Changelog

Fixed a major issue with addExperiments(), where some experimetal data was lost or misassigned.

addExperiments() is also used by runParameterEstimation() and setParameterEstimationSettings().
Deprecate the name parameter of setParameters().

Renaming parameters on a per reaction basis is not supported by COPASI.
Improved consistency of fetching of models from URLs.
Adjust for new BioModels URL scheme.

Added biomodels_url() helper function to assist with generating URLs where desirable.
Added support for Combine archives via loadCombineArchive() and saveCombineArchive().
Minor fixes and code cleanups.

Rebase on COPASI release 4.28 sources.
Add support for the time course automatic interval option.
Fix definition of experimental data with columns of type ‘ignore’.
Fix runParameterEstimation() output, in some cases, listing incorrect parameter start values.
Minor fixes and code cleanups.

Hotfix for windows build having an incorrect COPASI Version annotation.

The COPASI version was incorrectly reported to be 4.12.

Fix system compatility with various linux distros.

CoRC used to crash on various untested linux distros. Compatibility has now been confirmed with Ubuntu (16.04, 18.04, 20.04), CentOS (6, 7, 8), and Fedora (30, 32).
Use ‘readr’ package for write out of experimental data, to prevent erroneous conversion of NaN to NA.
Fix behaviour of autoplot.copasi_ts() function when a timeseries output named ‘Time’ exists.

‘Time’ output used to confilict with the invariant time column.
Rework tidyverse dependencies to be more light weight.
Minor fixes and code cleanups.

Rebase on COPASI release 4.27 sources.
Require at least R version 3.2.0.
Base the linux binaries on the manylinux2010 docker container.
Add parameter soft_error to runTimeCourse() to allow for readout of incomplete result tables for failed time courses.

Rebase on COPASI release 4.25 sources.
Add a preserve_concentrations argument to setCompartments() to preserve species concentrations instead of particle numbers on adjustment of compartment sizes.
Fix a bug where clearing initial expressions in setter functions prevented them from adjusting initial values.
Enable for getCopasi() to fall back on github as a download mirror.
Minor fixes and code cleanups.

Rebase on COPASI release 4.24 sources.
Fix sigma point method for cases other than two dependent variables.
Use parallel::parLapplyLB() for parallel processing as it was fixed in R version 3.5.
Minor fixes and code cleanups.

Rebase on latest COPASI development sources.
Add functions to handle SBML models as strings (loadSBMLFromString(), saveSBMLToString()).
Allow for currently running tasks to be terminated interactively (issue #3).
Fix loadSBML function failing for local files.
Fix installation on UNIX systems.
Minor fixes and improvements.

Rebase on latest COPASI development sources.
Add model event functioniality (event(), event_strict(), getEvents(), setEvents(), newEvent(), deleteEvent()).
The package now generally uses "" instead of NA to denote unset or empty expressions.
Allow expressions to be automatically coerced from finite numeric and logical values. E.g. getValue(1) instead of getValue("1").
Fix crashes on entity deletion. Deletion functions now delete recursively.
Generally warn if model fails to compile.
Fix errors with argument type of setCompartments() and setGlobalQuantities().
Use new Copasi XML parser.

CoRC 0.9.0 (2020-11-23)