longer need to have the reversible flag set. The default is FALSE, which is the opposite of Level 2: all of my reaction rate laws have always been positive, and a design objective I like is to keep SBMLR model files as lean as possible (subject to the constraint that they be valid R code).
Simulate handles lsoda() event dataframes, see simulate help.
curtoNatural.R (see Fig. 7 BMC Bioinformatics 2004, 5:190) is now in the models folder.
The SOD model of Kowald et al, JTB 238 (2006) 828–840 is now also in this folder.
Two pdfs of publications that are freely available were removed to make the package lighter.
Similarly, only manual.doc remains: its redundant pdf is now out.

SBMLR objects do need to have their reversible flag set in files, but do in SBMLR objects in R.