CHANGES IN VERSION 1.57.1 ------------------------ 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 ------------------------ 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)