parse_concide().In the future, this feature analysis will issue warnings only when it is a true conflict, not a possible conflict (e.g.: scheduled events modifying species that are subject to conservation law experssions)
options(uqsa.verbose=FALSE).errors seem to cause slow downs on windows when doing arithmetic, we now more carefully drop errors when a function doesn't need them.dll rather than so).abc_mcmc was introduced, it is a rewrite of the
older ABCMCMC function, with different arguments.KLD which can serve as
fallback if other packages are unavailable for KLD calculations.par and option settings on completion.Windows compatibility: all checks pass.
The way that we generate C code and how shared libraries are made has
changed. In the past we were aiming for a workflow, where a user would
have their model in a repository. This repository would have the
generated C code for their model as well, so that there was no need to
keep regenerating it. The same repository could have a copy of the
model in various formats such as mod, sbml, vf, etc.
However, these derived formats make it quite difficult to keep everything synchronized and up to date. Therefore we consider it the more common case that we frequently change the model TSV files and then update the C code.
The model, once converted to an ODE or CME (for chemical master
equation type models) now has a field for the C file storage location
and the shlib function uses this field to compile the model to a
shared library (same directory). The path to the so file is also
stored in the ODE or CME object.
Many other changes have been made to improve convenience, as well es to fix bugs.