CHANGES IN VERSION 1.57.1
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NEW FEATURES
o Added new function S4toS3() for converting S4 SBML models of rsbml into S3 SBMLR models.
o 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.
o Problem of libsbml allowing multiple args to multiplication operator was solved
by using prod(). Similarly for sum(). Note that "*"() is strictly a binary operator.
SIGNIFICANT USER-LEVEL CHANGES
o 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().
o 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).
o Simulate handles lsoda() event dataframes, see simulate help.
o curtoNatural.R (see Fig. 7 BMC Bioinformatics 2004, 5:190) is now in the models folder.
o The SOD model of Kowald et al, JTB 238 (2006) 828–840 is now also in this folder.
o Two pdfs of publications that are freely available were removed to make the package lighter.
o Similarly, only manual.doc remains: its redundant pdf is now out.
Notes
o SBMLR objects do need to have their reversible flag set in files, but do in SBMLR objects in R.
CHANGES IN VERSION 1.51.1
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NEW FEATURES
o Replaced odesolve dependence with deSolve dependence.
o Updated url in description
o This is the last version with changes logged in doc/readme.txt (3/20/2012)